McNamara 20161006 revised draft tables for CPHG Light ...

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From the SelectedWorks of George McNamara Fall October 3, 2016 McNamara 20161006 revised draſt tables for CPHG Light Microscopy and Image Analysis.pdf George McNamara is work is licensed under a Creative Commons CC_BY International License. Available at: hps://works.bepress.com/gmcnamara/77/

Transcript of McNamara 20161006 revised draft tables for CPHG Light ...

Page 1: McNamara 20161006 revised draft tables for CPHG Light ...

From the SelectedWorks of George McNamara

Fall October 3 2016

McNamara 20161006 revised draft tables forCPHG Light Microscopy and Image AnalysispdfGeorge McNamara

This work is licensed under a Creative Commons CC_BY International License

Available at httpsworksbepresscomgmcnamara77

Table 441 Useful Light Microscopy Web Sites

Light Microscopy (overview) Confocal Listserv (not just for confocal microscopes) httpslistsumneducgi-binwaA0=confocalmicroscopy G McNamara ndash Multi-Probe Microscopy (content last updated 2005 includes extensive glossary) httpsworksbepresscomgmcnamara2 Molecular Expressions National High Magnetic Field Laboratory (NHMFL) Florida State University httpmicromagnetfsuedu Microscopedia ndash Resources Guide To Light Microscopy httpwwwmicroscopediacomMicroscopyLight Molecular Probes Inc Invitrogen Thermo Fisher (Many links to useful and informative sites) httpswwwthermofishercomusenhomebrandsmolecular-probeshtml Photonics buyerrsquos guide (much more comprehensive than this list) httpwwwphotonicscomBuyersGuideaspx Science Exchange ndash Reproducibility Initiative (focus on commercial antibodies and uses) httpswwwscienceexchangecomapplicationsreproducibility Wikipedia - Chromosomes httpsenwikipediaorgwikiChromosome Wikipedia ndash Microscope httpenwikipediaorgwikiMicroscope Societies Association of Biomolecular Resource Facilities Light Microscopy Research Group (ABRF LMRG) httpsabrforgresearch-grouplight-microscopy-research-group-lmrg European Microscopy Society (EMS) httpwwweurmicsocorg International Society for Advancement of Cytometry (ISAC) httpisac-netorg Microscopy Society of America (MSA) httpwwwmicroscopyorg Royal Microscopical Society (RMS) httpwwwrmsorguk Major Microscope Companies Leica Microsystems Inc httpwwwleica-microsystemscom httpwwwleica-microsystemscomscience-lab httpwwwleica-microsystemscomproductsconfocal-microscopesdetailsproductleica-tcs-sp8-sted-3x

Nikon Instruments Inc httpswwwnikoninstrumentscom httpswwwmicroscopyucom

httpswwwnikoninstrumentscomProductsLive-Cell-Screening-SystemsBioStation-CT

Olympus America Inc httpwwwolympus-lifesciencecomen httpolympusmagnetfsuedu

Zeiss (Carl Zeiss Inc) httpwwwzeisscom httpwwwzeisscomcorporateen_ushomehtml httpzeiss-campusmagnetfsueduindexhtml httpwwwzeisscommicroscopyen_deproductsmicroscope-camerasaxiocam-702-monohtml

Karyotype Systems and Digital Pathology Digital Pathology Blog ndash see educational sponsors for comprehensive list of digital pathology vendors httptissuepathologycom 3DHistech ndash digital pathology Pannoramic scanners httpwww3dhistechcom Agilent Pathology Solutions Dako ndash IHC and ISH reagents autostainers httpwwwdakocomdkindexknowledgecenteromnishtm httpwwwdakocomdkar42productgroupshtm Applied Spectral Imaging ndash SKY Spectral karyotyping GenASIs digital pathology httpwwwspectral-imagingcom httpwwwspectral-imagingcomapplicationsspectral-imaging httpwwwspectral-imagingcomapplicationspathology Bioview ndash pathology and FISH cytogenetics scanners httpbioviewcom Definiens (MedImmuneAstraZeneca) - digital pathology image analysis (with deep learning algorithms) httpwwwdefinienscom Huron Digital Pathology ndash large area confocal scanning (entire human brain slices) httpwwwhurondigitalpathologycom Leica Biosystems ndash CytoVision CytogeneticsFISH Aperio digital pathology httpswwwleicabiosystemscomclinical-microscopy-surgery-radiologycytogenetics httpswwwleicabiosystemscomdigital-pathology MetaSystems International ndash karyotyping FISH digital pathology httpsmetasystems-internationalcomenproducts Molecular Probes ThermoFisher Scientific ndash Evos FL Auto and Evos Floid cell imaging stations high content screening (HCS) (Cellomics) httpswwwthermofishercomusenhomelife-sciencecell-analysiscellular-imagingcell-imaging-systemsevos-fl-autohtml httpswwwthermofishercomusenhomelife-sciencecell-analysiscellular-imagingcell-imaging-systemsfloid-cell-imaging-stationhtml httpswwwthermofishercomusenhomelife-sciencecell-analysiscellular-imaginghigh-content-screeninghigh-content-screening-instrumentshtml Philips ndash digital pathology httpwwwusaphilipscomhealthcaresolutionspathology Ventana Roche Digital Pathology ndash digital pathology FISH httpwwwventanacomdigitalpathology Visiopharm ndash digital pathology image analysis (with deep learning algorithms) stereology httpwwwvisiopharmcom

Filter and Filter Sets Manufacturers Alluxa httpwwwalluxacom BMV Optical wwwbmvopticalcom Chroma Technology httpwwwchromacom Edmund Optics ndash filters prisms httpwwwedmundopticscomopticsoptical-filtersbandpass-filtersfluorescence-filter-kits3226 httpwwwedmundopticscomopticsprisms Iridian Spectral Technologies httpwwwiridian-optical-filterscomproduct-categoryfluorescence-sets Newport (Spectra-Physics Oriel Bookham New Focus) httpswwwnewportcomcoptical-filters

Omega Optical httpwwwomegafilterscom Optolong (Kunming Yulong OpticalampElectronics Technology Co Ltd) httpwwwoptolongcomenproductsfluorescence-filters Schott Glass Technologies httpwwwschottcom httpwwwusschottcomadvanced_opticsenglishsynadvanced_opticsproductsoptical-componentsoptical-filtersinterference-filtersindexhtml Semrock Inc (IDEX CVI Melles Griot) httpsemrockcom ThorLabs ndash optical filters httpswwwthorlabscomnavigationcfmguide_id=21 Major scientific CMOS (sCMOS) camera companies (your next microscope cameras should likely be sCMOS not CCD or EMCCD) Andor Technology Ltd (Oxford Instruments) httpwwwandorcomscientific-camerasneo-and-zyla-scmos-cameras Hamamatsu httpswwwhamamatsucomusencommunitylife_science_camerasensor_technologiesscientific_cmos_scmos_image_sensorindexhtml httpwwwhamamatsucomusencommunitylife_science_cameraproductsearchC11440-22CUindexhtml PCO httpsuspco-techcomscmos-cameras Photometrics httpwwwphotometricscomproductsscmos Fluorescent Proteins Luciferases (DNA plasmids andor other expression products) 490BioTech ndash LuxABCDE

http490biotechcomvectors-2 Abberior httpwwwabberiorcomshopLabels-by-FunctionFluorescent-Proteins7_14html httpwwwabberiorcomshopLabels-by-Application1html Addgeneorg wwwaddgeneorg httpswwwaddgeneorgfluorescent-proteins httpswwwaddgeneorgfluorescent-proteinsbiosensors httpswwwaddgeneorgfluorescent-proteinslocalization httpswwwaddgeneorgoptogenetics httpswwwaddgeneorgfluorescent-proteinsdavidson httpswwwaddgeneorgRoger_Tsien Allele Biotechnology httpwwwallelebiotechcomFluorescent-Proteins Bell Biosystems ndash Magnelle living MRI contrast agents (magnetotactic bacteria taken up by human cells in vitro) with fluorescent proteins ndash in vivo cell tracking httpwwwbellbiosystemscomProducts-and-ServicesCell-Tracking-Solutions BioBricks Foundation httpbiobricksorg BioPop (Intrexon) ndash Dinoflagellates bioluminescence luciferaseluciferin httpsbiopopcomproducts Chromotek GmbH - Chromobodies Nano-Boosters (llama nanobodies attached to or detecting FP) httpwwwchromotekcomproductschromobodies httpwwwchromotekcomproductschromobodiescell-cycle-chromobodyr httpwwwchromotekcomproductsnano-boosters DNA 20 chromogenic and fluorescent protein paintbox (not really IP-Free) httpswwwdna20comproductsprotein-paintbox Evrogen httpevrogencomproductsbasicFPsshtml httpevrogencomproductsBiosensorsshtml httpevrogencomproductsOrganelle-labelingshtml iGEM BioBricks ndash reporter proteins including fluorescent proteins httppartsigemorgProtein_coding_sequencesReporters iGEM Registry of Standard Biological Parts httppartsigemorgMain_Page InvivoGen ndash GFP Lucia luciferase reporters httpwwwinvivogencomdual-reporter MBL International Corp ndash fluorescent proteins httpswwwmblintlcomproductsfluorescent-proteins httpruomblcojpbioeproductflproteinfuccihtml Millipore-Sigma Sigma-Aldrich ndash firefly luciferase D-luciferin httpwwwsigmaaldrichcomlife-sciencemetabolomicsenzyme-exploreranalytical-enzymesluciferasehtml Molecular Probes Inc Invitrogen Thermo Fisher ndash Bacmam 20 fluorescent proteins biosensors FUCCI httpwwwprobescom httpwwwthermofishercomusenhomebrandsmolecular-probeshtml httpswwwthermofishercomusenhomeindustrialpharma-biopharmadrug-discovery-developmenttarget-and-lead-identification-and-validationpathway-biologycellular-pathway-analysisbacmam-systembacmam-reagentshtml

Montana Molecular LLC - genetically encoded fluorescent biosensors and probes for cell-based assays and live cell imaging httpmontanamolecularcomproductsproducts-overview NanoLight Technologies ndash Renilla GFP luciferases httpwwwnanolightcomNanoFluorsGFP_Expression_Vectorshtml httpswwwbiotoycomenlearn n3D Biosciences ndash generate 3D cell spheroids high throughput screening image changes using smartphone camera inside incubator httpwwwn3dbiocomproductsmagnetic-3d-bioprinting httpwwwn3dbiocomproductsassays New England BioLabs (NEB) ndash Cypridina Gaussia luciferases httpswwwnebcomapplicationscellular-analysisreporter-systems Promega ndash Monster GFP NanoLuc httpswwwpromegacomproductsreporter-assays-and-transfectionreporter-vectors-and-cell-linesmonster-green-fluorescent-protein-phmgfp-vector httpswwwpromegacomproductsreporter-assays-and-transfectionreporter-vectors-and-cell-linesnanoluc-luciferase-reportersnanoluc-genetic-reporter-vectors Fluorescence Products (reagents) Advanced Cell Diagnostics (Bio-Techne) - branched DNA probe sets for RNA FISH httpsacdbiocomproducts Affymetrix eBioscience Thermo Fisher - branched DNA probe sets for RNA FISH httpwwwaffymetrixcomestorepromotionsviewrnaishindexaffx Anaspec ndash HiLyte Fluorophores FRET probes httpswwwanaspeccomproductsproductcategoryaspid=10 Antibody Resource Page httpwwwantibodyresourcecom Biocompare ndash Antibodies httpwwwbiocomparecomAntibodies Cell Signaling Technology ndash fluorescence antibodies httpswwwcellsignalcombrowseimmunofluorescence-immunocytochemistryif-paraffinif-frozen Essen Biosciences ndash Bacmam 30 ready to use FP gene transfection reagents httpwwwessenbiosciencecomenproductsreagents-consumablesincucyte-nuclight-red-bacmam-30-reagent-nuclear-labeling-cat-no-4621 GE Healthcare Amersham Biosciences httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usbrandscydye Global Biological Standards Institute (GBSI) ndash Antibody Validation Initiative httpwwwgbsiorgworkantibodies Goryo Chemical httpwwwgoryochemicalcom Human Protein Atlas (academic) Atlas Antibodies (commercial arm) US distributor httpwwwproteinatlasorg httpsatlasantibodiescom httpwwwsigmaaldrichcomlife-sciencecell-biologyantibodiesprestige-antibodieshtml

Integrated DNA Technologies (IDT) httpwwwidtdnacomsiteCatalogmodificationsdyes httpwwwidtdnacompagesproductsmodificationsfluorophoresfreedom-dyes httpwwwidtdnacomsiteCatalogModificationsCategory4 Jackson ImmunoResearch httpswwwjacksonimmunocom KPL (formerly Kirkegaard amp Perry Laboratories Inc) SeraCare httpwwwkplcom LGC Biosearch Technologies ndash dyes for oligonucleotides single molecular RNA FISH image gallery httpswwwbiosearchtechcomsupporteducationfluorophores-and-quenchers httpstellarisfishsmugmugcom httpsinglemoleculefishcom httpswwwbiosearchtechcomproductsrna-fish (typically 48 20 base oligonucleotides) Marker Gene Technologies Inc (MGT) httpwwwmarkergenecomfluorescent-reagent Miltenyi Biotec ndash REAfinity recombinant engineered antibodies (no Fc Receptor binding) FASER fluorescence amplification kits NiraWave fluorophores (indocyanine green formulations) httpwwwmiltenyibioteccomenproducts-and-servicesmacs-flow-cytometryreagentsantibodies-and-dyesrecombinant-antibodiesaspx httpwwwmiltenyibioteccomenproducts-and-servicesmacs-flow-cytometryreagentssupport-reagentsfaser-kitsaspx httpwwwmiltenyibioteccomenproducts-and-servicesviscover-imagingoptical-imagingaspx Molecular Probes Inc Invitrogen Thermo Fisher ndash largest vendor of fluorophores Molecular Probes Handbook (web resource) Tyramide Signal Amplification kits httpwwwprobescom httpswwwthermofishercomusenhomereferencesmolecular-probes-the-handbookhtml httpswwwthermofishercomusenhomereferencesmolecular-probes-the-handbooktablestyramide-signal-amplification-tsa-kitshtml NIRvana Sciences httpnirvanasciencescom httpnirvanasciencescompage_id=3088 One World Lab ndash antibody search httponeworldlabcomantibodies CytoCell Oxford Gene Technologies ndash DNA FISH probes human mouse pig chicken httpwwwcytocell-uscom Perkin Elmer ndash nucleotides labeling kits Tyramide Signal Amplification Kits (TSA) Opal 7plex discovery panel kit based on sequential TSA httpwwwperkinelmercomcategoryfluorescent-hapten-nucleotides httpwwwperkinelmercomcategoryfluorescent-agents-labeling-kits-dyes httpwwwperkinelmercomlab-solutionsresourcesdocsBRO_TSAsignalamplificationpdf httpwwwperkinelmercomproductopal-7-immunology-discovery-kit-op7ds1001kt

Rockland Inc httpwwwrockland-inccomcommerceindexjsp

TEFLabs ndash fluorescent ion indicators (Ca++ Cl- K+ Mg++ Na+ pH Zn++) ionophores fluorophores httpwwwteflabscomion-indicators Vector Laboratories Inc httpwwwvectorlabscom

Live cell imaging dishes and multi-well plates (ldquoglass bottom dishesrdquo)

We recommend these for simplified handing and processing vs either thick plastic dishesplates or having to handle loose coverslips with your valuable cells

Leicester Imaging Technologies (LITE) - University of Leicester - table of dishes for live cell imaging (our table has current links and bad links left out) httpwww2leacukcollegesmedbiopsychfacilities-and-servicescbsliteaiftips-and-tricks-1dishes-for-live-cell-imaging Bellco Glass Inc - glass flat bottom plate httpwwwbellcoglasscomnode1046 Bioptechs - interchangable coverslip dish ($036 per experiment) httpwwwbioptechscomproductinterchangeable-coverslip-dish Brooks Automation Inc - clar bottom optical imaging microplates httpwwwbrookscomproductslife-scienceconsumablesmatrical-microplates-microtubes-racks-lidsglass-bottom-optical-imaging-microplates Cell EampG - glass bottom cell sulture dishes plates httpcellegcomproducthtml Cellvis - glass bottom dishes and plates httpwwwcellviscom_35-mm-glass-bottom-dishes_products_by_categoryphpcat_id=3 Corning - glass bottom microplates httpcatalog2corningcomLifeSciencesen-USShoppingCategoryaspxcategoryname=Microplates20-202015(Lifesciences)|Assay20Microplates20-202015(Lifesciences) Design 1 Solutions - Custom microplates and fabrication services httpwwwdesign1solutionscomcustom-microplateshtml Eppendorf - cell imaging dishes imaging plates httpsonline-shopeppendorfcomOC-enCell-Culture-and-Imaging-Consumables-110320Cell-Imaging-Consumables-120210Eppendorf-Cell-Imaging-Dishes-PF-19457html httpsonline-shopeppendorfcomOC-enCell-Culture-and-Imaging-Consumables-110320Cell-Imaging-Consumables-120210Eppendorf-Cell-Imaging-Plates-PF-19458html Greiner Bio-One International - CellView glass bottom dishes quadrant dishes httpsshopgbocomenrowarticlescataloguearticle0110_0110_0040_002027513 ibidi - u-Plates glass bottom dishes microfluidic slides httpibidicomxtproductsenibidi-Labwarem-Plates httpibidicomxtproductsenibidi-Labware Matsunami Glass Ind Ltd httpwwwmatsunami-glasscojpenglishlifebiodata01html Mattek - glass bottom dishes and SBS plates httpswwwmattekcomstore-categoryculturewareglass-bottom-dishes Nunc - glass bottom dishes httpswwwthermofishercomordercatalogproduct150680 NEST Biotechnology Co Ltd Wuxi Jiangsu PRChina httpwwwnestscientificusacomproducts_detailproductId=31html PerkinElmer - glass bottom plates httpwwwperkinelmercomSECatalogCategoryIDMicroplates

Porvair Sciences - clear bottom assay plates httpwwwporvair-sciencescomenservices-menulife-sciencesclear-bottom-assay-plates Ted Pella Inc - glass bottom dishes clear wall or black wall (manufactured by WillCo Wells) httpswwwtedpellacomsection_html706dishhtm Warner Instruments (Harvard Apparatus) - culture dishes perfusion systems httpswwwwarneronlinecomproduct_cat_infocfmid=1322 Willco Wells - glass bottom dishes wwwwillcowellscom World Precision Instruments - Fluorodish glass bottom dishes httpswwwwpiinccomproductslaboratory-suppliesfd35-100-fluorodish-cell-culture-dish-35mm-23mm-well-pkg-of-100 Microscopes Microscopy Accessories (accessorize) Reagents Resources 3scan ndash knife edge scanning microscope (images slices repeats through specimen) httpwww3scancomdata-2 89North (affiliated with Chroma Technology Corp) httpwww89northcom Abberior Instruments ndash STED RESOLFT precision localization super-resolution microscopes STEDYCON convert any fluorescence microscope to STED httpabberior-instrumentscom httpabberior-instrumentscomproductscompact-lineabberior-stedy-con Acquifer ndash HIVE imaging machine (computer hardware) for high content screening big data httpswwwacquiferde Adobe Systems Inc httpwwwAdobecom httpscreativeadobecomproductsdownloadphotoshop Affymetrix eBioscience (ThermoFisher) - microarrays httpwwwaffymetrixcomestorebrowselevel_one_category_template_onejspparent=35796ampcategory=35796 httpwwwaffymetrixcomestorecatalog131547AFFYGeneChip26231743B+System+3000Dx+v22623423B1_1 Agilent Technologies ndash SureScan microarray scanner (array CGH microRNA SNPs CNV) httpwwwgenomicsagilentcomenMicroarray-Scanner-Processing-HardwareSureScan-Microarray-Scannercid=AG-PT-144 Andor Technology (Oxford Instruments) ndash sCMOS cameras Dragonfly spinning disk confocal Revolution DSD2 differential spinning disk confocal photostimulation (fluorescence recovery after photobleaching optogenetics) Mosaic3 DMDDLP high speed light patterning (optogenetics structured illumination) MicroPoint pulsed UV laser for ablation DNA damage photobleachingactivation uncaging accessories httpwwwandorcomscientific-camerasneo-and-zyla-scmos-cameras httpwwwandorcommicroscopy-systemsdragonfly httpwwwandorcommicroscopy-systemsrevolution-dsd httpwwwandorcommicroscopy-systemsphotostimulation httpwwwandorcommicroscopy-systemsphotostimulationmosaic httpwwwandorcommicroscopy-systemsphotostimulationmicropoint httpwwwandorcommicroscopy-systemsmicroscopy-components Apogee Instruments Inc (Andor Technology) ndash CCD cameras and filter wheels (mostly marketed for astronomy) httpwwwccdcomandorhtml Applied Scientific Instrumentation Inc ndash light sheet imager (iSPIM diSPIM)

wwwasiimagingcom httpwwwasiimagingcomindexphpproductslight-sheet-microscopyselective-plane-illumination-microscopy-ispim-dispim Applied NanoFluorescence LLC ndash NS1 NanoSpectralyzer (Raman and UV-VISNIR) NS MiniTracer near infrared spectrometer NFM NanoFluorescence microscope multi-laser light source single wall carbon nanotubes (NIR II fluorophores) httpappliednanocomproductshtml httpappliednanocomproductsns1html httpappliednanocomproductsproduct-list77-ns-minitracerhtml httpappliednanocomproductsnfmhtml httpappliednanocomproductsls-nhtml httpwwwnanowerkcomnewsnewsid=24132php Applied Spectral Imaging Inc httpwwwspectral-imagingcom ArgoLight ndash fluorescence resolution test target slides httpargolightcom AttoCube - attoMICROSCOPY overview attoCFM - Multichannel cryogenic (low temperature) confocal fluorescence microscopes 08 NA objective lenses 400-1000 nm spectral range httpwwwattocubecom httpwwwattocubecomattomicroscopyintroductiontab-2 httpwwwattocubecomattodownloads AutoQuant (Media Cybernetics) spatial deconvolution httpwwwmediacycomautoquantx3 Becker amp Hickl GmbH httpwwwbecker-hicklcomproductshtm Berkeley Lights Inc ndash manueuver into nanowells incubate recover 4000 single cells per chip httpswwwberkeleylightscomtechnology Bioaxial ndash Codim imaging conical diffraction beam shaper for super-resolution (4 sub-images) httpwwwbioaxialcomcodim-imaging Bioptechs - Live-Cell Micro-Observation Products httpwwwbioptechscom Bionumbers - database of useful biological numbers httpbionumbershmsharvardeduKeyNumbersaspx Biostatus ndash DRAQ5 DRAQ7 ApopTRAK CyTRAK Orange CyGel HypoxiTRAK httpwwwbiostatuscomProducts Bio-Tek ndash Cytation 3 Cell Imaging Multi-Mode Reader Lionheart FX Automated Live Cell Imager httpwwwbiotekcomproductsimagingcytation3_cell_imaging_multi_mode_readerhtml httpwwwbiotekcomproductsimaginglionheartfx_automated_live_cell_imagerhtml Biovision Technologies ndash distributor for several imagers including VT-iSIM instant super-resolution microscope httpbiovision-technologiescom httpbiovision-technologiescomsystemshtml httpbiovision-technologiescomvtisimhtml Bitplane (Andor Oxford Instruments) ndash Imaris imaging software httpwwwbitplanecom BMV Optical - custom lens assemblies and optical filters wwwbmvopticalcom

Bruker (previously Prairie Technologies Vutara) ndash Opterra confocal Ultima Multiphoton Vutara 352 single molecule localization microscopes httpswwwbrukercomproductsfluorescence-microscopesopterra-confocal-microscopyoverviewhtml httpswwwbrukercomproductsfluorescence-microscopesultima-multiphoton-microscopyhtml httpswwwbrukercomproductsfluorescence-microscopesvutara-super-resolution-microscopyoverviewhtml Cairn Research ndash standard and custom accessories ex Light Sheet Illuminator MultiCam (4 cameras) custom design httpswwwcairn-researchcouk httpswwwcairn-researchcoukproductl-spi-single-plane-illuminator (dual L-SPI for 4 illumination directions) httpswwwcairn-researchcoukproductmulticam httpswwwcairn-researchcoukcustom-design Cameca ndash NanoSIMS 50L (7plex stable isotope imaging) httpwwwcamecacominstruments-for-researchnanosimsaspx CellMic (formerly Holomic) - blood analysis or fluorescence imaging cytometer on a cell phone httpwwwcellmiccomcontentadvanced-technologies httpwwwcellmiccomcontentfluorescent-imaging-cytometry-and-e-coli-detection-on-a-cell-phone CellOptic ndash FINCH (Fresnel INcoherence Correlation Holography) httpwwwcellopticcomindex2html CellProfiler ndash High content screening (HCS) image processing and analysis software httpcellprofilerorg ClearLight Diagnostics - CLARITY Optimized Light Sheet Microscopy (3D tissue optical clearing + light sheet imaging) httpwwwclearlightdxcomindexhtml Confocalnl ndash Rescan confocal microscopy to obtain 170 nm resolution with any pinhole diameter httpwwwconfocalnl CoolLED ndash LED light sources httpwwwcoolledcomproduct-detailpe-4000 Crest Optics SRL ndash X-Light confocal X-Light V2 + VCS (VideoConfocal super-resolution) httpwwwcrestoptcom httpwwwcrestoptcomhtmlx-light_v2_vcshtml Cytoskeleton Inc - live cell imaging reagents Spirochrome SiR bioimaging probes httpwwwcytoskeletoncomlive-cell-reagents httpwwwcytoskeletoncomlive-cell-reagentsspirochrome CytoViva ndash darkfield imaging hypspectral imaging httpwwwcytovivacomproducts3d-enhanced-darkfield-imaging httpwwwcytovivacomproductshyperspectral-imaging-2hyperspectral-imaging Data Translation Inc - digitizer cards httpwwwdatxcom Delmic BV - combined correlative scanning electron microscope with inverted fluorescence microscope httpwwwdelmiccomdelphi httpswwwdelphimicroscopecom httpwwwdelmiccomsecom-super-resolution Digital Light Innovations (DLi) - CELscope C-mount LED Microscope using Texas Instruments DLP illuminator with a simple stand httpswwwdlinnovationscomdli-deep-dives-celscope-c-mount-led-microscope Double Helix LLC ndash single molecule localization microscope (Piestun) httpdoublehelixopticscom Edinburgh Super-resolution Imaging Consortium (ESRIC)

httpwwwesricorg Energetiq ndash Deep ultraviolet (DUV high radiance 170-2100 nm) laser driven light source (LDLS) httpwwwenergetiqcom Epi Technology - CaliCube - Cube for fluorescence light path to inspect epi Illumination light source (lamp) fiber optic or liquid light guide httpwwwepitechnologycomepitechnology-1 Essen Biosciences ndash Incucyte Zoom (imager inside incubator) httpwwwessenbiosciencecomenproductsincucyte Estigen Tissue Science ndash manual and automated tissue arrayer (tissue microarray maker) httpwwwestigencom Euro-Bioimaging httpwwweurobioimagingeu Excelitas Technologies (formerly Lumen Dynamics) ndash X-Cite LEDs httpwwwexcelitascomPagesProductX-Cite-LED-Solutionsaspx Expansion Technologies Inc (extbio) ndash Expansion microscopy httpwwwextbiocombuycell FEI (formerly Till Photonics) (Thermo Fisher) ndash correlative LM-EM single molecule Cryo-EM httpswwwfeicomlife-sciencescellular-biology httpswwwfeicomlife-sciencescellular-biologycorrelative-microscopy httpswwwfeicomlife-sciencesstructural-biology Femtonics - Multi-phton microscopes software accessories caged glutamate reagents services httpfemtonicseuproducts First Light Imaging ndash C-Red NIR imaging (800-2500 nm NIR windows I II III 650-950 nm 1100-1350 nm 1600-1870 nm[Shi et al 2015]) high speed visible EMCCD (400-1000 nm) httpwwwfirst-lightfrcategoryrangesinfrared Fluidigm ndash Helios imaging CyTOF mass cytometer (42plex) Callisto (32 independent chambers dose with up to 16 independent factors for 1-1000 cell populations culture up to 3 week) Polaris functional genomics meets imaging (48 single cells up to 24 hours after single cell selection from a population) httpswwwfluidigmcomproductshelios httpswwwfluidigmcomproductscallisto httpswwwfluidigmcomproductspolaris GattaQuant - nanorulers for high resolution microscopes and super-resolution microscopes performance testing httpwwwgattaquantcomNanoruler GE Healthcare life Sciences Applied Precision ndash DeltaVision deconvolution OMX OMX SR httpwwwgelifesciencescomwebappwcsstoresservletproductByIdenGELifeSciences-us29065728 httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usproductsAlternativeProductStructure_2380729065721 httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usproductsAlternativeProductStructure_2380729115476 German BioImagingorg httpwwwgermanbioimagingorgwikiindexphpMain_Page httpwwwgermanbioimagingorgwikiindexphpWorkgroup6SoftwarePackages GIGAmacro ndash Magnify2 gigapixel imagery oof macroscopic and microscopic objects Terapixel macro image httpwwwgigamacrocomgigapixel-macro-imaging-system httpwwwgigamacrocomworlds-first-terapixel-macro-image

Glencoe Software ndash OMERO Plus enterprise data management for scientific images and any associated metadata (OME = Open Microscopy Environment) DataViewer PathViewer httpsglencoesoftwarecomomeroplushtml httpsglencoesoftwarecomdataviewerhtml httpsglencoesoftwarecompathviewerhtml Gooch amp Housego ndash spectral imager httpsgoochandhousegocomminiature-spectral-imaging-camera httpwwwghinstrumentscomproductsspectral-imaging-synthesishsi-440c-hyperspectral-imaging-system Hindsight Imaging ndash spectral imaging httphindsight-imagingcom Horiba Scientific - SWIFT ultra-fast Raman confocal imaging Raman spectroscopy httpwwwhoribacomscientificproductsraman-spectroscopyraman-imagingswift httpwwwhoribacomscientificproductsraman-spectroscopyraman-imaging httpwwwhoribacomscientificproductsraman-spectroscopy IATIA Ultima Capital ndash QPm (quantitative phase microscopy) httpwwwultimacapitalnetiatiaimagingPublicationsIatia20ImagingapplicationNotesqpmApplicationWithConfocalMicroscopespdf Ibidi - heating and incubation systems optical O2 measurement systems Nanolive 3D Cell Explorer pump system gas incubation system httpibidicomxtproductsenInstruments-AccessoriesHeating-Incubation-Systems httpibidicomxtproductsenInstruments-Accessoriesibidi-OPAL-Optical-O2-Measurement-System httpibidicomxtproductsenInstruments-AccessoriesNanolive-3D-Cell-Explorer httpibidicomxtproductsenInstruments-Accessoriesibidi-Pump-System httpibidicomxtproductsenInstruments-AccessoriesHeating-Incubation-Systemsibidi-Gas-Incubation-System iLAbSolutions (Agilent Technologies) - Instrument management and scheduling software (cores and labs) httpwwwilabsolutionscominstrument-access-control ImageJ - Fiji ImageJ NIH ImageJ ImageJ ndash Fiji (Fiji is just ImageJ) is the main download site httpfijisc httpsimagejnihgovij wwwimagejnet Inscopix ndash nVista in vivo mouse brain imaging miniature microscope httpswwwinscopixcomproducts Intelligent Imaging Innovations Inc (3i) ndash Slidebook imaging software Lattice light sheet (high speed gentle to cells high resolution imaging) Dual-view Inverted Selective Plane Illumination (diSPIM) VIVO 2-Photon (VIVO 2P) multiphoton microscopy Everest intravital imaging Marianas 3D real-time deconvolution timelapse spinning disk FRAP TIRF FLIM single molecule environmental control Phasor - optogenetic photostimulation using digital holography Yokogawa spinning disk confocal units wwwintelligent-imagingcom httpswwwintelligent-imagingcomslidebookphp httpswwwintelligent-imagingcomsystemsphplattice httpswwwintelligent-imagingcomsystemsphpdispim httpswwwintelligent-imagingcomsystemsphptwophoton httpswwwintelligent-imagingcomsystemsphpeverest httpswwwintelligent-imagingcomsystemsphpmarianas httpswwwintelligent-imagingcomoptogeneticsphp httpswwwintelligent-imagingcomsdcphp ISS Inc ndash fluorescence lifetime imaging microscopy fluorescence correlation spectroscopy (FCS) confocal imaging httpwwwisscommicroscopyindexhtml JenLab GmbH cyto-microscopy multiphoton tomography httpwwwjenlabdeproducts250html httpwwwjenlabde2PM-Cryo1330html

httpwwwjenlabdeMultiphoton-Tomography680html Jenoptik - microscope cameras httpswwwjenoptikcomproductscameras-and-imaging-modulesmicroscope-cameras JPK Instruments - integrated atomic force microscope (AFM) force sensing optical tweezers optical trapping single cell force spectroscopy (SCFS) httpwwwjpkcomindex2enhtml httpusajpkcomoptical-tweezers-optical-trapping29ushtml httpusajpkcomcellular-adhesion-cytomechanics30ushtml Keyence ndash VK-X confocal (upright) BZ-X700 widefield (inverted) httpwwwkeyencecomssproductsmicroscopevkx httpwwwkeyencecomssproductsmicroscopebz-x700indexjsp KK Technology - CapiScope HVCS Handheld Video Capillaroscopy System (CytoScan) httpwwwkktechnologycomhvcshtml LaVision BioTec ndash TriMscope Multiphoton TriM Scope II Adaptive Optics UltraMicroscope II light sheet httpwwwlavisionbiotecde httpwwwlavisionbiotecdetrim-scope-overviewhtml httpwwwlavisionbiotecdetrim-scope-ii-adaptive-opticshtml httpwwwlavisionbiotecdeultramicroscope-ii-introductionhtml Laxco ndash upright and inverted microscopes httpwwwlaxcoinccomMICROSCOPES Lego ndash Lego Idea Microscopes httpsideaslegocomprojects44370 httpwwwnico71frlego-working-microscope Li-Cor ndash near-infared fluorescent dyes and in vivo imaging agents in vivo and Western blot imaging systems httpswwwlicorcombioproductsreagents httpswwwlicorcombioproductsreagentsirdyebrightsite_imaging_agents httpswwwlicorcombioproductsimaging_systemsodyssey_familyhtml httpswwwlicorcombioproductsimaging_systemspearl httpswwwlicorcombioproductsimaging_systemscdigit Life Imaging Services - ldquothe Ludin chamberrsquo ldquothe cube amp the boxrdquo httpwwwlischthechamberhtml httpwwwlischtheboxhtml Lightform Inc ndash PARISS imaging spectrometer httplightforminccom LMU Bioimaging httpwwwbioimagingbmcmeduni-muenchendelinkswebsitesindexhtml httpwwwbioimagingbmcmeduni-muenchendelearneduwebsitesindexhtml Ludl Electronic Products Ltd ndash automated XY stages focus motors filter wheels httpwwwludlcom

LumaCyte ndash Laser force Cytology (laser trap meets microfluidics to suspend and manipulate single cells) httpwwwlumacytecomabouttechnology Lumencor ndash LEDs fluorescence light sources httplumencorcomproducts Luxcel ndash mitochondrial and cellular functions O2 sensor reagents httpluxcelcomproduct+list Luxendo GmbH ndash light sheet imager

wwwluxendoeu Lyncee tec - digital holography microscopy (DHM) high content screening by DHM httpwwwlynceeteccom httpwwwlynceeteccomhigh-content-screening Mad City Labs Inc - nanopositioning wwwmadcitylabscom Mauna Kea Technologies ndash CellVizio confocal laser endomicroscopy httpwwwmaunakeatechcomenhealthcare-professionalscellvizio-endomicroscopy-0 MBF Bioscience - stereology and neuron morphology quantitative imaging httpwwwmbfbiosciencecom McCrone Group wwwmccronecominstrument-sales Media Cybernetics Inc ndash Image Premier 3D AutoQuant X3 deconvolution httpwwwmediacycom Meiji Techno America wwwmeijitechnocom MesoLens Ltd httpwwwmesolenscomproducttechnical-specifications httpwwwmesolenscomimages httpswwwbiophotonicsstrathacukresearch_1htm Meyer Instruments ndash Pathscan Enabler GigaMacro digital pathology telepathology httpmeyerinstcom httpmeyerinstcompathscan-enabler-5 httpmeyerinstcomgigamacro-gigapixel-macro-imaging httpmeyerinstcomhomescanners httprealtimetelepathologycom Microarrays - Large-Scale Gene Expression and Microarray Links and Resources httpswwwebiacukarrayexpress Micro-Manager ndash Device Support ndash tabulates many microscope cameras and motorized accessories every new camera and accessory should have a uManager driver to enable simple use with Fiji ImageJ httpsmicro-managerorg httpsmicro-managerorgwikiDevice_Support httpsopen-imagingcom Microvolution ndash (near) instant gratification spatial deconvolution using NVidia GPU card(s) httpmicrovolutioncom Mightex Systems ndash optogenetics DMDDLP illuminator (digital micro-mirror device digital light processing) httpwwwmightexsystemscomindexphpcPath=245 Millipore-Sigma Merck KGaA (Amnis Corp CellASIC EMD Millipore) ndash ImageStreamX and FlowSight imaging flow cytometers ONIX2 Microperfusion System for microscopes httpswwwemdmilliporecom httpswwwemdmilliporecomUSenlife-science-researchcell-analysisamnis-imaging-flow-cytometersQ6ubqBm3UAAAFLCKIpygJnav httpwwwemdmilliporecomUSenlife-science-researchcell-culture-systemscellASIC-live-cell-analysisd1CbqBw58AAAE_0j13MnAnav Mitutoyo America Corp wwwmitutoyocom httpecatalogmitutoyocomMF-U-Series-176-High-power-Multi-function-Measuring-Microscopes-C1413aspx

Molecular Devices Corporation Universal Imaging Corporation (Danaher) ndash MetaMorph MetaFluor high content systems (HCS) httpswwwmoleculardevicescomsystemsmetamorph-research-imaging httpmdccusthelpcomappanswersdetaila_id19319 httpswwwmoleculardevicescomsystemshigh-content-imaging Molecular Machines amp Industries - laser microdissection and tweezer systems httpwwwmolecular-machinescomhome MUSE Microscopy Inc ndash Deep UV illumination for shallow depth of field imaging httpwwwmusemicrocom Micro Video Instruments Inc - DarkLite illuminator httpwwwmvi-inccom NanoEnTek ndash JuLI Stage (imager inside incubator or on lab bench) httpwwwjulistagecom National Instruments ndash LabView software httpwwwnicomen-ushtml Navitar - Hoffman Modulation Contrast (HMC alternative to differential interference contrast phase contrast) custom lens design UVDUVNUV imaging lenses httpsnavitarcommarketsmicroscopy httpsnavitarcomproductsimaging-opticscustom-microscope-objectivescustom-microscope-objectives httpsnavitarcomproductsimaging-opticsuv-imaging National Center for X-ray Tomography (NCXT) ndash soft X-ray tomography (CT of hydrated cells) XM-2 dedicated biological SXT microscope Prof Carolyn Larabell Director (see also SiriusXT) httpncxtlblgov httpncxtlblgovsxt httpncxtlblgovmanual httpncxtlblgovq=carolyn Neogenomics (Clarient) ndash MultiOmyx immunofluorescence or DNA FISH (ldquo60plexrdquo) httpneogenomicscomPharma-ServicesLab-ServicesMultiOmyxTechnologyMultiOmyx-IF-Assay-DNA-FISH-assay-NGS-from-ROI Nexcelom ndash Celigo imaging cytometer Cellometer cell counters httpwwwnexcelomcomCeligoindexphp httpwwwnexcelomcomProducts Nikon ndash Ti-LAPP modular illumination system (for Nikon Ti series microscopes) TIRF Optogenetics httpswwwnikoninstrumentscomProductsPhotostimulation-and-TIRFTi-LAPP Nirmidas Biotech httpwwwnirmidascomtechnologynir httpwwwnirmidascomproductsniriidye NVidia ndash Pascal 10+ Gbps GPU cards for instant gratification deconvolution (software from Microvolutioncom SVInl) httpwwwgeforcecomhardware10seriesgeforce-gtx-1080 httpwwwgeforcecomhardware10seriestitan-x-pascal httpwwwnvidiacomobjectquadro-graphics-with-pascalhtml Ocean Optics ndash spectrometers httpoceanopticscomproduct-categorymodular-spectrometers Oko-Lab stage top incubator httpwwwoko-labcomstage-top Open Microscopy Environment (OME) ndash OMERO (see also Glencoe Software) Bio-Formats LOCI

httpswwwopenmicroscopyorgsite httpswwwopenmicroscopyorgsiteproductsomero httpswwwopenmicroscopyorgsiteproductsbio-formats httpswwwopenmicroscopyorgsitesupportbio-formats52supported-formatshtml httpswwwopenmicroscopyorgsiteaboutdevelopment-teamskevin OpenSPIM ndash do-it-yourself selective plane illumination microscopy (light sheet imaging) httpopenspimorgWelcome_to_the_OpenSPIM_Wiki OpenSpinMicroscopy ndash do-it-yourself SPIMDSLMOPT microscopes httpssitesgooglecomsiteopenspinmicroscopy Ovizio ndash differential digital holography (similar to quantitative phase imaging) httpwwwoviziocomenHome httpwwwoviziocomenMicroscopesQMod Oxford Gene Technologies ndash microarrays ndash cytogenetics molecule genetics cancer research pre-implantation genetic diagnosis httpwwwogtcomclinical_genetics Oxford Nanoimaging ndash single molecule(s) localization fluorescence resonance energy transfer (FRET) (Kapanidis) wwwoxfordnicom Pathology Devices ndash LiveCell stage top incubator amp controller tissue microarrayers (TMA makers) httpwwwpathologydevicescomLiveCellhtm httpwwwpathologydevicescomTMArrayerhtm PeCon GmbH ndash microscope incubators httpwwwpeconbiz Pembroke Instruments ndash spectrometers mini-lasers httppembrokeinstrumentscomqmini-spectrometer httppembrokeinstrumentscommini-lasers PerkinElmer ndash in vivo imaging systems (bioluminescence NIR fluorescence) Vectra digital slide scanner httpwwwperkinelmercomcategoryin-vivo-imaging-instruments httpwwwperkinelmercomcategoryquantitative-pathology-imaging-instruments Phi Optics ndash CellVista SLIM Pro (quantitative phase microscopy) httpphiopticscom Photometrics (Roper Scientific) ndash DualView QuadView httpwwwphotometricscom httpwwwphotometricscomproductsmultichannel Photon Technology International httpwwwpti-njcomindexhtml

PicoQuant GmbH ndash fluorescence lifetime imaging microscopes (FLIM) STED 3D-EasySTED httpswwwpicoquantcomproductscategoryfluorescence-microscopes httpswwwpicoquantcomapplicationscategorylife-sciencested httpwwweasystedorg Physik Instrumente GmbH amp Co KG (PI) - Nanopositioning Applications for Microscopy Neuroscience and Metrology httpswwwphysikinstrumentecomen httpwwwpi-usausindexphp PreSens Prescision Sensing GmbH - VisiSens measure and visualize Oxygen pH or carbon dioxide distributions httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-biological-researchhtml httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-life-science-researchhtml Prior Scientific

httpwwwprior-uscom Profusa Inc - Lumee tissue-integrated biosensors scaffolds httpprofusacomtechnology Reindeer Graphics Inc ndash OptiPix Fovea Pro 9plugins for Adobe Photoshop 6 and CS series) httpwwwreindeergraphicscom Renishaw - StreamLine fast chemical imaging Raman spectroscopy httpwwwrenishawcomenstreamline-generate-chemical-images-rapidly--9449 httpwwwrenishawcomenraman-spectroscopy--6150 Sanford Burnham Prebys ndash High Content Screening httpwwwsbpdiscoveryorgtechnologysrPagesLaJolla_HighContentScreeningaspx ScopeM - Scientific Center for Optical and Electron Microscopy - ETH Zurich httpwwwscopemethzch SiriusXT - soft X-ray tomography (SXT) microscope (CT scan hydrated cell) httpsiriusxtcom SpectraGenetics - Fluorogen Activating Peptides (FAPs) new genetically encoded ldquobinaryrdquo reporters httpspectrageneticscomproductsvectors-for-expressing-fluorogen-activating-proteinsfap-technology-overview Spirochrome - Silicon Rhodamine (SiR) and other fluorescent reagents probes for bioimaging httpspirochromecom Stanford Photonics Inc httpwwwstanfordphotonicscom httpwwwstanfordphotonicscomLife20SciencesLifeScihtm

Stream Technologies Inc ndash ColorFlow lens (multi-wavelength emission onto a camera) httpwwwstreamtechinccomproducts Sutter Instrument Company httpwwwsuttercom httpwwwsuttercomMICROSCOPESindexhtml httpwwwsuttercomIMAGINGindexhtml SVI Huygens ndash Professional (general image analysis) deconvolution NVidia GPU deconvolution httpssvinlHuygensProfessional httpssvinlHuygensDeconvolution httpssvinlHuygensGPU Sysmex Partex ndash CyScope httpwwwsysmex-parteccomproductsmicroscopyhtml httpwwwsysmex-parteccomproductsprdouct-detailviewcyscopeR-malaria-3238html Technical Instruments httpwwwtechinstcomproductsphp TESCAN Brno sro - Tescan Q-PHASE multimodal holographic quantitative phase imaging system (QPi) optional fluorescence httpwwwtescancomenproductsq-phaseq-phase httpq-phasetescancom httpq-phasetescancomindexphptechnologyspecifications Ted Pella Inc ndash specialty light microscopy and electron microscopy supplies httpswwwtedpellacom Texas Instruments ndash DLP 4100 development kit (digital light processingrsquo DMD digital micromirror device) httpwwwticomtooldlpd4x00kit

ThorLabs ndash iCyte imaging cytometer multiphoton confocal EnVista digital slide scanning microscopes httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7473 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7494 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=5696 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=6570 TIRF Labs lightguide TIRF prism TIRF TIRF-Electrochemistry httpwwwtirf-labscom httpwwwtirf-labscomtechnologieshtml TissueVision - Serial Two Photon Tomography (image volume ablate imaged volume with multiphoton laser repeat) httpwwwtissuevisioncomtechnology Tokai Hit - stage top incubator httpwwwtokaihitcomenglishproduct_guidanceoptionhtml TopoNomos Ltd ndash Toponome Imaging Cycler ndash immunofluorescence (100plex) httpwwwtoposnomoscomtechnologyhtml Ultivue Inc ndash DNA-PAINT ndash reagents data processing service httpwwwultivuecom httpwwwultivuecomproducts UMech Technologies ndash Cytovar HCS up to 16 excitation wavelengths httpcloudumechcomproducts httpcloudumechcomproductsmodelC16 Visitech ndash vt-iSIM instant super-resolution microscopy up to 1000 frames per second confocal scanners and light engines httpwwwvisitechcoukvt-isimhtml httpwwwvisitechcoukproductshtml Visitron Systems GmbH - high speed imaging systems httpwwwvisitronde Visualsonics (Fujifilm) - photoacoustic imaging httpwwwvisualsonicscomproductstechnology-overview Wicked Lasers httpwwwwickedlaserscom httpwwwwickedlaserscomarctic WITec Wissenschaftliche Instrumente und Technologie GmbH - imaging systems for FLIM Raman AFM and SNOM analysis httpwitecdeproducts httpwwwwitec-instrumentscom WM Keck Center for Adaptive Optical Microscopy (CfAOM) at UC Santa Cruz httpscfaomsoeucscedu httpcfaoucolickorgpgallery Yokogawa Corp ndash spinning disk confocal scanner live cell imager high content screener confocal quantitative cytometer httpwwwyokogawacomsolutionsproducts-platformslife-science httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-scanner-unit-csu httpwwwyokogawacomsolutionsproducts-platformslife-scienceall-in-one-live-cell-imaging-solution httpwwwyokogawacomsolutionsproducts-platformslife-sciencehigh-throughput-cytological-discovery-system httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-quantitative-image-cytometer Zellkraftwerk (ChipCytometry) ndash immunofluorescence (80plex) httpwwwzellkraftwerkcomProducts2phtml httpwwwzellkraftwerkcomZKWOnephtmlSoftware

httpwwwchipcytometrycomtechnologyphtml Fluorescence Spectra Data and Graphing Sites PubSpectra ndash Excel file data download httpsworksbepresscomgmcnamara9 BD Biosciences ndash spectrum viewer Brilliant fluorophores httpwwwbdbiosciencescomussspectrumviewer httpwwwbdbiosciencescomusapplicationssspectrumguidepage BioLegend ndash spectra analyzer Brilliant Violet fluorophores httpwwwbiolegendcomspectraanalyzer httpwwwbiolegendcombrilliantviolet Chroma Technology httpswwwchromacomspectra-viewer eBioscience (Affymetrix ThermoFisher) ndash fluorPlan ndash a multi-laser spectra viewer httpwwwebiosciencecomresourcesfluorplan-spectra-viewerhtm Spectra Viewer (requires Java) Evrogen ndash Spectrum Viewer httpevrogencomspectra-viewerflashviewerhtml Fluorophoresorg ndash Fluorescent Substances httpwwwfluorophorestugrazatsubstance I Love GFP httpssitesgooglecomsiteilovegfpHomefps Lambert and Thorn UCSF Fluorescent protein properties httpnicucsfeduFPvisualization Leica Microsystem - ldquoFluoScoutrdquo httpwwwleica-microsystemscomfluoscout

Molecular Probes Invitrogen Thermo Fisher ndash Fluorescence SpectraViewer httpwwwthermofishercomusenhomelife-sciencecell-analysislabeling-chemistryfluorescence-spectraviewerhtml httpsitunesapplecomusappfluorescence-spectraviewerid421031826 (iTunes App) Nightsea - Compendium of spectra web sites httpwwwnightseacomsfa-sharingfluorescence-spectra-viewers Omega Optical ldquoCurvomatricrdquo httpswwwomegafilterscomcurvomatic

PhotoChemCAD 20 (Jonathan S Lindsey) dye spectra database and chemistry calculator NIRvana Sciences httpwwwphotochemcadcom httpnirvanasciencescompage_id=3088 UCSF (Lambert Thorn 2016) - Fluorescent protein properties httpnicucsfeduFPvisualization University of Arizona - Fluorescent Spectra Database httpwwwspectraarizonaedu Semrock - Searchlight httpssearchlightsemrockcom Spectroscopy Ninja ndash links to spectral and fluorescence data Spekwin32 spectroscopy software httpwwweffemm2deinfoinfo_specdatahtml

httpwwweffemm2deindexhtml Zeiss ndash interactive fluorescence dye and filter database overview dyes overview filter sets httpswwwmicro-shopzeisscoms=50479761ad21e5ampl=enampp=usampf=fampa=i httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=d httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=f Researcher Labs Alby Diaspro ndash IIT httpwwwlambsitindexphppage=People Alice Ting ndash MIT httpwwwtinglaborgresearch Allen Institute for Brain Science httpwwwalleninstituteorgwhat-we-dobrain-science Allen Institute for Cell Science httpwwwalleninstituteorgwhat-we-docell-science Amina Qutub - Rice University - How are human cells designed lab httpsqutublaborgqutub-lab Amy Herr UC Berkeley ndash Single cell Westerns httpherrlabberkeleyedu Amy Palmer ndash UC Boulder httpspalmerlabcoloradoedu Andrew York ndash Calico Life Sciences httpswwwcalicolabscomteam-memberandrew-york Anne Carpenter ndash Broad Institute CellProfiler httpspersonalbroadinstituteorganne Arjun Raj UPenn single molecule RNA FISH quantitative understanding cellular functions httprajlabseasupenneduindexhtml httpwwwpopscicomsciencearticle2013-09arjun-raj Atsuko Miyawaki - Laboratory for Cell Function Dynamics (CFDS) Fucci2 fluorescent proteins cell cycle indicator httpwwwbrainrikenjpenfacultydetails30 httpcfdsbrainrikenjp httpcfdsbrainrikenjpFuccihtml Aydogan Ozcan - UCLA - new imaging and sensing architectures httpinnovateeeuclaeduwelcomehtml httpwwwhhmiorgscientistsaydogan-ozcan Badri Roysam - UH - FARSIGHT Toolkit httpwwweeuhedufacultyroysam httpwwwfarsight-toolkitorgwikiMain_Page Brian J Ford ndash microscopist and popularizer httpsuklinkedincominprofbrianjford Carolyn Larabell ndashNational Center for X-ray Tomography (LBNL) UCSF httpncxtlblgovq=carolyn httpprofilesucsfeducarolynlarabell Clare Waterman ndash NHLBI NIH

httpswwwnhlbinihgovresearchintramuralresearcherspiwaterman-clare Dana Peer - Columbia University - Computational Systems Biology viSNE and more software httpwwwc2b2columbiaedudanapeerlabhtml httpwwwc2b2columbiaedudanapeerlabhtmlcythtml David Mayerich - UH - STIM Laboratory Scalable Tissue Imaging and Modeling httpwwweeuhedufacultymayerich httpstimeeuhedu David Piston WUSTL httpwwwcellbiologywustledufacultytenureddavid-w-piston-phd Diane Lidke and Keith Lidke - University of New Mexico httppathologyunmeduresearchfaculty-laboratoriesthe-lidke-laboratoryindexhtml httppanda3physunmedu~klidke Donna Arndt-Jovin and Thomas Jovin - Max Planck Institute for Biophysical Chemistry Laboratory of Cellular Dynamics httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsDonnaArdndt-JovinResearchAreasAndProjects httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsChairmanThomasJovinResearchAreasAndProjects Ed Boyden ndash MIT Media Lab ndash expansion microscopy (ExM) optogenetics httpsyntheticneurobiologyorg httpsyntheticneurobiologyorgprotocols httpsyntheticneurobiologyorgpublications httpwwwtedcomtalksed_boyden_baby_diapers_inspired_this_new_way_to_study_the_brain httpwwwextbiocombuycell Elizabeth Blackburn ndash Salk Institute - Telomeres httpswwwsalkeduscientistelizabeth-blackburn httpsenwikipediaorgwikiElizabeth_Blackburn httpswwwnobelprizeorgnobel_prizesmedicinelaureates2009blackburn-factshtml Elizabeth Hillman - Columbia university - SCAPE (Swept Confocally-Aligned Planar Excitation) high speed 3D microscopy DyCE (dynamic contrast enhancement to image and segment small animal organs live) Neuroimaging amp Neurovascular Coupling httporionbmecolumbiaedu~hillmanInstrumentationhtml httporionbmecolumbiaedu~hillmanSCAPEhtml httporionbmecolumbiaedu~hillmanMolecularhtml httporionbmecolumbiaedu~hillmanBrain_Imaginghtml Eric Betzig ndash UCSF (moving from HHMI Janelia Farm in 2016) httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014betzig-factshtml Eva Sevick-Muraca ndash UT Health Science Center at Houston molecular imaging clinical NIR fluoresceince imaging httpswwwutheduimmprofilehtmid=1005459 httpswwwutheduimmcentersmolecular-imaginghtm Evelin Schrock - Technische Universitaumlt Dresden spectral karyotyping cytogenetics httpswwwresearchgatenetprofileEvelin_Schrock Garry Nolan Stanford University ndash Mass cytometry MIBI-ToF high throughput imaging mass cytometry (42plex) httpwebstanfordedugroupnolanresourceshtml httpwebstanfordedugroupnolantechnologieshtml George McNamara ndash Cell Morphometry (41) Figure 1 right top two panels (55) The Chase (2016 temporal area maps lsquodynamic morphologyrsquo) (76) newsletter series on ldquoThe Chaserdquo (73) direct Vimeo movie of ldquoThe Chaserdquo Tiki_Goddess linkedin 10+plex blog httpsworksbepresscomgmcnamara41 httpsworksbepresscomgmcnamara55 httpsworksbepresscomgmcnamara76

httpsworksbepresscomgmcnamara73 httpsvimeocom175151196 httphomeearthlinknet~tiki_goddess httpswwwlinkedincomingeorgemcnamara httpswwwlinkedincompulsebd-biosciences-listed-tandems-horizon-brilliant-violets-mcnamara Gillian Griffiths - University of Cambridge - T-cell immunological synapse httpwwwcimrcamacukresearchprincipal-investigatorsprincipal-investigators-a-hgriffiths Hari Shroff NIBIB NIH httpswwwnibibnihgovlabs-at-nibibsection-high-resolution-optical-imaging-hroi HHMI Janelia Farm Research Campus (JFRC) - Advanced Imaging Center Open Science httpswwwjaneliaorgopen-scienceadvanced-imaging-center-aic httpswwwjaneliaorgopen-science Jeanne Lawrence University of Massachussetts Medical School httpwwwumassmededucellbiolabslawrencepersonnelprincipal-investigator Jennifer Lippincott-Schwartz ndash HHMI Janelia Farm httpswwwjaneliaorgpeoplejennifer-lippincott-schwartz Jin Zhang ndash UCSD httpprofilesucsdedujinzhang Joe DeRisi - UCSF - 3D printable lab stuff httpderisilabucsfeduindexphppage=3D John Russ Chris Russ Fovea Pro plugins for Adobe Photoshop httpwwwdrjohnrusscomindexhtml httpwwwdrjohnrusscombookshtml httpwwwreindeergraphicscomfoveaprotutorialhtml Julie Theriot httpcmgmstanfordedutheriot Karl Deisseroth ndash Stanford University ndash CLARITY optical tissue clearing Optogenetics httpclarityresourcecenterorg httpwebstanfordedugroupdlaboptogeneticsindexhtml Karsten Koumlnig (Koenig) - Saarland University and JenLab GmbH - biophotonics httpwwwbltuni-saarlanddeindex_ehtm httpwwwjenlabde httpwwwthelastescape-filmcom Karsten Rodenacker ndash image measurements httpkaro03bplacednetkaroMeMisc_WWWpdfMicrosoftWord-EQUAPATpdf Kevin Eliceiri ndash UW-Madison Open Source Photonics and Software Laboratory for Optical and Computational Instrumentation (LOCI) wwwlociwiscedu Klaus Kemp ndash Microlife Services ndash diatoms and other prepared microscope slides httpwwwdiatomscouk Kurt Thorn UCSF httpthornlabucsfedu httpsnicucsfedublog httpnicucsfeduFPvisualization httpgigapancomgigapans163370 Lihong Wang - WUSTL - Optical Imaging Laboratory photoacoustic tomography

httpoilabseaswustledu httpoilabseaswustleduresearch_0html Loren Looger - HHMI JFRC - iGluSnFr fluorescent protein biosensor httpswwwjaneliaorglablooger-lab Mary-Lou Pardue ndash MIT (first ever in situ hybridization with J Gall) httpsbiologymitedupeoplemary_lou_pardue httpsenwikipediaorgwikiMary-Lou_Pardue Nancy Allbritton - UNC - Chemical cytometry microraft arrays organ-on-a-chip httpswwwbmencsueduindexphpcomponentcomprofileruserprofilenlallbri httpwwwbmeuncedulabsallbritton Navin Varadarajan - UH - single-cell Lab httpwwwcheeuhedufacultyvaradarajan httpsinglecellcheeuheducontacthtml Nicholas Shaner - Scintillon Institute - mNeonGreen httpwwwscintillonorgshaner_lab Rebecca Richards-Kortum httpbioengineeringriceedufacultyrebecca_richards-kortumaspx Robert Campbell - Fluorescent proteins optogenetic proteins httpcampbellwebchemualbertaca httpcampbellwebchemualbertacaprojects-2 Robert Murphy ndash Cell measurements web services httpmurphylabwebcmueduservices Sabine Mai - University of Manitoba - Genomic Centre for Cancer Research and Diagnosis (GCCRD) - httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBPlatformsGCCRDhtml httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBScientistsMaiAwardshtml Sally Ward and Raimund Ober - Texas AampM University - httpwwwwardoberlabcom Simon Watkins - U Pittsburgh Center for Biologic Imaging httpwwwcbppittedufacultywatkinshtml httpwwwcbppittedufacultylabwatkinshtml httpwwwcbipittedu Stefan Hell ndash Deparment Hell NanoBiopohotonics httpwwwmpibpcmpgdehell httpsenwikipediaorgwikiStefan_Hell httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014hell-factshtml Sunney Xie Harvard httpsbernsteinharvardedu Susan Cox ndash 3B microscopy httpwwwcoxphysicscomindexhtml httpwwwcoxphysicscom3b Radim Chmeliacutek - Center for innovative microscopy Experimental biophotonics group httpswwwceiteceuceitec-butexperimental-biophotonicsrg3 httpwwwbiophotczhome Taekjip Ha ndash Johns Hopkins University ndash single molecules httphamedjhmiedu

Thomas Ried ndash NCI NIH SKYM-FISH and CGH Database httpsccrcancergovGenetics-Branchthomas-ried httpsccrcancergovGenetics-Branchthomas-riedqt-staff_profile_tabs=9qt-staff_profile_tabs ftpftpncbinlmnihgovsky-cghDATA httpswwwncbinlmnihgovdbvar Viviana Gradinaru ndash CalTech ndash CLARITYPACT Optogenetics httpwwwbbecaltecheducontentviviana-gradinaru httpglabcaltechedu Vladislav Verkhusha - near infrared fluorescent proteins httpwwweinsteinyuedulabsvlad-verkhushadefaultaspx httpwwweinsteinyueduresearchfacilitiesfluorescent WE Moerner ndash Stanford University httpwebstanfordedugroupmoerner Willard Wiggans ndash micro gallery httpwwwwillard-wigancomgallery Wolf Frommer ndash Molecular sensors httpbiosensordpbcarnegiescienceedu (fluorescent protein biosensors table) Xiaowei Zhuang = Harvard httpzhuangharvardedu Yuval Garini - Bar-Ilan University - Nano-Bio-Photonics laboratory httpgarinilabbiuacil Microscopy Magazines Imaging amp Microscopy httpwwwimaging-gitcommagazine Laser Focus World httpwwwlaserfocusworldcomindexhtml Microscopy amp Analysis httpwwwmicroscopy-analysiscom Microscopy Today httpwwwmicroscopy-todaycom Microscopy-UK httpwwwmicroscopy-ukorguk Photonics Spectra Biophotonics httpwwwphotonicscomPublicationsaspx The Microscope Journal httpmcriorgv72the-microscope-journal RMS Infocus Magazine httpwwwrmsorgukstudy-readinfocus-magazinehtml Nobel Prizes in Light Microscopy and Related Fields Chemistry 1925 colloids (light sheet) Zsigmondy (Siedentopf Zsigmondy 1902) httpswwwnobelprizeorgnobel_prizeschemistrylaureates1925

Chemistry 2000 conductive polymers Heeger MacDiarmid Shirakawa (Brilliant Violets Ultraviolets Blues) httpwwwnobelprizeorgnobel_prizeschemistrylaureates2000 Chemistry 2008 green fluorescent protein GFP Shimomura Chalfie Tsien httpwwwnobelprizeorgnobel_prizeschemistrylaureates2008 Chemistry 2014 super-resolved fluorescence microscopy Betzig Hell Moerner httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014 Physics 1953 Phase Contrast Zernike httpswwwnobelprizeorgnobel_prizesphysicslaureates1953 Physics 2009 invention of an imaging semiconductor circuit ndash the CCD sensor Kao Boyle Smith httpwwwnobelprizeorgnobel_prizesphysicslaureates2009 Physics 2014 efficient blue light emitting diodes Akasaki Amano Nakamura httpwwwnobelprizeorgnobel_prizesphysicslaureates2014 Physiology or Medicine 2006 Fire and Mello RNA interference ndash gene silencing by double stranded RNA httpwwwnobelprizeorgnobel_prizesmedicinelaureates2006 Physiology or Medicine 2006 Capecchi Evans Smithies specific gene modifications in mice by the use of embryonic stem cells httpwwwnobelprizeorgnobel_prizesmedicinelaureates2007 Physiology or Medicine 2009 Blackburn Greider Szostak how chromosomes are protected by telomeres and telomerase httpwwwnobelprizeorgnobel_prizesmedicinelaureates2009 Physiology or Medicine 2012 Gurdon Yamamanka matured cells can be reprogrammed to become pluripotent httpwwwnobelprizeorgnobel_prizesmedicinelaureates2012

Table 442 Fluorophores Photophysics Data

Fluorophore Abs or Ex max (nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Acridine orange 271 520 27000 020 5

Alexa Fluor 430 431 541 16000 055 9

Alexa Fluor 488 495 519 71000 094 67

Alexa Fluor 532 532 553 81000 080 65

Alexa Fluor 546 556 573 104000 096 100

Alexa Fluor 568 578 603 91300 075 69

Alexa Fluor 594 590 617 73000 064 47

Allophycocyanin (APC) 650 660 700000 068 476

Atto 390 390 479 24000 090 22

Atto 425 436 484 45000 065 29

Atto 430LS 433 547 32000 065 21

Atto 465 453 508 75000 075 56

Atto 490LS 496 661 40000 030 12

Atto 520 525 547 105000 095 100

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 2: McNamara 20161006 revised draft tables for CPHG Light ...

Table 441 Useful Light Microscopy Web Sites

Light Microscopy (overview) Confocal Listserv (not just for confocal microscopes) httpslistsumneducgi-binwaA0=confocalmicroscopy G McNamara ndash Multi-Probe Microscopy (content last updated 2005 includes extensive glossary) httpsworksbepresscomgmcnamara2 Molecular Expressions National High Magnetic Field Laboratory (NHMFL) Florida State University httpmicromagnetfsuedu Microscopedia ndash Resources Guide To Light Microscopy httpwwwmicroscopediacomMicroscopyLight Molecular Probes Inc Invitrogen Thermo Fisher (Many links to useful and informative sites) httpswwwthermofishercomusenhomebrandsmolecular-probeshtml Photonics buyerrsquos guide (much more comprehensive than this list) httpwwwphotonicscomBuyersGuideaspx Science Exchange ndash Reproducibility Initiative (focus on commercial antibodies and uses) httpswwwscienceexchangecomapplicationsreproducibility Wikipedia - Chromosomes httpsenwikipediaorgwikiChromosome Wikipedia ndash Microscope httpenwikipediaorgwikiMicroscope Societies Association of Biomolecular Resource Facilities Light Microscopy Research Group (ABRF LMRG) httpsabrforgresearch-grouplight-microscopy-research-group-lmrg European Microscopy Society (EMS) httpwwweurmicsocorg International Society for Advancement of Cytometry (ISAC) httpisac-netorg Microscopy Society of America (MSA) httpwwwmicroscopyorg Royal Microscopical Society (RMS) httpwwwrmsorguk Major Microscope Companies Leica Microsystems Inc httpwwwleica-microsystemscom httpwwwleica-microsystemscomscience-lab httpwwwleica-microsystemscomproductsconfocal-microscopesdetailsproductleica-tcs-sp8-sted-3x

Nikon Instruments Inc httpswwwnikoninstrumentscom httpswwwmicroscopyucom

httpswwwnikoninstrumentscomProductsLive-Cell-Screening-SystemsBioStation-CT

Olympus America Inc httpwwwolympus-lifesciencecomen httpolympusmagnetfsuedu

Zeiss (Carl Zeiss Inc) httpwwwzeisscom httpwwwzeisscomcorporateen_ushomehtml httpzeiss-campusmagnetfsueduindexhtml httpwwwzeisscommicroscopyen_deproductsmicroscope-camerasaxiocam-702-monohtml

Karyotype Systems and Digital Pathology Digital Pathology Blog ndash see educational sponsors for comprehensive list of digital pathology vendors httptissuepathologycom 3DHistech ndash digital pathology Pannoramic scanners httpwww3dhistechcom Agilent Pathology Solutions Dako ndash IHC and ISH reagents autostainers httpwwwdakocomdkindexknowledgecenteromnishtm httpwwwdakocomdkar42productgroupshtm Applied Spectral Imaging ndash SKY Spectral karyotyping GenASIs digital pathology httpwwwspectral-imagingcom httpwwwspectral-imagingcomapplicationsspectral-imaging httpwwwspectral-imagingcomapplicationspathology Bioview ndash pathology and FISH cytogenetics scanners httpbioviewcom Definiens (MedImmuneAstraZeneca) - digital pathology image analysis (with deep learning algorithms) httpwwwdefinienscom Huron Digital Pathology ndash large area confocal scanning (entire human brain slices) httpwwwhurondigitalpathologycom Leica Biosystems ndash CytoVision CytogeneticsFISH Aperio digital pathology httpswwwleicabiosystemscomclinical-microscopy-surgery-radiologycytogenetics httpswwwleicabiosystemscomdigital-pathology MetaSystems International ndash karyotyping FISH digital pathology httpsmetasystems-internationalcomenproducts Molecular Probes ThermoFisher Scientific ndash Evos FL Auto and Evos Floid cell imaging stations high content screening (HCS) (Cellomics) httpswwwthermofishercomusenhomelife-sciencecell-analysiscellular-imagingcell-imaging-systemsevos-fl-autohtml httpswwwthermofishercomusenhomelife-sciencecell-analysiscellular-imagingcell-imaging-systemsfloid-cell-imaging-stationhtml httpswwwthermofishercomusenhomelife-sciencecell-analysiscellular-imaginghigh-content-screeninghigh-content-screening-instrumentshtml Philips ndash digital pathology httpwwwusaphilipscomhealthcaresolutionspathology Ventana Roche Digital Pathology ndash digital pathology FISH httpwwwventanacomdigitalpathology Visiopharm ndash digital pathology image analysis (with deep learning algorithms) stereology httpwwwvisiopharmcom

Filter and Filter Sets Manufacturers Alluxa httpwwwalluxacom BMV Optical wwwbmvopticalcom Chroma Technology httpwwwchromacom Edmund Optics ndash filters prisms httpwwwedmundopticscomopticsoptical-filtersbandpass-filtersfluorescence-filter-kits3226 httpwwwedmundopticscomopticsprisms Iridian Spectral Technologies httpwwwiridian-optical-filterscomproduct-categoryfluorescence-sets Newport (Spectra-Physics Oriel Bookham New Focus) httpswwwnewportcomcoptical-filters

Omega Optical httpwwwomegafilterscom Optolong (Kunming Yulong OpticalampElectronics Technology Co Ltd) httpwwwoptolongcomenproductsfluorescence-filters Schott Glass Technologies httpwwwschottcom httpwwwusschottcomadvanced_opticsenglishsynadvanced_opticsproductsoptical-componentsoptical-filtersinterference-filtersindexhtml Semrock Inc (IDEX CVI Melles Griot) httpsemrockcom ThorLabs ndash optical filters httpswwwthorlabscomnavigationcfmguide_id=21 Major scientific CMOS (sCMOS) camera companies (your next microscope cameras should likely be sCMOS not CCD or EMCCD) Andor Technology Ltd (Oxford Instruments) httpwwwandorcomscientific-camerasneo-and-zyla-scmos-cameras Hamamatsu httpswwwhamamatsucomusencommunitylife_science_camerasensor_technologiesscientific_cmos_scmos_image_sensorindexhtml httpwwwhamamatsucomusencommunitylife_science_cameraproductsearchC11440-22CUindexhtml PCO httpsuspco-techcomscmos-cameras Photometrics httpwwwphotometricscomproductsscmos Fluorescent Proteins Luciferases (DNA plasmids andor other expression products) 490BioTech ndash LuxABCDE

http490biotechcomvectors-2 Abberior httpwwwabberiorcomshopLabels-by-FunctionFluorescent-Proteins7_14html httpwwwabberiorcomshopLabels-by-Application1html Addgeneorg wwwaddgeneorg httpswwwaddgeneorgfluorescent-proteins httpswwwaddgeneorgfluorescent-proteinsbiosensors httpswwwaddgeneorgfluorescent-proteinslocalization httpswwwaddgeneorgoptogenetics httpswwwaddgeneorgfluorescent-proteinsdavidson httpswwwaddgeneorgRoger_Tsien Allele Biotechnology httpwwwallelebiotechcomFluorescent-Proteins Bell Biosystems ndash Magnelle living MRI contrast agents (magnetotactic bacteria taken up by human cells in vitro) with fluorescent proteins ndash in vivo cell tracking httpwwwbellbiosystemscomProducts-and-ServicesCell-Tracking-Solutions BioBricks Foundation httpbiobricksorg BioPop (Intrexon) ndash Dinoflagellates bioluminescence luciferaseluciferin httpsbiopopcomproducts Chromotek GmbH - Chromobodies Nano-Boosters (llama nanobodies attached to or detecting FP) httpwwwchromotekcomproductschromobodies httpwwwchromotekcomproductschromobodiescell-cycle-chromobodyr httpwwwchromotekcomproductsnano-boosters DNA 20 chromogenic and fluorescent protein paintbox (not really IP-Free) httpswwwdna20comproductsprotein-paintbox Evrogen httpevrogencomproductsbasicFPsshtml httpevrogencomproductsBiosensorsshtml httpevrogencomproductsOrganelle-labelingshtml iGEM BioBricks ndash reporter proteins including fluorescent proteins httppartsigemorgProtein_coding_sequencesReporters iGEM Registry of Standard Biological Parts httppartsigemorgMain_Page InvivoGen ndash GFP Lucia luciferase reporters httpwwwinvivogencomdual-reporter MBL International Corp ndash fluorescent proteins httpswwwmblintlcomproductsfluorescent-proteins httpruomblcojpbioeproductflproteinfuccihtml Millipore-Sigma Sigma-Aldrich ndash firefly luciferase D-luciferin httpwwwsigmaaldrichcomlife-sciencemetabolomicsenzyme-exploreranalytical-enzymesluciferasehtml Molecular Probes Inc Invitrogen Thermo Fisher ndash Bacmam 20 fluorescent proteins biosensors FUCCI httpwwwprobescom httpwwwthermofishercomusenhomebrandsmolecular-probeshtml httpswwwthermofishercomusenhomeindustrialpharma-biopharmadrug-discovery-developmenttarget-and-lead-identification-and-validationpathway-biologycellular-pathway-analysisbacmam-systembacmam-reagentshtml

Montana Molecular LLC - genetically encoded fluorescent biosensors and probes for cell-based assays and live cell imaging httpmontanamolecularcomproductsproducts-overview NanoLight Technologies ndash Renilla GFP luciferases httpwwwnanolightcomNanoFluorsGFP_Expression_Vectorshtml httpswwwbiotoycomenlearn n3D Biosciences ndash generate 3D cell spheroids high throughput screening image changes using smartphone camera inside incubator httpwwwn3dbiocomproductsmagnetic-3d-bioprinting httpwwwn3dbiocomproductsassays New England BioLabs (NEB) ndash Cypridina Gaussia luciferases httpswwwnebcomapplicationscellular-analysisreporter-systems Promega ndash Monster GFP NanoLuc httpswwwpromegacomproductsreporter-assays-and-transfectionreporter-vectors-and-cell-linesmonster-green-fluorescent-protein-phmgfp-vector httpswwwpromegacomproductsreporter-assays-and-transfectionreporter-vectors-and-cell-linesnanoluc-luciferase-reportersnanoluc-genetic-reporter-vectors Fluorescence Products (reagents) Advanced Cell Diagnostics (Bio-Techne) - branched DNA probe sets for RNA FISH httpsacdbiocomproducts Affymetrix eBioscience Thermo Fisher - branched DNA probe sets for RNA FISH httpwwwaffymetrixcomestorepromotionsviewrnaishindexaffx Anaspec ndash HiLyte Fluorophores FRET probes httpswwwanaspeccomproductsproductcategoryaspid=10 Antibody Resource Page httpwwwantibodyresourcecom Biocompare ndash Antibodies httpwwwbiocomparecomAntibodies Cell Signaling Technology ndash fluorescence antibodies httpswwwcellsignalcombrowseimmunofluorescence-immunocytochemistryif-paraffinif-frozen Essen Biosciences ndash Bacmam 30 ready to use FP gene transfection reagents httpwwwessenbiosciencecomenproductsreagents-consumablesincucyte-nuclight-red-bacmam-30-reagent-nuclear-labeling-cat-no-4621 GE Healthcare Amersham Biosciences httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usbrandscydye Global Biological Standards Institute (GBSI) ndash Antibody Validation Initiative httpwwwgbsiorgworkantibodies Goryo Chemical httpwwwgoryochemicalcom Human Protein Atlas (academic) Atlas Antibodies (commercial arm) US distributor httpwwwproteinatlasorg httpsatlasantibodiescom httpwwwsigmaaldrichcomlife-sciencecell-biologyantibodiesprestige-antibodieshtml

Integrated DNA Technologies (IDT) httpwwwidtdnacomsiteCatalogmodificationsdyes httpwwwidtdnacompagesproductsmodificationsfluorophoresfreedom-dyes httpwwwidtdnacomsiteCatalogModificationsCategory4 Jackson ImmunoResearch httpswwwjacksonimmunocom KPL (formerly Kirkegaard amp Perry Laboratories Inc) SeraCare httpwwwkplcom LGC Biosearch Technologies ndash dyes for oligonucleotides single molecular RNA FISH image gallery httpswwwbiosearchtechcomsupporteducationfluorophores-and-quenchers httpstellarisfishsmugmugcom httpsinglemoleculefishcom httpswwwbiosearchtechcomproductsrna-fish (typically 48 20 base oligonucleotides) Marker Gene Technologies Inc (MGT) httpwwwmarkergenecomfluorescent-reagent Miltenyi Biotec ndash REAfinity recombinant engineered antibodies (no Fc Receptor binding) FASER fluorescence amplification kits NiraWave fluorophores (indocyanine green formulations) httpwwwmiltenyibioteccomenproducts-and-servicesmacs-flow-cytometryreagentsantibodies-and-dyesrecombinant-antibodiesaspx httpwwwmiltenyibioteccomenproducts-and-servicesmacs-flow-cytometryreagentssupport-reagentsfaser-kitsaspx httpwwwmiltenyibioteccomenproducts-and-servicesviscover-imagingoptical-imagingaspx Molecular Probes Inc Invitrogen Thermo Fisher ndash largest vendor of fluorophores Molecular Probes Handbook (web resource) Tyramide Signal Amplification kits httpwwwprobescom httpswwwthermofishercomusenhomereferencesmolecular-probes-the-handbookhtml httpswwwthermofishercomusenhomereferencesmolecular-probes-the-handbooktablestyramide-signal-amplification-tsa-kitshtml NIRvana Sciences httpnirvanasciencescom httpnirvanasciencescompage_id=3088 One World Lab ndash antibody search httponeworldlabcomantibodies CytoCell Oxford Gene Technologies ndash DNA FISH probes human mouse pig chicken httpwwwcytocell-uscom Perkin Elmer ndash nucleotides labeling kits Tyramide Signal Amplification Kits (TSA) Opal 7plex discovery panel kit based on sequential TSA httpwwwperkinelmercomcategoryfluorescent-hapten-nucleotides httpwwwperkinelmercomcategoryfluorescent-agents-labeling-kits-dyes httpwwwperkinelmercomlab-solutionsresourcesdocsBRO_TSAsignalamplificationpdf httpwwwperkinelmercomproductopal-7-immunology-discovery-kit-op7ds1001kt

Rockland Inc httpwwwrockland-inccomcommerceindexjsp

TEFLabs ndash fluorescent ion indicators (Ca++ Cl- K+ Mg++ Na+ pH Zn++) ionophores fluorophores httpwwwteflabscomion-indicators Vector Laboratories Inc httpwwwvectorlabscom

Live cell imaging dishes and multi-well plates (ldquoglass bottom dishesrdquo)

We recommend these for simplified handing and processing vs either thick plastic dishesplates or having to handle loose coverslips with your valuable cells

Leicester Imaging Technologies (LITE) - University of Leicester - table of dishes for live cell imaging (our table has current links and bad links left out) httpwww2leacukcollegesmedbiopsychfacilities-and-servicescbsliteaiftips-and-tricks-1dishes-for-live-cell-imaging Bellco Glass Inc - glass flat bottom plate httpwwwbellcoglasscomnode1046 Bioptechs - interchangable coverslip dish ($036 per experiment) httpwwwbioptechscomproductinterchangeable-coverslip-dish Brooks Automation Inc - clar bottom optical imaging microplates httpwwwbrookscomproductslife-scienceconsumablesmatrical-microplates-microtubes-racks-lidsglass-bottom-optical-imaging-microplates Cell EampG - glass bottom cell sulture dishes plates httpcellegcomproducthtml Cellvis - glass bottom dishes and plates httpwwwcellviscom_35-mm-glass-bottom-dishes_products_by_categoryphpcat_id=3 Corning - glass bottom microplates httpcatalog2corningcomLifeSciencesen-USShoppingCategoryaspxcategoryname=Microplates20-202015(Lifesciences)|Assay20Microplates20-202015(Lifesciences) Design 1 Solutions - Custom microplates and fabrication services httpwwwdesign1solutionscomcustom-microplateshtml Eppendorf - cell imaging dishes imaging plates httpsonline-shopeppendorfcomOC-enCell-Culture-and-Imaging-Consumables-110320Cell-Imaging-Consumables-120210Eppendorf-Cell-Imaging-Dishes-PF-19457html httpsonline-shopeppendorfcomOC-enCell-Culture-and-Imaging-Consumables-110320Cell-Imaging-Consumables-120210Eppendorf-Cell-Imaging-Plates-PF-19458html Greiner Bio-One International - CellView glass bottom dishes quadrant dishes httpsshopgbocomenrowarticlescataloguearticle0110_0110_0040_002027513 ibidi - u-Plates glass bottom dishes microfluidic slides httpibidicomxtproductsenibidi-Labwarem-Plates httpibidicomxtproductsenibidi-Labware Matsunami Glass Ind Ltd httpwwwmatsunami-glasscojpenglishlifebiodata01html Mattek - glass bottom dishes and SBS plates httpswwwmattekcomstore-categoryculturewareglass-bottom-dishes Nunc - glass bottom dishes httpswwwthermofishercomordercatalogproduct150680 NEST Biotechnology Co Ltd Wuxi Jiangsu PRChina httpwwwnestscientificusacomproducts_detailproductId=31html PerkinElmer - glass bottom plates httpwwwperkinelmercomSECatalogCategoryIDMicroplates

Porvair Sciences - clear bottom assay plates httpwwwporvair-sciencescomenservices-menulife-sciencesclear-bottom-assay-plates Ted Pella Inc - glass bottom dishes clear wall or black wall (manufactured by WillCo Wells) httpswwwtedpellacomsection_html706dishhtm Warner Instruments (Harvard Apparatus) - culture dishes perfusion systems httpswwwwarneronlinecomproduct_cat_infocfmid=1322 Willco Wells - glass bottom dishes wwwwillcowellscom World Precision Instruments - Fluorodish glass bottom dishes httpswwwwpiinccomproductslaboratory-suppliesfd35-100-fluorodish-cell-culture-dish-35mm-23mm-well-pkg-of-100 Microscopes Microscopy Accessories (accessorize) Reagents Resources 3scan ndash knife edge scanning microscope (images slices repeats through specimen) httpwww3scancomdata-2 89North (affiliated with Chroma Technology Corp) httpwww89northcom Abberior Instruments ndash STED RESOLFT precision localization super-resolution microscopes STEDYCON convert any fluorescence microscope to STED httpabberior-instrumentscom httpabberior-instrumentscomproductscompact-lineabberior-stedy-con Acquifer ndash HIVE imaging machine (computer hardware) for high content screening big data httpswwwacquiferde Adobe Systems Inc httpwwwAdobecom httpscreativeadobecomproductsdownloadphotoshop Affymetrix eBioscience (ThermoFisher) - microarrays httpwwwaffymetrixcomestorebrowselevel_one_category_template_onejspparent=35796ampcategory=35796 httpwwwaffymetrixcomestorecatalog131547AFFYGeneChip26231743B+System+3000Dx+v22623423B1_1 Agilent Technologies ndash SureScan microarray scanner (array CGH microRNA SNPs CNV) httpwwwgenomicsagilentcomenMicroarray-Scanner-Processing-HardwareSureScan-Microarray-Scannercid=AG-PT-144 Andor Technology (Oxford Instruments) ndash sCMOS cameras Dragonfly spinning disk confocal Revolution DSD2 differential spinning disk confocal photostimulation (fluorescence recovery after photobleaching optogenetics) Mosaic3 DMDDLP high speed light patterning (optogenetics structured illumination) MicroPoint pulsed UV laser for ablation DNA damage photobleachingactivation uncaging accessories httpwwwandorcomscientific-camerasneo-and-zyla-scmos-cameras httpwwwandorcommicroscopy-systemsdragonfly httpwwwandorcommicroscopy-systemsrevolution-dsd httpwwwandorcommicroscopy-systemsphotostimulation httpwwwandorcommicroscopy-systemsphotostimulationmosaic httpwwwandorcommicroscopy-systemsphotostimulationmicropoint httpwwwandorcommicroscopy-systemsmicroscopy-components Apogee Instruments Inc (Andor Technology) ndash CCD cameras and filter wheels (mostly marketed for astronomy) httpwwwccdcomandorhtml Applied Scientific Instrumentation Inc ndash light sheet imager (iSPIM diSPIM)

wwwasiimagingcom httpwwwasiimagingcomindexphpproductslight-sheet-microscopyselective-plane-illumination-microscopy-ispim-dispim Applied NanoFluorescence LLC ndash NS1 NanoSpectralyzer (Raman and UV-VISNIR) NS MiniTracer near infrared spectrometer NFM NanoFluorescence microscope multi-laser light source single wall carbon nanotubes (NIR II fluorophores) httpappliednanocomproductshtml httpappliednanocomproductsns1html httpappliednanocomproductsproduct-list77-ns-minitracerhtml httpappliednanocomproductsnfmhtml httpappliednanocomproductsls-nhtml httpwwwnanowerkcomnewsnewsid=24132php Applied Spectral Imaging Inc httpwwwspectral-imagingcom ArgoLight ndash fluorescence resolution test target slides httpargolightcom AttoCube - attoMICROSCOPY overview attoCFM - Multichannel cryogenic (low temperature) confocal fluorescence microscopes 08 NA objective lenses 400-1000 nm spectral range httpwwwattocubecom httpwwwattocubecomattomicroscopyintroductiontab-2 httpwwwattocubecomattodownloads AutoQuant (Media Cybernetics) spatial deconvolution httpwwwmediacycomautoquantx3 Becker amp Hickl GmbH httpwwwbecker-hicklcomproductshtm Berkeley Lights Inc ndash manueuver into nanowells incubate recover 4000 single cells per chip httpswwwberkeleylightscomtechnology Bioaxial ndash Codim imaging conical diffraction beam shaper for super-resolution (4 sub-images) httpwwwbioaxialcomcodim-imaging Bioptechs - Live-Cell Micro-Observation Products httpwwwbioptechscom Bionumbers - database of useful biological numbers httpbionumbershmsharvardeduKeyNumbersaspx Biostatus ndash DRAQ5 DRAQ7 ApopTRAK CyTRAK Orange CyGel HypoxiTRAK httpwwwbiostatuscomProducts Bio-Tek ndash Cytation 3 Cell Imaging Multi-Mode Reader Lionheart FX Automated Live Cell Imager httpwwwbiotekcomproductsimagingcytation3_cell_imaging_multi_mode_readerhtml httpwwwbiotekcomproductsimaginglionheartfx_automated_live_cell_imagerhtml Biovision Technologies ndash distributor for several imagers including VT-iSIM instant super-resolution microscope httpbiovision-technologiescom httpbiovision-technologiescomsystemshtml httpbiovision-technologiescomvtisimhtml Bitplane (Andor Oxford Instruments) ndash Imaris imaging software httpwwwbitplanecom BMV Optical - custom lens assemblies and optical filters wwwbmvopticalcom

Bruker (previously Prairie Technologies Vutara) ndash Opterra confocal Ultima Multiphoton Vutara 352 single molecule localization microscopes httpswwwbrukercomproductsfluorescence-microscopesopterra-confocal-microscopyoverviewhtml httpswwwbrukercomproductsfluorescence-microscopesultima-multiphoton-microscopyhtml httpswwwbrukercomproductsfluorescence-microscopesvutara-super-resolution-microscopyoverviewhtml Cairn Research ndash standard and custom accessories ex Light Sheet Illuminator MultiCam (4 cameras) custom design httpswwwcairn-researchcouk httpswwwcairn-researchcoukproductl-spi-single-plane-illuminator (dual L-SPI for 4 illumination directions) httpswwwcairn-researchcoukproductmulticam httpswwwcairn-researchcoukcustom-design Cameca ndash NanoSIMS 50L (7plex stable isotope imaging) httpwwwcamecacominstruments-for-researchnanosimsaspx CellMic (formerly Holomic) - blood analysis or fluorescence imaging cytometer on a cell phone httpwwwcellmiccomcontentadvanced-technologies httpwwwcellmiccomcontentfluorescent-imaging-cytometry-and-e-coli-detection-on-a-cell-phone CellOptic ndash FINCH (Fresnel INcoherence Correlation Holography) httpwwwcellopticcomindex2html CellProfiler ndash High content screening (HCS) image processing and analysis software httpcellprofilerorg ClearLight Diagnostics - CLARITY Optimized Light Sheet Microscopy (3D tissue optical clearing + light sheet imaging) httpwwwclearlightdxcomindexhtml Confocalnl ndash Rescan confocal microscopy to obtain 170 nm resolution with any pinhole diameter httpwwwconfocalnl CoolLED ndash LED light sources httpwwwcoolledcomproduct-detailpe-4000 Crest Optics SRL ndash X-Light confocal X-Light V2 + VCS (VideoConfocal super-resolution) httpwwwcrestoptcom httpwwwcrestoptcomhtmlx-light_v2_vcshtml Cytoskeleton Inc - live cell imaging reagents Spirochrome SiR bioimaging probes httpwwwcytoskeletoncomlive-cell-reagents httpwwwcytoskeletoncomlive-cell-reagentsspirochrome CytoViva ndash darkfield imaging hypspectral imaging httpwwwcytovivacomproducts3d-enhanced-darkfield-imaging httpwwwcytovivacomproductshyperspectral-imaging-2hyperspectral-imaging Data Translation Inc - digitizer cards httpwwwdatxcom Delmic BV - combined correlative scanning electron microscope with inverted fluorescence microscope httpwwwdelmiccomdelphi httpswwwdelphimicroscopecom httpwwwdelmiccomsecom-super-resolution Digital Light Innovations (DLi) - CELscope C-mount LED Microscope using Texas Instruments DLP illuminator with a simple stand httpswwwdlinnovationscomdli-deep-dives-celscope-c-mount-led-microscope Double Helix LLC ndash single molecule localization microscope (Piestun) httpdoublehelixopticscom Edinburgh Super-resolution Imaging Consortium (ESRIC)

httpwwwesricorg Energetiq ndash Deep ultraviolet (DUV high radiance 170-2100 nm) laser driven light source (LDLS) httpwwwenergetiqcom Epi Technology - CaliCube - Cube for fluorescence light path to inspect epi Illumination light source (lamp) fiber optic or liquid light guide httpwwwepitechnologycomepitechnology-1 Essen Biosciences ndash Incucyte Zoom (imager inside incubator) httpwwwessenbiosciencecomenproductsincucyte Estigen Tissue Science ndash manual and automated tissue arrayer (tissue microarray maker) httpwwwestigencom Euro-Bioimaging httpwwweurobioimagingeu Excelitas Technologies (formerly Lumen Dynamics) ndash X-Cite LEDs httpwwwexcelitascomPagesProductX-Cite-LED-Solutionsaspx Expansion Technologies Inc (extbio) ndash Expansion microscopy httpwwwextbiocombuycell FEI (formerly Till Photonics) (Thermo Fisher) ndash correlative LM-EM single molecule Cryo-EM httpswwwfeicomlife-sciencescellular-biology httpswwwfeicomlife-sciencescellular-biologycorrelative-microscopy httpswwwfeicomlife-sciencesstructural-biology Femtonics - Multi-phton microscopes software accessories caged glutamate reagents services httpfemtonicseuproducts First Light Imaging ndash C-Red NIR imaging (800-2500 nm NIR windows I II III 650-950 nm 1100-1350 nm 1600-1870 nm[Shi et al 2015]) high speed visible EMCCD (400-1000 nm) httpwwwfirst-lightfrcategoryrangesinfrared Fluidigm ndash Helios imaging CyTOF mass cytometer (42plex) Callisto (32 independent chambers dose with up to 16 independent factors for 1-1000 cell populations culture up to 3 week) Polaris functional genomics meets imaging (48 single cells up to 24 hours after single cell selection from a population) httpswwwfluidigmcomproductshelios httpswwwfluidigmcomproductscallisto httpswwwfluidigmcomproductspolaris GattaQuant - nanorulers for high resolution microscopes and super-resolution microscopes performance testing httpwwwgattaquantcomNanoruler GE Healthcare life Sciences Applied Precision ndash DeltaVision deconvolution OMX OMX SR httpwwwgelifesciencescomwebappwcsstoresservletproductByIdenGELifeSciences-us29065728 httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usproductsAlternativeProductStructure_2380729065721 httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usproductsAlternativeProductStructure_2380729115476 German BioImagingorg httpwwwgermanbioimagingorgwikiindexphpMain_Page httpwwwgermanbioimagingorgwikiindexphpWorkgroup6SoftwarePackages GIGAmacro ndash Magnify2 gigapixel imagery oof macroscopic and microscopic objects Terapixel macro image httpwwwgigamacrocomgigapixel-macro-imaging-system httpwwwgigamacrocomworlds-first-terapixel-macro-image

Glencoe Software ndash OMERO Plus enterprise data management for scientific images and any associated metadata (OME = Open Microscopy Environment) DataViewer PathViewer httpsglencoesoftwarecomomeroplushtml httpsglencoesoftwarecomdataviewerhtml httpsglencoesoftwarecompathviewerhtml Gooch amp Housego ndash spectral imager httpsgoochandhousegocomminiature-spectral-imaging-camera httpwwwghinstrumentscomproductsspectral-imaging-synthesishsi-440c-hyperspectral-imaging-system Hindsight Imaging ndash spectral imaging httphindsight-imagingcom Horiba Scientific - SWIFT ultra-fast Raman confocal imaging Raman spectroscopy httpwwwhoribacomscientificproductsraman-spectroscopyraman-imagingswift httpwwwhoribacomscientificproductsraman-spectroscopyraman-imaging httpwwwhoribacomscientificproductsraman-spectroscopy IATIA Ultima Capital ndash QPm (quantitative phase microscopy) httpwwwultimacapitalnetiatiaimagingPublicationsIatia20ImagingapplicationNotesqpmApplicationWithConfocalMicroscopespdf Ibidi - heating and incubation systems optical O2 measurement systems Nanolive 3D Cell Explorer pump system gas incubation system httpibidicomxtproductsenInstruments-AccessoriesHeating-Incubation-Systems httpibidicomxtproductsenInstruments-Accessoriesibidi-OPAL-Optical-O2-Measurement-System httpibidicomxtproductsenInstruments-AccessoriesNanolive-3D-Cell-Explorer httpibidicomxtproductsenInstruments-Accessoriesibidi-Pump-System httpibidicomxtproductsenInstruments-AccessoriesHeating-Incubation-Systemsibidi-Gas-Incubation-System iLAbSolutions (Agilent Technologies) - Instrument management and scheduling software (cores and labs) httpwwwilabsolutionscominstrument-access-control ImageJ - Fiji ImageJ NIH ImageJ ImageJ ndash Fiji (Fiji is just ImageJ) is the main download site httpfijisc httpsimagejnihgovij wwwimagejnet Inscopix ndash nVista in vivo mouse brain imaging miniature microscope httpswwwinscopixcomproducts Intelligent Imaging Innovations Inc (3i) ndash Slidebook imaging software Lattice light sheet (high speed gentle to cells high resolution imaging) Dual-view Inverted Selective Plane Illumination (diSPIM) VIVO 2-Photon (VIVO 2P) multiphoton microscopy Everest intravital imaging Marianas 3D real-time deconvolution timelapse spinning disk FRAP TIRF FLIM single molecule environmental control Phasor - optogenetic photostimulation using digital holography Yokogawa spinning disk confocal units wwwintelligent-imagingcom httpswwwintelligent-imagingcomslidebookphp httpswwwintelligent-imagingcomsystemsphplattice httpswwwintelligent-imagingcomsystemsphpdispim httpswwwintelligent-imagingcomsystemsphptwophoton httpswwwintelligent-imagingcomsystemsphpeverest httpswwwintelligent-imagingcomsystemsphpmarianas httpswwwintelligent-imagingcomoptogeneticsphp httpswwwintelligent-imagingcomsdcphp ISS Inc ndash fluorescence lifetime imaging microscopy fluorescence correlation spectroscopy (FCS) confocal imaging httpwwwisscommicroscopyindexhtml JenLab GmbH cyto-microscopy multiphoton tomography httpwwwjenlabdeproducts250html httpwwwjenlabde2PM-Cryo1330html

httpwwwjenlabdeMultiphoton-Tomography680html Jenoptik - microscope cameras httpswwwjenoptikcomproductscameras-and-imaging-modulesmicroscope-cameras JPK Instruments - integrated atomic force microscope (AFM) force sensing optical tweezers optical trapping single cell force spectroscopy (SCFS) httpwwwjpkcomindex2enhtml httpusajpkcomoptical-tweezers-optical-trapping29ushtml httpusajpkcomcellular-adhesion-cytomechanics30ushtml Keyence ndash VK-X confocal (upright) BZ-X700 widefield (inverted) httpwwwkeyencecomssproductsmicroscopevkx httpwwwkeyencecomssproductsmicroscopebz-x700indexjsp KK Technology - CapiScope HVCS Handheld Video Capillaroscopy System (CytoScan) httpwwwkktechnologycomhvcshtml LaVision BioTec ndash TriMscope Multiphoton TriM Scope II Adaptive Optics UltraMicroscope II light sheet httpwwwlavisionbiotecde httpwwwlavisionbiotecdetrim-scope-overviewhtml httpwwwlavisionbiotecdetrim-scope-ii-adaptive-opticshtml httpwwwlavisionbiotecdeultramicroscope-ii-introductionhtml Laxco ndash upright and inverted microscopes httpwwwlaxcoinccomMICROSCOPES Lego ndash Lego Idea Microscopes httpsideaslegocomprojects44370 httpwwwnico71frlego-working-microscope Li-Cor ndash near-infared fluorescent dyes and in vivo imaging agents in vivo and Western blot imaging systems httpswwwlicorcombioproductsreagents httpswwwlicorcombioproductsreagentsirdyebrightsite_imaging_agents httpswwwlicorcombioproductsimaging_systemsodyssey_familyhtml httpswwwlicorcombioproductsimaging_systemspearl httpswwwlicorcombioproductsimaging_systemscdigit Life Imaging Services - ldquothe Ludin chamberrsquo ldquothe cube amp the boxrdquo httpwwwlischthechamberhtml httpwwwlischtheboxhtml Lightform Inc ndash PARISS imaging spectrometer httplightforminccom LMU Bioimaging httpwwwbioimagingbmcmeduni-muenchendelinkswebsitesindexhtml httpwwwbioimagingbmcmeduni-muenchendelearneduwebsitesindexhtml Ludl Electronic Products Ltd ndash automated XY stages focus motors filter wheels httpwwwludlcom

LumaCyte ndash Laser force Cytology (laser trap meets microfluidics to suspend and manipulate single cells) httpwwwlumacytecomabouttechnology Lumencor ndash LEDs fluorescence light sources httplumencorcomproducts Luxcel ndash mitochondrial and cellular functions O2 sensor reagents httpluxcelcomproduct+list Luxendo GmbH ndash light sheet imager

wwwluxendoeu Lyncee tec - digital holography microscopy (DHM) high content screening by DHM httpwwwlynceeteccom httpwwwlynceeteccomhigh-content-screening Mad City Labs Inc - nanopositioning wwwmadcitylabscom Mauna Kea Technologies ndash CellVizio confocal laser endomicroscopy httpwwwmaunakeatechcomenhealthcare-professionalscellvizio-endomicroscopy-0 MBF Bioscience - stereology and neuron morphology quantitative imaging httpwwwmbfbiosciencecom McCrone Group wwwmccronecominstrument-sales Media Cybernetics Inc ndash Image Premier 3D AutoQuant X3 deconvolution httpwwwmediacycom Meiji Techno America wwwmeijitechnocom MesoLens Ltd httpwwwmesolenscomproducttechnical-specifications httpwwwmesolenscomimages httpswwwbiophotonicsstrathacukresearch_1htm Meyer Instruments ndash Pathscan Enabler GigaMacro digital pathology telepathology httpmeyerinstcom httpmeyerinstcompathscan-enabler-5 httpmeyerinstcomgigamacro-gigapixel-macro-imaging httpmeyerinstcomhomescanners httprealtimetelepathologycom Microarrays - Large-Scale Gene Expression and Microarray Links and Resources httpswwwebiacukarrayexpress Micro-Manager ndash Device Support ndash tabulates many microscope cameras and motorized accessories every new camera and accessory should have a uManager driver to enable simple use with Fiji ImageJ httpsmicro-managerorg httpsmicro-managerorgwikiDevice_Support httpsopen-imagingcom Microvolution ndash (near) instant gratification spatial deconvolution using NVidia GPU card(s) httpmicrovolutioncom Mightex Systems ndash optogenetics DMDDLP illuminator (digital micro-mirror device digital light processing) httpwwwmightexsystemscomindexphpcPath=245 Millipore-Sigma Merck KGaA (Amnis Corp CellASIC EMD Millipore) ndash ImageStreamX and FlowSight imaging flow cytometers ONIX2 Microperfusion System for microscopes httpswwwemdmilliporecom httpswwwemdmilliporecomUSenlife-science-researchcell-analysisamnis-imaging-flow-cytometersQ6ubqBm3UAAAFLCKIpygJnav httpwwwemdmilliporecomUSenlife-science-researchcell-culture-systemscellASIC-live-cell-analysisd1CbqBw58AAAE_0j13MnAnav Mitutoyo America Corp wwwmitutoyocom httpecatalogmitutoyocomMF-U-Series-176-High-power-Multi-function-Measuring-Microscopes-C1413aspx

Molecular Devices Corporation Universal Imaging Corporation (Danaher) ndash MetaMorph MetaFluor high content systems (HCS) httpswwwmoleculardevicescomsystemsmetamorph-research-imaging httpmdccusthelpcomappanswersdetaila_id19319 httpswwwmoleculardevicescomsystemshigh-content-imaging Molecular Machines amp Industries - laser microdissection and tweezer systems httpwwwmolecular-machinescomhome MUSE Microscopy Inc ndash Deep UV illumination for shallow depth of field imaging httpwwwmusemicrocom Micro Video Instruments Inc - DarkLite illuminator httpwwwmvi-inccom NanoEnTek ndash JuLI Stage (imager inside incubator or on lab bench) httpwwwjulistagecom National Instruments ndash LabView software httpwwwnicomen-ushtml Navitar - Hoffman Modulation Contrast (HMC alternative to differential interference contrast phase contrast) custom lens design UVDUVNUV imaging lenses httpsnavitarcommarketsmicroscopy httpsnavitarcomproductsimaging-opticscustom-microscope-objectivescustom-microscope-objectives httpsnavitarcomproductsimaging-opticsuv-imaging National Center for X-ray Tomography (NCXT) ndash soft X-ray tomography (CT of hydrated cells) XM-2 dedicated biological SXT microscope Prof Carolyn Larabell Director (see also SiriusXT) httpncxtlblgov httpncxtlblgovsxt httpncxtlblgovmanual httpncxtlblgovq=carolyn Neogenomics (Clarient) ndash MultiOmyx immunofluorescence or DNA FISH (ldquo60plexrdquo) httpneogenomicscomPharma-ServicesLab-ServicesMultiOmyxTechnologyMultiOmyx-IF-Assay-DNA-FISH-assay-NGS-from-ROI Nexcelom ndash Celigo imaging cytometer Cellometer cell counters httpwwwnexcelomcomCeligoindexphp httpwwwnexcelomcomProducts Nikon ndash Ti-LAPP modular illumination system (for Nikon Ti series microscopes) TIRF Optogenetics httpswwwnikoninstrumentscomProductsPhotostimulation-and-TIRFTi-LAPP Nirmidas Biotech httpwwwnirmidascomtechnologynir httpwwwnirmidascomproductsniriidye NVidia ndash Pascal 10+ Gbps GPU cards for instant gratification deconvolution (software from Microvolutioncom SVInl) httpwwwgeforcecomhardware10seriesgeforce-gtx-1080 httpwwwgeforcecomhardware10seriestitan-x-pascal httpwwwnvidiacomobjectquadro-graphics-with-pascalhtml Ocean Optics ndash spectrometers httpoceanopticscomproduct-categorymodular-spectrometers Oko-Lab stage top incubator httpwwwoko-labcomstage-top Open Microscopy Environment (OME) ndash OMERO (see also Glencoe Software) Bio-Formats LOCI

httpswwwopenmicroscopyorgsite httpswwwopenmicroscopyorgsiteproductsomero httpswwwopenmicroscopyorgsiteproductsbio-formats httpswwwopenmicroscopyorgsitesupportbio-formats52supported-formatshtml httpswwwopenmicroscopyorgsiteaboutdevelopment-teamskevin OpenSPIM ndash do-it-yourself selective plane illumination microscopy (light sheet imaging) httpopenspimorgWelcome_to_the_OpenSPIM_Wiki OpenSpinMicroscopy ndash do-it-yourself SPIMDSLMOPT microscopes httpssitesgooglecomsiteopenspinmicroscopy Ovizio ndash differential digital holography (similar to quantitative phase imaging) httpwwwoviziocomenHome httpwwwoviziocomenMicroscopesQMod Oxford Gene Technologies ndash microarrays ndash cytogenetics molecule genetics cancer research pre-implantation genetic diagnosis httpwwwogtcomclinical_genetics Oxford Nanoimaging ndash single molecule(s) localization fluorescence resonance energy transfer (FRET) (Kapanidis) wwwoxfordnicom Pathology Devices ndash LiveCell stage top incubator amp controller tissue microarrayers (TMA makers) httpwwwpathologydevicescomLiveCellhtm httpwwwpathologydevicescomTMArrayerhtm PeCon GmbH ndash microscope incubators httpwwwpeconbiz Pembroke Instruments ndash spectrometers mini-lasers httppembrokeinstrumentscomqmini-spectrometer httppembrokeinstrumentscommini-lasers PerkinElmer ndash in vivo imaging systems (bioluminescence NIR fluorescence) Vectra digital slide scanner httpwwwperkinelmercomcategoryin-vivo-imaging-instruments httpwwwperkinelmercomcategoryquantitative-pathology-imaging-instruments Phi Optics ndash CellVista SLIM Pro (quantitative phase microscopy) httpphiopticscom Photometrics (Roper Scientific) ndash DualView QuadView httpwwwphotometricscom httpwwwphotometricscomproductsmultichannel Photon Technology International httpwwwpti-njcomindexhtml

PicoQuant GmbH ndash fluorescence lifetime imaging microscopes (FLIM) STED 3D-EasySTED httpswwwpicoquantcomproductscategoryfluorescence-microscopes httpswwwpicoquantcomapplicationscategorylife-sciencested httpwwweasystedorg Physik Instrumente GmbH amp Co KG (PI) - Nanopositioning Applications for Microscopy Neuroscience and Metrology httpswwwphysikinstrumentecomen httpwwwpi-usausindexphp PreSens Prescision Sensing GmbH - VisiSens measure and visualize Oxygen pH or carbon dioxide distributions httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-biological-researchhtml httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-life-science-researchhtml Prior Scientific

httpwwwprior-uscom Profusa Inc - Lumee tissue-integrated biosensors scaffolds httpprofusacomtechnology Reindeer Graphics Inc ndash OptiPix Fovea Pro 9plugins for Adobe Photoshop 6 and CS series) httpwwwreindeergraphicscom Renishaw - StreamLine fast chemical imaging Raman spectroscopy httpwwwrenishawcomenstreamline-generate-chemical-images-rapidly--9449 httpwwwrenishawcomenraman-spectroscopy--6150 Sanford Burnham Prebys ndash High Content Screening httpwwwsbpdiscoveryorgtechnologysrPagesLaJolla_HighContentScreeningaspx ScopeM - Scientific Center for Optical and Electron Microscopy - ETH Zurich httpwwwscopemethzch SiriusXT - soft X-ray tomography (SXT) microscope (CT scan hydrated cell) httpsiriusxtcom SpectraGenetics - Fluorogen Activating Peptides (FAPs) new genetically encoded ldquobinaryrdquo reporters httpspectrageneticscomproductsvectors-for-expressing-fluorogen-activating-proteinsfap-technology-overview Spirochrome - Silicon Rhodamine (SiR) and other fluorescent reagents probes for bioimaging httpspirochromecom Stanford Photonics Inc httpwwwstanfordphotonicscom httpwwwstanfordphotonicscomLife20SciencesLifeScihtm

Stream Technologies Inc ndash ColorFlow lens (multi-wavelength emission onto a camera) httpwwwstreamtechinccomproducts Sutter Instrument Company httpwwwsuttercom httpwwwsuttercomMICROSCOPESindexhtml httpwwwsuttercomIMAGINGindexhtml SVI Huygens ndash Professional (general image analysis) deconvolution NVidia GPU deconvolution httpssvinlHuygensProfessional httpssvinlHuygensDeconvolution httpssvinlHuygensGPU Sysmex Partex ndash CyScope httpwwwsysmex-parteccomproductsmicroscopyhtml httpwwwsysmex-parteccomproductsprdouct-detailviewcyscopeR-malaria-3238html Technical Instruments httpwwwtechinstcomproductsphp TESCAN Brno sro - Tescan Q-PHASE multimodal holographic quantitative phase imaging system (QPi) optional fluorescence httpwwwtescancomenproductsq-phaseq-phase httpq-phasetescancom httpq-phasetescancomindexphptechnologyspecifications Ted Pella Inc ndash specialty light microscopy and electron microscopy supplies httpswwwtedpellacom Texas Instruments ndash DLP 4100 development kit (digital light processingrsquo DMD digital micromirror device) httpwwwticomtooldlpd4x00kit

ThorLabs ndash iCyte imaging cytometer multiphoton confocal EnVista digital slide scanning microscopes httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7473 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7494 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=5696 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=6570 TIRF Labs lightguide TIRF prism TIRF TIRF-Electrochemistry httpwwwtirf-labscom httpwwwtirf-labscomtechnologieshtml TissueVision - Serial Two Photon Tomography (image volume ablate imaged volume with multiphoton laser repeat) httpwwwtissuevisioncomtechnology Tokai Hit - stage top incubator httpwwwtokaihitcomenglishproduct_guidanceoptionhtml TopoNomos Ltd ndash Toponome Imaging Cycler ndash immunofluorescence (100plex) httpwwwtoposnomoscomtechnologyhtml Ultivue Inc ndash DNA-PAINT ndash reagents data processing service httpwwwultivuecom httpwwwultivuecomproducts UMech Technologies ndash Cytovar HCS up to 16 excitation wavelengths httpcloudumechcomproducts httpcloudumechcomproductsmodelC16 Visitech ndash vt-iSIM instant super-resolution microscopy up to 1000 frames per second confocal scanners and light engines httpwwwvisitechcoukvt-isimhtml httpwwwvisitechcoukproductshtml Visitron Systems GmbH - high speed imaging systems httpwwwvisitronde Visualsonics (Fujifilm) - photoacoustic imaging httpwwwvisualsonicscomproductstechnology-overview Wicked Lasers httpwwwwickedlaserscom httpwwwwickedlaserscomarctic WITec Wissenschaftliche Instrumente und Technologie GmbH - imaging systems for FLIM Raman AFM and SNOM analysis httpwitecdeproducts httpwwwwitec-instrumentscom WM Keck Center for Adaptive Optical Microscopy (CfAOM) at UC Santa Cruz httpscfaomsoeucscedu httpcfaoucolickorgpgallery Yokogawa Corp ndash spinning disk confocal scanner live cell imager high content screener confocal quantitative cytometer httpwwwyokogawacomsolutionsproducts-platformslife-science httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-scanner-unit-csu httpwwwyokogawacomsolutionsproducts-platformslife-scienceall-in-one-live-cell-imaging-solution httpwwwyokogawacomsolutionsproducts-platformslife-sciencehigh-throughput-cytological-discovery-system httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-quantitative-image-cytometer Zellkraftwerk (ChipCytometry) ndash immunofluorescence (80plex) httpwwwzellkraftwerkcomProducts2phtml httpwwwzellkraftwerkcomZKWOnephtmlSoftware

httpwwwchipcytometrycomtechnologyphtml Fluorescence Spectra Data and Graphing Sites PubSpectra ndash Excel file data download httpsworksbepresscomgmcnamara9 BD Biosciences ndash spectrum viewer Brilliant fluorophores httpwwwbdbiosciencescomussspectrumviewer httpwwwbdbiosciencescomusapplicationssspectrumguidepage BioLegend ndash spectra analyzer Brilliant Violet fluorophores httpwwwbiolegendcomspectraanalyzer httpwwwbiolegendcombrilliantviolet Chroma Technology httpswwwchromacomspectra-viewer eBioscience (Affymetrix ThermoFisher) ndash fluorPlan ndash a multi-laser spectra viewer httpwwwebiosciencecomresourcesfluorplan-spectra-viewerhtm Spectra Viewer (requires Java) Evrogen ndash Spectrum Viewer httpevrogencomspectra-viewerflashviewerhtml Fluorophoresorg ndash Fluorescent Substances httpwwwfluorophorestugrazatsubstance I Love GFP httpssitesgooglecomsiteilovegfpHomefps Lambert and Thorn UCSF Fluorescent protein properties httpnicucsfeduFPvisualization Leica Microsystem - ldquoFluoScoutrdquo httpwwwleica-microsystemscomfluoscout

Molecular Probes Invitrogen Thermo Fisher ndash Fluorescence SpectraViewer httpwwwthermofishercomusenhomelife-sciencecell-analysislabeling-chemistryfluorescence-spectraviewerhtml httpsitunesapplecomusappfluorescence-spectraviewerid421031826 (iTunes App) Nightsea - Compendium of spectra web sites httpwwwnightseacomsfa-sharingfluorescence-spectra-viewers Omega Optical ldquoCurvomatricrdquo httpswwwomegafilterscomcurvomatic

PhotoChemCAD 20 (Jonathan S Lindsey) dye spectra database and chemistry calculator NIRvana Sciences httpwwwphotochemcadcom httpnirvanasciencescompage_id=3088 UCSF (Lambert Thorn 2016) - Fluorescent protein properties httpnicucsfeduFPvisualization University of Arizona - Fluorescent Spectra Database httpwwwspectraarizonaedu Semrock - Searchlight httpssearchlightsemrockcom Spectroscopy Ninja ndash links to spectral and fluorescence data Spekwin32 spectroscopy software httpwwweffemm2deinfoinfo_specdatahtml

httpwwweffemm2deindexhtml Zeiss ndash interactive fluorescence dye and filter database overview dyes overview filter sets httpswwwmicro-shopzeisscoms=50479761ad21e5ampl=enampp=usampf=fampa=i httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=d httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=f Researcher Labs Alby Diaspro ndash IIT httpwwwlambsitindexphppage=People Alice Ting ndash MIT httpwwwtinglaborgresearch Allen Institute for Brain Science httpwwwalleninstituteorgwhat-we-dobrain-science Allen Institute for Cell Science httpwwwalleninstituteorgwhat-we-docell-science Amina Qutub - Rice University - How are human cells designed lab httpsqutublaborgqutub-lab Amy Herr UC Berkeley ndash Single cell Westerns httpherrlabberkeleyedu Amy Palmer ndash UC Boulder httpspalmerlabcoloradoedu Andrew York ndash Calico Life Sciences httpswwwcalicolabscomteam-memberandrew-york Anne Carpenter ndash Broad Institute CellProfiler httpspersonalbroadinstituteorganne Arjun Raj UPenn single molecule RNA FISH quantitative understanding cellular functions httprajlabseasupenneduindexhtml httpwwwpopscicomsciencearticle2013-09arjun-raj Atsuko Miyawaki - Laboratory for Cell Function Dynamics (CFDS) Fucci2 fluorescent proteins cell cycle indicator httpwwwbrainrikenjpenfacultydetails30 httpcfdsbrainrikenjp httpcfdsbrainrikenjpFuccihtml Aydogan Ozcan - UCLA - new imaging and sensing architectures httpinnovateeeuclaeduwelcomehtml httpwwwhhmiorgscientistsaydogan-ozcan Badri Roysam - UH - FARSIGHT Toolkit httpwwweeuhedufacultyroysam httpwwwfarsight-toolkitorgwikiMain_Page Brian J Ford ndash microscopist and popularizer httpsuklinkedincominprofbrianjford Carolyn Larabell ndashNational Center for X-ray Tomography (LBNL) UCSF httpncxtlblgovq=carolyn httpprofilesucsfeducarolynlarabell Clare Waterman ndash NHLBI NIH

httpswwwnhlbinihgovresearchintramuralresearcherspiwaterman-clare Dana Peer - Columbia University - Computational Systems Biology viSNE and more software httpwwwc2b2columbiaedudanapeerlabhtml httpwwwc2b2columbiaedudanapeerlabhtmlcythtml David Mayerich - UH - STIM Laboratory Scalable Tissue Imaging and Modeling httpwwweeuhedufacultymayerich httpstimeeuhedu David Piston WUSTL httpwwwcellbiologywustledufacultytenureddavid-w-piston-phd Diane Lidke and Keith Lidke - University of New Mexico httppathologyunmeduresearchfaculty-laboratoriesthe-lidke-laboratoryindexhtml httppanda3physunmedu~klidke Donna Arndt-Jovin and Thomas Jovin - Max Planck Institute for Biophysical Chemistry Laboratory of Cellular Dynamics httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsDonnaArdndt-JovinResearchAreasAndProjects httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsChairmanThomasJovinResearchAreasAndProjects Ed Boyden ndash MIT Media Lab ndash expansion microscopy (ExM) optogenetics httpsyntheticneurobiologyorg httpsyntheticneurobiologyorgprotocols httpsyntheticneurobiologyorgpublications httpwwwtedcomtalksed_boyden_baby_diapers_inspired_this_new_way_to_study_the_brain httpwwwextbiocombuycell Elizabeth Blackburn ndash Salk Institute - Telomeres httpswwwsalkeduscientistelizabeth-blackburn httpsenwikipediaorgwikiElizabeth_Blackburn httpswwwnobelprizeorgnobel_prizesmedicinelaureates2009blackburn-factshtml Elizabeth Hillman - Columbia university - SCAPE (Swept Confocally-Aligned Planar Excitation) high speed 3D microscopy DyCE (dynamic contrast enhancement to image and segment small animal organs live) Neuroimaging amp Neurovascular Coupling httporionbmecolumbiaedu~hillmanInstrumentationhtml httporionbmecolumbiaedu~hillmanSCAPEhtml httporionbmecolumbiaedu~hillmanMolecularhtml httporionbmecolumbiaedu~hillmanBrain_Imaginghtml Eric Betzig ndash UCSF (moving from HHMI Janelia Farm in 2016) httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014betzig-factshtml Eva Sevick-Muraca ndash UT Health Science Center at Houston molecular imaging clinical NIR fluoresceince imaging httpswwwutheduimmprofilehtmid=1005459 httpswwwutheduimmcentersmolecular-imaginghtm Evelin Schrock - Technische Universitaumlt Dresden spectral karyotyping cytogenetics httpswwwresearchgatenetprofileEvelin_Schrock Garry Nolan Stanford University ndash Mass cytometry MIBI-ToF high throughput imaging mass cytometry (42plex) httpwebstanfordedugroupnolanresourceshtml httpwebstanfordedugroupnolantechnologieshtml George McNamara ndash Cell Morphometry (41) Figure 1 right top two panels (55) The Chase (2016 temporal area maps lsquodynamic morphologyrsquo) (76) newsletter series on ldquoThe Chaserdquo (73) direct Vimeo movie of ldquoThe Chaserdquo Tiki_Goddess linkedin 10+plex blog httpsworksbepresscomgmcnamara41 httpsworksbepresscomgmcnamara55 httpsworksbepresscomgmcnamara76

httpsworksbepresscomgmcnamara73 httpsvimeocom175151196 httphomeearthlinknet~tiki_goddess httpswwwlinkedincomingeorgemcnamara httpswwwlinkedincompulsebd-biosciences-listed-tandems-horizon-brilliant-violets-mcnamara Gillian Griffiths - University of Cambridge - T-cell immunological synapse httpwwwcimrcamacukresearchprincipal-investigatorsprincipal-investigators-a-hgriffiths Hari Shroff NIBIB NIH httpswwwnibibnihgovlabs-at-nibibsection-high-resolution-optical-imaging-hroi HHMI Janelia Farm Research Campus (JFRC) - Advanced Imaging Center Open Science httpswwwjaneliaorgopen-scienceadvanced-imaging-center-aic httpswwwjaneliaorgopen-science Jeanne Lawrence University of Massachussetts Medical School httpwwwumassmededucellbiolabslawrencepersonnelprincipal-investigator Jennifer Lippincott-Schwartz ndash HHMI Janelia Farm httpswwwjaneliaorgpeoplejennifer-lippincott-schwartz Jin Zhang ndash UCSD httpprofilesucsdedujinzhang Joe DeRisi - UCSF - 3D printable lab stuff httpderisilabucsfeduindexphppage=3D John Russ Chris Russ Fovea Pro plugins for Adobe Photoshop httpwwwdrjohnrusscomindexhtml httpwwwdrjohnrusscombookshtml httpwwwreindeergraphicscomfoveaprotutorialhtml Julie Theriot httpcmgmstanfordedutheriot Karl Deisseroth ndash Stanford University ndash CLARITY optical tissue clearing Optogenetics httpclarityresourcecenterorg httpwebstanfordedugroupdlaboptogeneticsindexhtml Karsten Koumlnig (Koenig) - Saarland University and JenLab GmbH - biophotonics httpwwwbltuni-saarlanddeindex_ehtm httpwwwjenlabde httpwwwthelastescape-filmcom Karsten Rodenacker ndash image measurements httpkaro03bplacednetkaroMeMisc_WWWpdfMicrosoftWord-EQUAPATpdf Kevin Eliceiri ndash UW-Madison Open Source Photonics and Software Laboratory for Optical and Computational Instrumentation (LOCI) wwwlociwiscedu Klaus Kemp ndash Microlife Services ndash diatoms and other prepared microscope slides httpwwwdiatomscouk Kurt Thorn UCSF httpthornlabucsfedu httpsnicucsfedublog httpnicucsfeduFPvisualization httpgigapancomgigapans163370 Lihong Wang - WUSTL - Optical Imaging Laboratory photoacoustic tomography

httpoilabseaswustledu httpoilabseaswustleduresearch_0html Loren Looger - HHMI JFRC - iGluSnFr fluorescent protein biosensor httpswwwjaneliaorglablooger-lab Mary-Lou Pardue ndash MIT (first ever in situ hybridization with J Gall) httpsbiologymitedupeoplemary_lou_pardue httpsenwikipediaorgwikiMary-Lou_Pardue Nancy Allbritton - UNC - Chemical cytometry microraft arrays organ-on-a-chip httpswwwbmencsueduindexphpcomponentcomprofileruserprofilenlallbri httpwwwbmeuncedulabsallbritton Navin Varadarajan - UH - single-cell Lab httpwwwcheeuhedufacultyvaradarajan httpsinglecellcheeuheducontacthtml Nicholas Shaner - Scintillon Institute - mNeonGreen httpwwwscintillonorgshaner_lab Rebecca Richards-Kortum httpbioengineeringriceedufacultyrebecca_richards-kortumaspx Robert Campbell - Fluorescent proteins optogenetic proteins httpcampbellwebchemualbertaca httpcampbellwebchemualbertacaprojects-2 Robert Murphy ndash Cell measurements web services httpmurphylabwebcmueduservices Sabine Mai - University of Manitoba - Genomic Centre for Cancer Research and Diagnosis (GCCRD) - httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBPlatformsGCCRDhtml httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBScientistsMaiAwardshtml Sally Ward and Raimund Ober - Texas AampM University - httpwwwwardoberlabcom Simon Watkins - U Pittsburgh Center for Biologic Imaging httpwwwcbppittedufacultywatkinshtml httpwwwcbppittedufacultylabwatkinshtml httpwwwcbipittedu Stefan Hell ndash Deparment Hell NanoBiopohotonics httpwwwmpibpcmpgdehell httpsenwikipediaorgwikiStefan_Hell httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014hell-factshtml Sunney Xie Harvard httpsbernsteinharvardedu Susan Cox ndash 3B microscopy httpwwwcoxphysicscomindexhtml httpwwwcoxphysicscom3b Radim Chmeliacutek - Center for innovative microscopy Experimental biophotonics group httpswwwceiteceuceitec-butexperimental-biophotonicsrg3 httpwwwbiophotczhome Taekjip Ha ndash Johns Hopkins University ndash single molecules httphamedjhmiedu

Thomas Ried ndash NCI NIH SKYM-FISH and CGH Database httpsccrcancergovGenetics-Branchthomas-ried httpsccrcancergovGenetics-Branchthomas-riedqt-staff_profile_tabs=9qt-staff_profile_tabs ftpftpncbinlmnihgovsky-cghDATA httpswwwncbinlmnihgovdbvar Viviana Gradinaru ndash CalTech ndash CLARITYPACT Optogenetics httpwwwbbecaltecheducontentviviana-gradinaru httpglabcaltechedu Vladislav Verkhusha - near infrared fluorescent proteins httpwwweinsteinyuedulabsvlad-verkhushadefaultaspx httpwwweinsteinyueduresearchfacilitiesfluorescent WE Moerner ndash Stanford University httpwebstanfordedugroupmoerner Willard Wiggans ndash micro gallery httpwwwwillard-wigancomgallery Wolf Frommer ndash Molecular sensors httpbiosensordpbcarnegiescienceedu (fluorescent protein biosensors table) Xiaowei Zhuang = Harvard httpzhuangharvardedu Yuval Garini - Bar-Ilan University - Nano-Bio-Photonics laboratory httpgarinilabbiuacil Microscopy Magazines Imaging amp Microscopy httpwwwimaging-gitcommagazine Laser Focus World httpwwwlaserfocusworldcomindexhtml Microscopy amp Analysis httpwwwmicroscopy-analysiscom Microscopy Today httpwwwmicroscopy-todaycom Microscopy-UK httpwwwmicroscopy-ukorguk Photonics Spectra Biophotonics httpwwwphotonicscomPublicationsaspx The Microscope Journal httpmcriorgv72the-microscope-journal RMS Infocus Magazine httpwwwrmsorgukstudy-readinfocus-magazinehtml Nobel Prizes in Light Microscopy and Related Fields Chemistry 1925 colloids (light sheet) Zsigmondy (Siedentopf Zsigmondy 1902) httpswwwnobelprizeorgnobel_prizeschemistrylaureates1925

Chemistry 2000 conductive polymers Heeger MacDiarmid Shirakawa (Brilliant Violets Ultraviolets Blues) httpwwwnobelprizeorgnobel_prizeschemistrylaureates2000 Chemistry 2008 green fluorescent protein GFP Shimomura Chalfie Tsien httpwwwnobelprizeorgnobel_prizeschemistrylaureates2008 Chemistry 2014 super-resolved fluorescence microscopy Betzig Hell Moerner httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014 Physics 1953 Phase Contrast Zernike httpswwwnobelprizeorgnobel_prizesphysicslaureates1953 Physics 2009 invention of an imaging semiconductor circuit ndash the CCD sensor Kao Boyle Smith httpwwwnobelprizeorgnobel_prizesphysicslaureates2009 Physics 2014 efficient blue light emitting diodes Akasaki Amano Nakamura httpwwwnobelprizeorgnobel_prizesphysicslaureates2014 Physiology or Medicine 2006 Fire and Mello RNA interference ndash gene silencing by double stranded RNA httpwwwnobelprizeorgnobel_prizesmedicinelaureates2006 Physiology or Medicine 2006 Capecchi Evans Smithies specific gene modifications in mice by the use of embryonic stem cells httpwwwnobelprizeorgnobel_prizesmedicinelaureates2007 Physiology or Medicine 2009 Blackburn Greider Szostak how chromosomes are protected by telomeres and telomerase httpwwwnobelprizeorgnobel_prizesmedicinelaureates2009 Physiology or Medicine 2012 Gurdon Yamamanka matured cells can be reprogrammed to become pluripotent httpwwwnobelprizeorgnobel_prizesmedicinelaureates2012

Table 442 Fluorophores Photophysics Data

Fluorophore Abs or Ex max (nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Acridine orange 271 520 27000 020 5

Alexa Fluor 430 431 541 16000 055 9

Alexa Fluor 488 495 519 71000 094 67

Alexa Fluor 532 532 553 81000 080 65

Alexa Fluor 546 556 573 104000 096 100

Alexa Fluor 568 578 603 91300 075 69

Alexa Fluor 594 590 617 73000 064 47

Allophycocyanin (APC) 650 660 700000 068 476

Atto 390 390 479 24000 090 22

Atto 425 436 484 45000 065 29

Atto 430LS 433 547 32000 065 21

Atto 465 453 508 75000 075 56

Atto 490LS 496 661 40000 030 12

Atto 520 525 547 105000 095 100

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 3: McNamara 20161006 revised draft tables for CPHG Light ...

httpswwwnikoninstrumentscomProductsLive-Cell-Screening-SystemsBioStation-CT

Olympus America Inc httpwwwolympus-lifesciencecomen httpolympusmagnetfsuedu

Zeiss (Carl Zeiss Inc) httpwwwzeisscom httpwwwzeisscomcorporateen_ushomehtml httpzeiss-campusmagnetfsueduindexhtml httpwwwzeisscommicroscopyen_deproductsmicroscope-camerasaxiocam-702-monohtml

Karyotype Systems and Digital Pathology Digital Pathology Blog ndash see educational sponsors for comprehensive list of digital pathology vendors httptissuepathologycom 3DHistech ndash digital pathology Pannoramic scanners httpwww3dhistechcom Agilent Pathology Solutions Dako ndash IHC and ISH reagents autostainers httpwwwdakocomdkindexknowledgecenteromnishtm httpwwwdakocomdkar42productgroupshtm Applied Spectral Imaging ndash SKY Spectral karyotyping GenASIs digital pathology httpwwwspectral-imagingcom httpwwwspectral-imagingcomapplicationsspectral-imaging httpwwwspectral-imagingcomapplicationspathology Bioview ndash pathology and FISH cytogenetics scanners httpbioviewcom Definiens (MedImmuneAstraZeneca) - digital pathology image analysis (with deep learning algorithms) httpwwwdefinienscom Huron Digital Pathology ndash large area confocal scanning (entire human brain slices) httpwwwhurondigitalpathologycom Leica Biosystems ndash CytoVision CytogeneticsFISH Aperio digital pathology httpswwwleicabiosystemscomclinical-microscopy-surgery-radiologycytogenetics httpswwwleicabiosystemscomdigital-pathology MetaSystems International ndash karyotyping FISH digital pathology httpsmetasystems-internationalcomenproducts Molecular Probes ThermoFisher Scientific ndash Evos FL Auto and Evos Floid cell imaging stations high content screening (HCS) (Cellomics) httpswwwthermofishercomusenhomelife-sciencecell-analysiscellular-imagingcell-imaging-systemsevos-fl-autohtml httpswwwthermofishercomusenhomelife-sciencecell-analysiscellular-imagingcell-imaging-systemsfloid-cell-imaging-stationhtml httpswwwthermofishercomusenhomelife-sciencecell-analysiscellular-imaginghigh-content-screeninghigh-content-screening-instrumentshtml Philips ndash digital pathology httpwwwusaphilipscomhealthcaresolutionspathology Ventana Roche Digital Pathology ndash digital pathology FISH httpwwwventanacomdigitalpathology Visiopharm ndash digital pathology image analysis (with deep learning algorithms) stereology httpwwwvisiopharmcom

Filter and Filter Sets Manufacturers Alluxa httpwwwalluxacom BMV Optical wwwbmvopticalcom Chroma Technology httpwwwchromacom Edmund Optics ndash filters prisms httpwwwedmundopticscomopticsoptical-filtersbandpass-filtersfluorescence-filter-kits3226 httpwwwedmundopticscomopticsprisms Iridian Spectral Technologies httpwwwiridian-optical-filterscomproduct-categoryfluorescence-sets Newport (Spectra-Physics Oriel Bookham New Focus) httpswwwnewportcomcoptical-filters

Omega Optical httpwwwomegafilterscom Optolong (Kunming Yulong OpticalampElectronics Technology Co Ltd) httpwwwoptolongcomenproductsfluorescence-filters Schott Glass Technologies httpwwwschottcom httpwwwusschottcomadvanced_opticsenglishsynadvanced_opticsproductsoptical-componentsoptical-filtersinterference-filtersindexhtml Semrock Inc (IDEX CVI Melles Griot) httpsemrockcom ThorLabs ndash optical filters httpswwwthorlabscomnavigationcfmguide_id=21 Major scientific CMOS (sCMOS) camera companies (your next microscope cameras should likely be sCMOS not CCD or EMCCD) Andor Technology Ltd (Oxford Instruments) httpwwwandorcomscientific-camerasneo-and-zyla-scmos-cameras Hamamatsu httpswwwhamamatsucomusencommunitylife_science_camerasensor_technologiesscientific_cmos_scmos_image_sensorindexhtml httpwwwhamamatsucomusencommunitylife_science_cameraproductsearchC11440-22CUindexhtml PCO httpsuspco-techcomscmos-cameras Photometrics httpwwwphotometricscomproductsscmos Fluorescent Proteins Luciferases (DNA plasmids andor other expression products) 490BioTech ndash LuxABCDE

http490biotechcomvectors-2 Abberior httpwwwabberiorcomshopLabels-by-FunctionFluorescent-Proteins7_14html httpwwwabberiorcomshopLabels-by-Application1html Addgeneorg wwwaddgeneorg httpswwwaddgeneorgfluorescent-proteins httpswwwaddgeneorgfluorescent-proteinsbiosensors httpswwwaddgeneorgfluorescent-proteinslocalization httpswwwaddgeneorgoptogenetics httpswwwaddgeneorgfluorescent-proteinsdavidson httpswwwaddgeneorgRoger_Tsien Allele Biotechnology httpwwwallelebiotechcomFluorescent-Proteins Bell Biosystems ndash Magnelle living MRI contrast agents (magnetotactic bacteria taken up by human cells in vitro) with fluorescent proteins ndash in vivo cell tracking httpwwwbellbiosystemscomProducts-and-ServicesCell-Tracking-Solutions BioBricks Foundation httpbiobricksorg BioPop (Intrexon) ndash Dinoflagellates bioluminescence luciferaseluciferin httpsbiopopcomproducts Chromotek GmbH - Chromobodies Nano-Boosters (llama nanobodies attached to or detecting FP) httpwwwchromotekcomproductschromobodies httpwwwchromotekcomproductschromobodiescell-cycle-chromobodyr httpwwwchromotekcomproductsnano-boosters DNA 20 chromogenic and fluorescent protein paintbox (not really IP-Free) httpswwwdna20comproductsprotein-paintbox Evrogen httpevrogencomproductsbasicFPsshtml httpevrogencomproductsBiosensorsshtml httpevrogencomproductsOrganelle-labelingshtml iGEM BioBricks ndash reporter proteins including fluorescent proteins httppartsigemorgProtein_coding_sequencesReporters iGEM Registry of Standard Biological Parts httppartsigemorgMain_Page InvivoGen ndash GFP Lucia luciferase reporters httpwwwinvivogencomdual-reporter MBL International Corp ndash fluorescent proteins httpswwwmblintlcomproductsfluorescent-proteins httpruomblcojpbioeproductflproteinfuccihtml Millipore-Sigma Sigma-Aldrich ndash firefly luciferase D-luciferin httpwwwsigmaaldrichcomlife-sciencemetabolomicsenzyme-exploreranalytical-enzymesluciferasehtml Molecular Probes Inc Invitrogen Thermo Fisher ndash Bacmam 20 fluorescent proteins biosensors FUCCI httpwwwprobescom httpwwwthermofishercomusenhomebrandsmolecular-probeshtml httpswwwthermofishercomusenhomeindustrialpharma-biopharmadrug-discovery-developmenttarget-and-lead-identification-and-validationpathway-biologycellular-pathway-analysisbacmam-systembacmam-reagentshtml

Montana Molecular LLC - genetically encoded fluorescent biosensors and probes for cell-based assays and live cell imaging httpmontanamolecularcomproductsproducts-overview NanoLight Technologies ndash Renilla GFP luciferases httpwwwnanolightcomNanoFluorsGFP_Expression_Vectorshtml httpswwwbiotoycomenlearn n3D Biosciences ndash generate 3D cell spheroids high throughput screening image changes using smartphone camera inside incubator httpwwwn3dbiocomproductsmagnetic-3d-bioprinting httpwwwn3dbiocomproductsassays New England BioLabs (NEB) ndash Cypridina Gaussia luciferases httpswwwnebcomapplicationscellular-analysisreporter-systems Promega ndash Monster GFP NanoLuc httpswwwpromegacomproductsreporter-assays-and-transfectionreporter-vectors-and-cell-linesmonster-green-fluorescent-protein-phmgfp-vector httpswwwpromegacomproductsreporter-assays-and-transfectionreporter-vectors-and-cell-linesnanoluc-luciferase-reportersnanoluc-genetic-reporter-vectors Fluorescence Products (reagents) Advanced Cell Diagnostics (Bio-Techne) - branched DNA probe sets for RNA FISH httpsacdbiocomproducts Affymetrix eBioscience Thermo Fisher - branched DNA probe sets for RNA FISH httpwwwaffymetrixcomestorepromotionsviewrnaishindexaffx Anaspec ndash HiLyte Fluorophores FRET probes httpswwwanaspeccomproductsproductcategoryaspid=10 Antibody Resource Page httpwwwantibodyresourcecom Biocompare ndash Antibodies httpwwwbiocomparecomAntibodies Cell Signaling Technology ndash fluorescence antibodies httpswwwcellsignalcombrowseimmunofluorescence-immunocytochemistryif-paraffinif-frozen Essen Biosciences ndash Bacmam 30 ready to use FP gene transfection reagents httpwwwessenbiosciencecomenproductsreagents-consumablesincucyte-nuclight-red-bacmam-30-reagent-nuclear-labeling-cat-no-4621 GE Healthcare Amersham Biosciences httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usbrandscydye Global Biological Standards Institute (GBSI) ndash Antibody Validation Initiative httpwwwgbsiorgworkantibodies Goryo Chemical httpwwwgoryochemicalcom Human Protein Atlas (academic) Atlas Antibodies (commercial arm) US distributor httpwwwproteinatlasorg httpsatlasantibodiescom httpwwwsigmaaldrichcomlife-sciencecell-biologyantibodiesprestige-antibodieshtml

Integrated DNA Technologies (IDT) httpwwwidtdnacomsiteCatalogmodificationsdyes httpwwwidtdnacompagesproductsmodificationsfluorophoresfreedom-dyes httpwwwidtdnacomsiteCatalogModificationsCategory4 Jackson ImmunoResearch httpswwwjacksonimmunocom KPL (formerly Kirkegaard amp Perry Laboratories Inc) SeraCare httpwwwkplcom LGC Biosearch Technologies ndash dyes for oligonucleotides single molecular RNA FISH image gallery httpswwwbiosearchtechcomsupporteducationfluorophores-and-quenchers httpstellarisfishsmugmugcom httpsinglemoleculefishcom httpswwwbiosearchtechcomproductsrna-fish (typically 48 20 base oligonucleotides) Marker Gene Technologies Inc (MGT) httpwwwmarkergenecomfluorescent-reagent Miltenyi Biotec ndash REAfinity recombinant engineered antibodies (no Fc Receptor binding) FASER fluorescence amplification kits NiraWave fluorophores (indocyanine green formulations) httpwwwmiltenyibioteccomenproducts-and-servicesmacs-flow-cytometryreagentsantibodies-and-dyesrecombinant-antibodiesaspx httpwwwmiltenyibioteccomenproducts-and-servicesmacs-flow-cytometryreagentssupport-reagentsfaser-kitsaspx httpwwwmiltenyibioteccomenproducts-and-servicesviscover-imagingoptical-imagingaspx Molecular Probes Inc Invitrogen Thermo Fisher ndash largest vendor of fluorophores Molecular Probes Handbook (web resource) Tyramide Signal Amplification kits httpwwwprobescom httpswwwthermofishercomusenhomereferencesmolecular-probes-the-handbookhtml httpswwwthermofishercomusenhomereferencesmolecular-probes-the-handbooktablestyramide-signal-amplification-tsa-kitshtml NIRvana Sciences httpnirvanasciencescom httpnirvanasciencescompage_id=3088 One World Lab ndash antibody search httponeworldlabcomantibodies CytoCell Oxford Gene Technologies ndash DNA FISH probes human mouse pig chicken httpwwwcytocell-uscom Perkin Elmer ndash nucleotides labeling kits Tyramide Signal Amplification Kits (TSA) Opal 7plex discovery panel kit based on sequential TSA httpwwwperkinelmercomcategoryfluorescent-hapten-nucleotides httpwwwperkinelmercomcategoryfluorescent-agents-labeling-kits-dyes httpwwwperkinelmercomlab-solutionsresourcesdocsBRO_TSAsignalamplificationpdf httpwwwperkinelmercomproductopal-7-immunology-discovery-kit-op7ds1001kt

Rockland Inc httpwwwrockland-inccomcommerceindexjsp

TEFLabs ndash fluorescent ion indicators (Ca++ Cl- K+ Mg++ Na+ pH Zn++) ionophores fluorophores httpwwwteflabscomion-indicators Vector Laboratories Inc httpwwwvectorlabscom

Live cell imaging dishes and multi-well plates (ldquoglass bottom dishesrdquo)

We recommend these for simplified handing and processing vs either thick plastic dishesplates or having to handle loose coverslips with your valuable cells

Leicester Imaging Technologies (LITE) - University of Leicester - table of dishes for live cell imaging (our table has current links and bad links left out) httpwww2leacukcollegesmedbiopsychfacilities-and-servicescbsliteaiftips-and-tricks-1dishes-for-live-cell-imaging Bellco Glass Inc - glass flat bottom plate httpwwwbellcoglasscomnode1046 Bioptechs - interchangable coverslip dish ($036 per experiment) httpwwwbioptechscomproductinterchangeable-coverslip-dish Brooks Automation Inc - clar bottom optical imaging microplates httpwwwbrookscomproductslife-scienceconsumablesmatrical-microplates-microtubes-racks-lidsglass-bottom-optical-imaging-microplates Cell EampG - glass bottom cell sulture dishes plates httpcellegcomproducthtml Cellvis - glass bottom dishes and plates httpwwwcellviscom_35-mm-glass-bottom-dishes_products_by_categoryphpcat_id=3 Corning - glass bottom microplates httpcatalog2corningcomLifeSciencesen-USShoppingCategoryaspxcategoryname=Microplates20-202015(Lifesciences)|Assay20Microplates20-202015(Lifesciences) Design 1 Solutions - Custom microplates and fabrication services httpwwwdesign1solutionscomcustom-microplateshtml Eppendorf - cell imaging dishes imaging plates httpsonline-shopeppendorfcomOC-enCell-Culture-and-Imaging-Consumables-110320Cell-Imaging-Consumables-120210Eppendorf-Cell-Imaging-Dishes-PF-19457html httpsonline-shopeppendorfcomOC-enCell-Culture-and-Imaging-Consumables-110320Cell-Imaging-Consumables-120210Eppendorf-Cell-Imaging-Plates-PF-19458html Greiner Bio-One International - CellView glass bottom dishes quadrant dishes httpsshopgbocomenrowarticlescataloguearticle0110_0110_0040_002027513 ibidi - u-Plates glass bottom dishes microfluidic slides httpibidicomxtproductsenibidi-Labwarem-Plates httpibidicomxtproductsenibidi-Labware Matsunami Glass Ind Ltd httpwwwmatsunami-glasscojpenglishlifebiodata01html Mattek - glass bottom dishes and SBS plates httpswwwmattekcomstore-categoryculturewareglass-bottom-dishes Nunc - glass bottom dishes httpswwwthermofishercomordercatalogproduct150680 NEST Biotechnology Co Ltd Wuxi Jiangsu PRChina httpwwwnestscientificusacomproducts_detailproductId=31html PerkinElmer - glass bottom plates httpwwwperkinelmercomSECatalogCategoryIDMicroplates

Porvair Sciences - clear bottom assay plates httpwwwporvair-sciencescomenservices-menulife-sciencesclear-bottom-assay-plates Ted Pella Inc - glass bottom dishes clear wall or black wall (manufactured by WillCo Wells) httpswwwtedpellacomsection_html706dishhtm Warner Instruments (Harvard Apparatus) - culture dishes perfusion systems httpswwwwarneronlinecomproduct_cat_infocfmid=1322 Willco Wells - glass bottom dishes wwwwillcowellscom World Precision Instruments - Fluorodish glass bottom dishes httpswwwwpiinccomproductslaboratory-suppliesfd35-100-fluorodish-cell-culture-dish-35mm-23mm-well-pkg-of-100 Microscopes Microscopy Accessories (accessorize) Reagents Resources 3scan ndash knife edge scanning microscope (images slices repeats through specimen) httpwww3scancomdata-2 89North (affiliated with Chroma Technology Corp) httpwww89northcom Abberior Instruments ndash STED RESOLFT precision localization super-resolution microscopes STEDYCON convert any fluorescence microscope to STED httpabberior-instrumentscom httpabberior-instrumentscomproductscompact-lineabberior-stedy-con Acquifer ndash HIVE imaging machine (computer hardware) for high content screening big data httpswwwacquiferde Adobe Systems Inc httpwwwAdobecom httpscreativeadobecomproductsdownloadphotoshop Affymetrix eBioscience (ThermoFisher) - microarrays httpwwwaffymetrixcomestorebrowselevel_one_category_template_onejspparent=35796ampcategory=35796 httpwwwaffymetrixcomestorecatalog131547AFFYGeneChip26231743B+System+3000Dx+v22623423B1_1 Agilent Technologies ndash SureScan microarray scanner (array CGH microRNA SNPs CNV) httpwwwgenomicsagilentcomenMicroarray-Scanner-Processing-HardwareSureScan-Microarray-Scannercid=AG-PT-144 Andor Technology (Oxford Instruments) ndash sCMOS cameras Dragonfly spinning disk confocal Revolution DSD2 differential spinning disk confocal photostimulation (fluorescence recovery after photobleaching optogenetics) Mosaic3 DMDDLP high speed light patterning (optogenetics structured illumination) MicroPoint pulsed UV laser for ablation DNA damage photobleachingactivation uncaging accessories httpwwwandorcomscientific-camerasneo-and-zyla-scmos-cameras httpwwwandorcommicroscopy-systemsdragonfly httpwwwandorcommicroscopy-systemsrevolution-dsd httpwwwandorcommicroscopy-systemsphotostimulation httpwwwandorcommicroscopy-systemsphotostimulationmosaic httpwwwandorcommicroscopy-systemsphotostimulationmicropoint httpwwwandorcommicroscopy-systemsmicroscopy-components Apogee Instruments Inc (Andor Technology) ndash CCD cameras and filter wheels (mostly marketed for astronomy) httpwwwccdcomandorhtml Applied Scientific Instrumentation Inc ndash light sheet imager (iSPIM diSPIM)

wwwasiimagingcom httpwwwasiimagingcomindexphpproductslight-sheet-microscopyselective-plane-illumination-microscopy-ispim-dispim Applied NanoFluorescence LLC ndash NS1 NanoSpectralyzer (Raman and UV-VISNIR) NS MiniTracer near infrared spectrometer NFM NanoFluorescence microscope multi-laser light source single wall carbon nanotubes (NIR II fluorophores) httpappliednanocomproductshtml httpappliednanocomproductsns1html httpappliednanocomproductsproduct-list77-ns-minitracerhtml httpappliednanocomproductsnfmhtml httpappliednanocomproductsls-nhtml httpwwwnanowerkcomnewsnewsid=24132php Applied Spectral Imaging Inc httpwwwspectral-imagingcom ArgoLight ndash fluorescence resolution test target slides httpargolightcom AttoCube - attoMICROSCOPY overview attoCFM - Multichannel cryogenic (low temperature) confocal fluorescence microscopes 08 NA objective lenses 400-1000 nm spectral range httpwwwattocubecom httpwwwattocubecomattomicroscopyintroductiontab-2 httpwwwattocubecomattodownloads AutoQuant (Media Cybernetics) spatial deconvolution httpwwwmediacycomautoquantx3 Becker amp Hickl GmbH httpwwwbecker-hicklcomproductshtm Berkeley Lights Inc ndash manueuver into nanowells incubate recover 4000 single cells per chip httpswwwberkeleylightscomtechnology Bioaxial ndash Codim imaging conical diffraction beam shaper for super-resolution (4 sub-images) httpwwwbioaxialcomcodim-imaging Bioptechs - Live-Cell Micro-Observation Products httpwwwbioptechscom Bionumbers - database of useful biological numbers httpbionumbershmsharvardeduKeyNumbersaspx Biostatus ndash DRAQ5 DRAQ7 ApopTRAK CyTRAK Orange CyGel HypoxiTRAK httpwwwbiostatuscomProducts Bio-Tek ndash Cytation 3 Cell Imaging Multi-Mode Reader Lionheart FX Automated Live Cell Imager httpwwwbiotekcomproductsimagingcytation3_cell_imaging_multi_mode_readerhtml httpwwwbiotekcomproductsimaginglionheartfx_automated_live_cell_imagerhtml Biovision Technologies ndash distributor for several imagers including VT-iSIM instant super-resolution microscope httpbiovision-technologiescom httpbiovision-technologiescomsystemshtml httpbiovision-technologiescomvtisimhtml Bitplane (Andor Oxford Instruments) ndash Imaris imaging software httpwwwbitplanecom BMV Optical - custom lens assemblies and optical filters wwwbmvopticalcom

Bruker (previously Prairie Technologies Vutara) ndash Opterra confocal Ultima Multiphoton Vutara 352 single molecule localization microscopes httpswwwbrukercomproductsfluorescence-microscopesopterra-confocal-microscopyoverviewhtml httpswwwbrukercomproductsfluorescence-microscopesultima-multiphoton-microscopyhtml httpswwwbrukercomproductsfluorescence-microscopesvutara-super-resolution-microscopyoverviewhtml Cairn Research ndash standard and custom accessories ex Light Sheet Illuminator MultiCam (4 cameras) custom design httpswwwcairn-researchcouk httpswwwcairn-researchcoukproductl-spi-single-plane-illuminator (dual L-SPI for 4 illumination directions) httpswwwcairn-researchcoukproductmulticam httpswwwcairn-researchcoukcustom-design Cameca ndash NanoSIMS 50L (7plex stable isotope imaging) httpwwwcamecacominstruments-for-researchnanosimsaspx CellMic (formerly Holomic) - blood analysis or fluorescence imaging cytometer on a cell phone httpwwwcellmiccomcontentadvanced-technologies httpwwwcellmiccomcontentfluorescent-imaging-cytometry-and-e-coli-detection-on-a-cell-phone CellOptic ndash FINCH (Fresnel INcoherence Correlation Holography) httpwwwcellopticcomindex2html CellProfiler ndash High content screening (HCS) image processing and analysis software httpcellprofilerorg ClearLight Diagnostics - CLARITY Optimized Light Sheet Microscopy (3D tissue optical clearing + light sheet imaging) httpwwwclearlightdxcomindexhtml Confocalnl ndash Rescan confocal microscopy to obtain 170 nm resolution with any pinhole diameter httpwwwconfocalnl CoolLED ndash LED light sources httpwwwcoolledcomproduct-detailpe-4000 Crest Optics SRL ndash X-Light confocal X-Light V2 + VCS (VideoConfocal super-resolution) httpwwwcrestoptcom httpwwwcrestoptcomhtmlx-light_v2_vcshtml Cytoskeleton Inc - live cell imaging reagents Spirochrome SiR bioimaging probes httpwwwcytoskeletoncomlive-cell-reagents httpwwwcytoskeletoncomlive-cell-reagentsspirochrome CytoViva ndash darkfield imaging hypspectral imaging httpwwwcytovivacomproducts3d-enhanced-darkfield-imaging httpwwwcytovivacomproductshyperspectral-imaging-2hyperspectral-imaging Data Translation Inc - digitizer cards httpwwwdatxcom Delmic BV - combined correlative scanning electron microscope with inverted fluorescence microscope httpwwwdelmiccomdelphi httpswwwdelphimicroscopecom httpwwwdelmiccomsecom-super-resolution Digital Light Innovations (DLi) - CELscope C-mount LED Microscope using Texas Instruments DLP illuminator with a simple stand httpswwwdlinnovationscomdli-deep-dives-celscope-c-mount-led-microscope Double Helix LLC ndash single molecule localization microscope (Piestun) httpdoublehelixopticscom Edinburgh Super-resolution Imaging Consortium (ESRIC)

httpwwwesricorg Energetiq ndash Deep ultraviolet (DUV high radiance 170-2100 nm) laser driven light source (LDLS) httpwwwenergetiqcom Epi Technology - CaliCube - Cube for fluorescence light path to inspect epi Illumination light source (lamp) fiber optic or liquid light guide httpwwwepitechnologycomepitechnology-1 Essen Biosciences ndash Incucyte Zoom (imager inside incubator) httpwwwessenbiosciencecomenproductsincucyte Estigen Tissue Science ndash manual and automated tissue arrayer (tissue microarray maker) httpwwwestigencom Euro-Bioimaging httpwwweurobioimagingeu Excelitas Technologies (formerly Lumen Dynamics) ndash X-Cite LEDs httpwwwexcelitascomPagesProductX-Cite-LED-Solutionsaspx Expansion Technologies Inc (extbio) ndash Expansion microscopy httpwwwextbiocombuycell FEI (formerly Till Photonics) (Thermo Fisher) ndash correlative LM-EM single molecule Cryo-EM httpswwwfeicomlife-sciencescellular-biology httpswwwfeicomlife-sciencescellular-biologycorrelative-microscopy httpswwwfeicomlife-sciencesstructural-biology Femtonics - Multi-phton microscopes software accessories caged glutamate reagents services httpfemtonicseuproducts First Light Imaging ndash C-Red NIR imaging (800-2500 nm NIR windows I II III 650-950 nm 1100-1350 nm 1600-1870 nm[Shi et al 2015]) high speed visible EMCCD (400-1000 nm) httpwwwfirst-lightfrcategoryrangesinfrared Fluidigm ndash Helios imaging CyTOF mass cytometer (42plex) Callisto (32 independent chambers dose with up to 16 independent factors for 1-1000 cell populations culture up to 3 week) Polaris functional genomics meets imaging (48 single cells up to 24 hours after single cell selection from a population) httpswwwfluidigmcomproductshelios httpswwwfluidigmcomproductscallisto httpswwwfluidigmcomproductspolaris GattaQuant - nanorulers for high resolution microscopes and super-resolution microscopes performance testing httpwwwgattaquantcomNanoruler GE Healthcare life Sciences Applied Precision ndash DeltaVision deconvolution OMX OMX SR httpwwwgelifesciencescomwebappwcsstoresservletproductByIdenGELifeSciences-us29065728 httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usproductsAlternativeProductStructure_2380729065721 httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usproductsAlternativeProductStructure_2380729115476 German BioImagingorg httpwwwgermanbioimagingorgwikiindexphpMain_Page httpwwwgermanbioimagingorgwikiindexphpWorkgroup6SoftwarePackages GIGAmacro ndash Magnify2 gigapixel imagery oof macroscopic and microscopic objects Terapixel macro image httpwwwgigamacrocomgigapixel-macro-imaging-system httpwwwgigamacrocomworlds-first-terapixel-macro-image

Glencoe Software ndash OMERO Plus enterprise data management for scientific images and any associated metadata (OME = Open Microscopy Environment) DataViewer PathViewer httpsglencoesoftwarecomomeroplushtml httpsglencoesoftwarecomdataviewerhtml httpsglencoesoftwarecompathviewerhtml Gooch amp Housego ndash spectral imager httpsgoochandhousegocomminiature-spectral-imaging-camera httpwwwghinstrumentscomproductsspectral-imaging-synthesishsi-440c-hyperspectral-imaging-system Hindsight Imaging ndash spectral imaging httphindsight-imagingcom Horiba Scientific - SWIFT ultra-fast Raman confocal imaging Raman spectroscopy httpwwwhoribacomscientificproductsraman-spectroscopyraman-imagingswift httpwwwhoribacomscientificproductsraman-spectroscopyraman-imaging httpwwwhoribacomscientificproductsraman-spectroscopy IATIA Ultima Capital ndash QPm (quantitative phase microscopy) httpwwwultimacapitalnetiatiaimagingPublicationsIatia20ImagingapplicationNotesqpmApplicationWithConfocalMicroscopespdf Ibidi - heating and incubation systems optical O2 measurement systems Nanolive 3D Cell Explorer pump system gas incubation system httpibidicomxtproductsenInstruments-AccessoriesHeating-Incubation-Systems httpibidicomxtproductsenInstruments-Accessoriesibidi-OPAL-Optical-O2-Measurement-System httpibidicomxtproductsenInstruments-AccessoriesNanolive-3D-Cell-Explorer httpibidicomxtproductsenInstruments-Accessoriesibidi-Pump-System httpibidicomxtproductsenInstruments-AccessoriesHeating-Incubation-Systemsibidi-Gas-Incubation-System iLAbSolutions (Agilent Technologies) - Instrument management and scheduling software (cores and labs) httpwwwilabsolutionscominstrument-access-control ImageJ - Fiji ImageJ NIH ImageJ ImageJ ndash Fiji (Fiji is just ImageJ) is the main download site httpfijisc httpsimagejnihgovij wwwimagejnet Inscopix ndash nVista in vivo mouse brain imaging miniature microscope httpswwwinscopixcomproducts Intelligent Imaging Innovations Inc (3i) ndash Slidebook imaging software Lattice light sheet (high speed gentle to cells high resolution imaging) Dual-view Inverted Selective Plane Illumination (diSPIM) VIVO 2-Photon (VIVO 2P) multiphoton microscopy Everest intravital imaging Marianas 3D real-time deconvolution timelapse spinning disk FRAP TIRF FLIM single molecule environmental control Phasor - optogenetic photostimulation using digital holography Yokogawa spinning disk confocal units wwwintelligent-imagingcom httpswwwintelligent-imagingcomslidebookphp httpswwwintelligent-imagingcomsystemsphplattice httpswwwintelligent-imagingcomsystemsphpdispim httpswwwintelligent-imagingcomsystemsphptwophoton httpswwwintelligent-imagingcomsystemsphpeverest httpswwwintelligent-imagingcomsystemsphpmarianas httpswwwintelligent-imagingcomoptogeneticsphp httpswwwintelligent-imagingcomsdcphp ISS Inc ndash fluorescence lifetime imaging microscopy fluorescence correlation spectroscopy (FCS) confocal imaging httpwwwisscommicroscopyindexhtml JenLab GmbH cyto-microscopy multiphoton tomography httpwwwjenlabdeproducts250html httpwwwjenlabde2PM-Cryo1330html

httpwwwjenlabdeMultiphoton-Tomography680html Jenoptik - microscope cameras httpswwwjenoptikcomproductscameras-and-imaging-modulesmicroscope-cameras JPK Instruments - integrated atomic force microscope (AFM) force sensing optical tweezers optical trapping single cell force spectroscopy (SCFS) httpwwwjpkcomindex2enhtml httpusajpkcomoptical-tweezers-optical-trapping29ushtml httpusajpkcomcellular-adhesion-cytomechanics30ushtml Keyence ndash VK-X confocal (upright) BZ-X700 widefield (inverted) httpwwwkeyencecomssproductsmicroscopevkx httpwwwkeyencecomssproductsmicroscopebz-x700indexjsp KK Technology - CapiScope HVCS Handheld Video Capillaroscopy System (CytoScan) httpwwwkktechnologycomhvcshtml LaVision BioTec ndash TriMscope Multiphoton TriM Scope II Adaptive Optics UltraMicroscope II light sheet httpwwwlavisionbiotecde httpwwwlavisionbiotecdetrim-scope-overviewhtml httpwwwlavisionbiotecdetrim-scope-ii-adaptive-opticshtml httpwwwlavisionbiotecdeultramicroscope-ii-introductionhtml Laxco ndash upright and inverted microscopes httpwwwlaxcoinccomMICROSCOPES Lego ndash Lego Idea Microscopes httpsideaslegocomprojects44370 httpwwwnico71frlego-working-microscope Li-Cor ndash near-infared fluorescent dyes and in vivo imaging agents in vivo and Western blot imaging systems httpswwwlicorcombioproductsreagents httpswwwlicorcombioproductsreagentsirdyebrightsite_imaging_agents httpswwwlicorcombioproductsimaging_systemsodyssey_familyhtml httpswwwlicorcombioproductsimaging_systemspearl httpswwwlicorcombioproductsimaging_systemscdigit Life Imaging Services - ldquothe Ludin chamberrsquo ldquothe cube amp the boxrdquo httpwwwlischthechamberhtml httpwwwlischtheboxhtml Lightform Inc ndash PARISS imaging spectrometer httplightforminccom LMU Bioimaging httpwwwbioimagingbmcmeduni-muenchendelinkswebsitesindexhtml httpwwwbioimagingbmcmeduni-muenchendelearneduwebsitesindexhtml Ludl Electronic Products Ltd ndash automated XY stages focus motors filter wheels httpwwwludlcom

LumaCyte ndash Laser force Cytology (laser trap meets microfluidics to suspend and manipulate single cells) httpwwwlumacytecomabouttechnology Lumencor ndash LEDs fluorescence light sources httplumencorcomproducts Luxcel ndash mitochondrial and cellular functions O2 sensor reagents httpluxcelcomproduct+list Luxendo GmbH ndash light sheet imager

wwwluxendoeu Lyncee tec - digital holography microscopy (DHM) high content screening by DHM httpwwwlynceeteccom httpwwwlynceeteccomhigh-content-screening Mad City Labs Inc - nanopositioning wwwmadcitylabscom Mauna Kea Technologies ndash CellVizio confocal laser endomicroscopy httpwwwmaunakeatechcomenhealthcare-professionalscellvizio-endomicroscopy-0 MBF Bioscience - stereology and neuron morphology quantitative imaging httpwwwmbfbiosciencecom McCrone Group wwwmccronecominstrument-sales Media Cybernetics Inc ndash Image Premier 3D AutoQuant X3 deconvolution httpwwwmediacycom Meiji Techno America wwwmeijitechnocom MesoLens Ltd httpwwwmesolenscomproducttechnical-specifications httpwwwmesolenscomimages httpswwwbiophotonicsstrathacukresearch_1htm Meyer Instruments ndash Pathscan Enabler GigaMacro digital pathology telepathology httpmeyerinstcom httpmeyerinstcompathscan-enabler-5 httpmeyerinstcomgigamacro-gigapixel-macro-imaging httpmeyerinstcomhomescanners httprealtimetelepathologycom Microarrays - Large-Scale Gene Expression and Microarray Links and Resources httpswwwebiacukarrayexpress Micro-Manager ndash Device Support ndash tabulates many microscope cameras and motorized accessories every new camera and accessory should have a uManager driver to enable simple use with Fiji ImageJ httpsmicro-managerorg httpsmicro-managerorgwikiDevice_Support httpsopen-imagingcom Microvolution ndash (near) instant gratification spatial deconvolution using NVidia GPU card(s) httpmicrovolutioncom Mightex Systems ndash optogenetics DMDDLP illuminator (digital micro-mirror device digital light processing) httpwwwmightexsystemscomindexphpcPath=245 Millipore-Sigma Merck KGaA (Amnis Corp CellASIC EMD Millipore) ndash ImageStreamX and FlowSight imaging flow cytometers ONIX2 Microperfusion System for microscopes httpswwwemdmilliporecom httpswwwemdmilliporecomUSenlife-science-researchcell-analysisamnis-imaging-flow-cytometersQ6ubqBm3UAAAFLCKIpygJnav httpwwwemdmilliporecomUSenlife-science-researchcell-culture-systemscellASIC-live-cell-analysisd1CbqBw58AAAE_0j13MnAnav Mitutoyo America Corp wwwmitutoyocom httpecatalogmitutoyocomMF-U-Series-176-High-power-Multi-function-Measuring-Microscopes-C1413aspx

Molecular Devices Corporation Universal Imaging Corporation (Danaher) ndash MetaMorph MetaFluor high content systems (HCS) httpswwwmoleculardevicescomsystemsmetamorph-research-imaging httpmdccusthelpcomappanswersdetaila_id19319 httpswwwmoleculardevicescomsystemshigh-content-imaging Molecular Machines amp Industries - laser microdissection and tweezer systems httpwwwmolecular-machinescomhome MUSE Microscopy Inc ndash Deep UV illumination for shallow depth of field imaging httpwwwmusemicrocom Micro Video Instruments Inc - DarkLite illuminator httpwwwmvi-inccom NanoEnTek ndash JuLI Stage (imager inside incubator or on lab bench) httpwwwjulistagecom National Instruments ndash LabView software httpwwwnicomen-ushtml Navitar - Hoffman Modulation Contrast (HMC alternative to differential interference contrast phase contrast) custom lens design UVDUVNUV imaging lenses httpsnavitarcommarketsmicroscopy httpsnavitarcomproductsimaging-opticscustom-microscope-objectivescustom-microscope-objectives httpsnavitarcomproductsimaging-opticsuv-imaging National Center for X-ray Tomography (NCXT) ndash soft X-ray tomography (CT of hydrated cells) XM-2 dedicated biological SXT microscope Prof Carolyn Larabell Director (see also SiriusXT) httpncxtlblgov httpncxtlblgovsxt httpncxtlblgovmanual httpncxtlblgovq=carolyn Neogenomics (Clarient) ndash MultiOmyx immunofluorescence or DNA FISH (ldquo60plexrdquo) httpneogenomicscomPharma-ServicesLab-ServicesMultiOmyxTechnologyMultiOmyx-IF-Assay-DNA-FISH-assay-NGS-from-ROI Nexcelom ndash Celigo imaging cytometer Cellometer cell counters httpwwwnexcelomcomCeligoindexphp httpwwwnexcelomcomProducts Nikon ndash Ti-LAPP modular illumination system (for Nikon Ti series microscopes) TIRF Optogenetics httpswwwnikoninstrumentscomProductsPhotostimulation-and-TIRFTi-LAPP Nirmidas Biotech httpwwwnirmidascomtechnologynir httpwwwnirmidascomproductsniriidye NVidia ndash Pascal 10+ Gbps GPU cards for instant gratification deconvolution (software from Microvolutioncom SVInl) httpwwwgeforcecomhardware10seriesgeforce-gtx-1080 httpwwwgeforcecomhardware10seriestitan-x-pascal httpwwwnvidiacomobjectquadro-graphics-with-pascalhtml Ocean Optics ndash spectrometers httpoceanopticscomproduct-categorymodular-spectrometers Oko-Lab stage top incubator httpwwwoko-labcomstage-top Open Microscopy Environment (OME) ndash OMERO (see also Glencoe Software) Bio-Formats LOCI

httpswwwopenmicroscopyorgsite httpswwwopenmicroscopyorgsiteproductsomero httpswwwopenmicroscopyorgsiteproductsbio-formats httpswwwopenmicroscopyorgsitesupportbio-formats52supported-formatshtml httpswwwopenmicroscopyorgsiteaboutdevelopment-teamskevin OpenSPIM ndash do-it-yourself selective plane illumination microscopy (light sheet imaging) httpopenspimorgWelcome_to_the_OpenSPIM_Wiki OpenSpinMicroscopy ndash do-it-yourself SPIMDSLMOPT microscopes httpssitesgooglecomsiteopenspinmicroscopy Ovizio ndash differential digital holography (similar to quantitative phase imaging) httpwwwoviziocomenHome httpwwwoviziocomenMicroscopesQMod Oxford Gene Technologies ndash microarrays ndash cytogenetics molecule genetics cancer research pre-implantation genetic diagnosis httpwwwogtcomclinical_genetics Oxford Nanoimaging ndash single molecule(s) localization fluorescence resonance energy transfer (FRET) (Kapanidis) wwwoxfordnicom Pathology Devices ndash LiveCell stage top incubator amp controller tissue microarrayers (TMA makers) httpwwwpathologydevicescomLiveCellhtm httpwwwpathologydevicescomTMArrayerhtm PeCon GmbH ndash microscope incubators httpwwwpeconbiz Pembroke Instruments ndash spectrometers mini-lasers httppembrokeinstrumentscomqmini-spectrometer httppembrokeinstrumentscommini-lasers PerkinElmer ndash in vivo imaging systems (bioluminescence NIR fluorescence) Vectra digital slide scanner httpwwwperkinelmercomcategoryin-vivo-imaging-instruments httpwwwperkinelmercomcategoryquantitative-pathology-imaging-instruments Phi Optics ndash CellVista SLIM Pro (quantitative phase microscopy) httpphiopticscom Photometrics (Roper Scientific) ndash DualView QuadView httpwwwphotometricscom httpwwwphotometricscomproductsmultichannel Photon Technology International httpwwwpti-njcomindexhtml

PicoQuant GmbH ndash fluorescence lifetime imaging microscopes (FLIM) STED 3D-EasySTED httpswwwpicoquantcomproductscategoryfluorescence-microscopes httpswwwpicoquantcomapplicationscategorylife-sciencested httpwwweasystedorg Physik Instrumente GmbH amp Co KG (PI) - Nanopositioning Applications for Microscopy Neuroscience and Metrology httpswwwphysikinstrumentecomen httpwwwpi-usausindexphp PreSens Prescision Sensing GmbH - VisiSens measure and visualize Oxygen pH or carbon dioxide distributions httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-biological-researchhtml httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-life-science-researchhtml Prior Scientific

httpwwwprior-uscom Profusa Inc - Lumee tissue-integrated biosensors scaffolds httpprofusacomtechnology Reindeer Graphics Inc ndash OptiPix Fovea Pro 9plugins for Adobe Photoshop 6 and CS series) httpwwwreindeergraphicscom Renishaw - StreamLine fast chemical imaging Raman spectroscopy httpwwwrenishawcomenstreamline-generate-chemical-images-rapidly--9449 httpwwwrenishawcomenraman-spectroscopy--6150 Sanford Burnham Prebys ndash High Content Screening httpwwwsbpdiscoveryorgtechnologysrPagesLaJolla_HighContentScreeningaspx ScopeM - Scientific Center for Optical and Electron Microscopy - ETH Zurich httpwwwscopemethzch SiriusXT - soft X-ray tomography (SXT) microscope (CT scan hydrated cell) httpsiriusxtcom SpectraGenetics - Fluorogen Activating Peptides (FAPs) new genetically encoded ldquobinaryrdquo reporters httpspectrageneticscomproductsvectors-for-expressing-fluorogen-activating-proteinsfap-technology-overview Spirochrome - Silicon Rhodamine (SiR) and other fluorescent reagents probes for bioimaging httpspirochromecom Stanford Photonics Inc httpwwwstanfordphotonicscom httpwwwstanfordphotonicscomLife20SciencesLifeScihtm

Stream Technologies Inc ndash ColorFlow lens (multi-wavelength emission onto a camera) httpwwwstreamtechinccomproducts Sutter Instrument Company httpwwwsuttercom httpwwwsuttercomMICROSCOPESindexhtml httpwwwsuttercomIMAGINGindexhtml SVI Huygens ndash Professional (general image analysis) deconvolution NVidia GPU deconvolution httpssvinlHuygensProfessional httpssvinlHuygensDeconvolution httpssvinlHuygensGPU Sysmex Partex ndash CyScope httpwwwsysmex-parteccomproductsmicroscopyhtml httpwwwsysmex-parteccomproductsprdouct-detailviewcyscopeR-malaria-3238html Technical Instruments httpwwwtechinstcomproductsphp TESCAN Brno sro - Tescan Q-PHASE multimodal holographic quantitative phase imaging system (QPi) optional fluorescence httpwwwtescancomenproductsq-phaseq-phase httpq-phasetescancom httpq-phasetescancomindexphptechnologyspecifications Ted Pella Inc ndash specialty light microscopy and electron microscopy supplies httpswwwtedpellacom Texas Instruments ndash DLP 4100 development kit (digital light processingrsquo DMD digital micromirror device) httpwwwticomtooldlpd4x00kit

ThorLabs ndash iCyte imaging cytometer multiphoton confocal EnVista digital slide scanning microscopes httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7473 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7494 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=5696 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=6570 TIRF Labs lightguide TIRF prism TIRF TIRF-Electrochemistry httpwwwtirf-labscom httpwwwtirf-labscomtechnologieshtml TissueVision - Serial Two Photon Tomography (image volume ablate imaged volume with multiphoton laser repeat) httpwwwtissuevisioncomtechnology Tokai Hit - stage top incubator httpwwwtokaihitcomenglishproduct_guidanceoptionhtml TopoNomos Ltd ndash Toponome Imaging Cycler ndash immunofluorescence (100plex) httpwwwtoposnomoscomtechnologyhtml Ultivue Inc ndash DNA-PAINT ndash reagents data processing service httpwwwultivuecom httpwwwultivuecomproducts UMech Technologies ndash Cytovar HCS up to 16 excitation wavelengths httpcloudumechcomproducts httpcloudumechcomproductsmodelC16 Visitech ndash vt-iSIM instant super-resolution microscopy up to 1000 frames per second confocal scanners and light engines httpwwwvisitechcoukvt-isimhtml httpwwwvisitechcoukproductshtml Visitron Systems GmbH - high speed imaging systems httpwwwvisitronde Visualsonics (Fujifilm) - photoacoustic imaging httpwwwvisualsonicscomproductstechnology-overview Wicked Lasers httpwwwwickedlaserscom httpwwwwickedlaserscomarctic WITec Wissenschaftliche Instrumente und Technologie GmbH - imaging systems for FLIM Raman AFM and SNOM analysis httpwitecdeproducts httpwwwwitec-instrumentscom WM Keck Center for Adaptive Optical Microscopy (CfAOM) at UC Santa Cruz httpscfaomsoeucscedu httpcfaoucolickorgpgallery Yokogawa Corp ndash spinning disk confocal scanner live cell imager high content screener confocal quantitative cytometer httpwwwyokogawacomsolutionsproducts-platformslife-science httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-scanner-unit-csu httpwwwyokogawacomsolutionsproducts-platformslife-scienceall-in-one-live-cell-imaging-solution httpwwwyokogawacomsolutionsproducts-platformslife-sciencehigh-throughput-cytological-discovery-system httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-quantitative-image-cytometer Zellkraftwerk (ChipCytometry) ndash immunofluorescence (80plex) httpwwwzellkraftwerkcomProducts2phtml httpwwwzellkraftwerkcomZKWOnephtmlSoftware

httpwwwchipcytometrycomtechnologyphtml Fluorescence Spectra Data and Graphing Sites PubSpectra ndash Excel file data download httpsworksbepresscomgmcnamara9 BD Biosciences ndash spectrum viewer Brilliant fluorophores httpwwwbdbiosciencescomussspectrumviewer httpwwwbdbiosciencescomusapplicationssspectrumguidepage BioLegend ndash spectra analyzer Brilliant Violet fluorophores httpwwwbiolegendcomspectraanalyzer httpwwwbiolegendcombrilliantviolet Chroma Technology httpswwwchromacomspectra-viewer eBioscience (Affymetrix ThermoFisher) ndash fluorPlan ndash a multi-laser spectra viewer httpwwwebiosciencecomresourcesfluorplan-spectra-viewerhtm Spectra Viewer (requires Java) Evrogen ndash Spectrum Viewer httpevrogencomspectra-viewerflashviewerhtml Fluorophoresorg ndash Fluorescent Substances httpwwwfluorophorestugrazatsubstance I Love GFP httpssitesgooglecomsiteilovegfpHomefps Lambert and Thorn UCSF Fluorescent protein properties httpnicucsfeduFPvisualization Leica Microsystem - ldquoFluoScoutrdquo httpwwwleica-microsystemscomfluoscout

Molecular Probes Invitrogen Thermo Fisher ndash Fluorescence SpectraViewer httpwwwthermofishercomusenhomelife-sciencecell-analysislabeling-chemistryfluorescence-spectraviewerhtml httpsitunesapplecomusappfluorescence-spectraviewerid421031826 (iTunes App) Nightsea - Compendium of spectra web sites httpwwwnightseacomsfa-sharingfluorescence-spectra-viewers Omega Optical ldquoCurvomatricrdquo httpswwwomegafilterscomcurvomatic

PhotoChemCAD 20 (Jonathan S Lindsey) dye spectra database and chemistry calculator NIRvana Sciences httpwwwphotochemcadcom httpnirvanasciencescompage_id=3088 UCSF (Lambert Thorn 2016) - Fluorescent protein properties httpnicucsfeduFPvisualization University of Arizona - Fluorescent Spectra Database httpwwwspectraarizonaedu Semrock - Searchlight httpssearchlightsemrockcom Spectroscopy Ninja ndash links to spectral and fluorescence data Spekwin32 spectroscopy software httpwwweffemm2deinfoinfo_specdatahtml

httpwwweffemm2deindexhtml Zeiss ndash interactive fluorescence dye and filter database overview dyes overview filter sets httpswwwmicro-shopzeisscoms=50479761ad21e5ampl=enampp=usampf=fampa=i httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=d httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=f Researcher Labs Alby Diaspro ndash IIT httpwwwlambsitindexphppage=People Alice Ting ndash MIT httpwwwtinglaborgresearch Allen Institute for Brain Science httpwwwalleninstituteorgwhat-we-dobrain-science Allen Institute for Cell Science httpwwwalleninstituteorgwhat-we-docell-science Amina Qutub - Rice University - How are human cells designed lab httpsqutublaborgqutub-lab Amy Herr UC Berkeley ndash Single cell Westerns httpherrlabberkeleyedu Amy Palmer ndash UC Boulder httpspalmerlabcoloradoedu Andrew York ndash Calico Life Sciences httpswwwcalicolabscomteam-memberandrew-york Anne Carpenter ndash Broad Institute CellProfiler httpspersonalbroadinstituteorganne Arjun Raj UPenn single molecule RNA FISH quantitative understanding cellular functions httprajlabseasupenneduindexhtml httpwwwpopscicomsciencearticle2013-09arjun-raj Atsuko Miyawaki - Laboratory for Cell Function Dynamics (CFDS) Fucci2 fluorescent proteins cell cycle indicator httpwwwbrainrikenjpenfacultydetails30 httpcfdsbrainrikenjp httpcfdsbrainrikenjpFuccihtml Aydogan Ozcan - UCLA - new imaging and sensing architectures httpinnovateeeuclaeduwelcomehtml httpwwwhhmiorgscientistsaydogan-ozcan Badri Roysam - UH - FARSIGHT Toolkit httpwwweeuhedufacultyroysam httpwwwfarsight-toolkitorgwikiMain_Page Brian J Ford ndash microscopist and popularizer httpsuklinkedincominprofbrianjford Carolyn Larabell ndashNational Center for X-ray Tomography (LBNL) UCSF httpncxtlblgovq=carolyn httpprofilesucsfeducarolynlarabell Clare Waterman ndash NHLBI NIH

httpswwwnhlbinihgovresearchintramuralresearcherspiwaterman-clare Dana Peer - Columbia University - Computational Systems Biology viSNE and more software httpwwwc2b2columbiaedudanapeerlabhtml httpwwwc2b2columbiaedudanapeerlabhtmlcythtml David Mayerich - UH - STIM Laboratory Scalable Tissue Imaging and Modeling httpwwweeuhedufacultymayerich httpstimeeuhedu David Piston WUSTL httpwwwcellbiologywustledufacultytenureddavid-w-piston-phd Diane Lidke and Keith Lidke - University of New Mexico httppathologyunmeduresearchfaculty-laboratoriesthe-lidke-laboratoryindexhtml httppanda3physunmedu~klidke Donna Arndt-Jovin and Thomas Jovin - Max Planck Institute for Biophysical Chemistry Laboratory of Cellular Dynamics httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsDonnaArdndt-JovinResearchAreasAndProjects httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsChairmanThomasJovinResearchAreasAndProjects Ed Boyden ndash MIT Media Lab ndash expansion microscopy (ExM) optogenetics httpsyntheticneurobiologyorg httpsyntheticneurobiologyorgprotocols httpsyntheticneurobiologyorgpublications httpwwwtedcomtalksed_boyden_baby_diapers_inspired_this_new_way_to_study_the_brain httpwwwextbiocombuycell Elizabeth Blackburn ndash Salk Institute - Telomeres httpswwwsalkeduscientistelizabeth-blackburn httpsenwikipediaorgwikiElizabeth_Blackburn httpswwwnobelprizeorgnobel_prizesmedicinelaureates2009blackburn-factshtml Elizabeth Hillman - Columbia university - SCAPE (Swept Confocally-Aligned Planar Excitation) high speed 3D microscopy DyCE (dynamic contrast enhancement to image and segment small animal organs live) Neuroimaging amp Neurovascular Coupling httporionbmecolumbiaedu~hillmanInstrumentationhtml httporionbmecolumbiaedu~hillmanSCAPEhtml httporionbmecolumbiaedu~hillmanMolecularhtml httporionbmecolumbiaedu~hillmanBrain_Imaginghtml Eric Betzig ndash UCSF (moving from HHMI Janelia Farm in 2016) httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014betzig-factshtml Eva Sevick-Muraca ndash UT Health Science Center at Houston molecular imaging clinical NIR fluoresceince imaging httpswwwutheduimmprofilehtmid=1005459 httpswwwutheduimmcentersmolecular-imaginghtm Evelin Schrock - Technische Universitaumlt Dresden spectral karyotyping cytogenetics httpswwwresearchgatenetprofileEvelin_Schrock Garry Nolan Stanford University ndash Mass cytometry MIBI-ToF high throughput imaging mass cytometry (42plex) httpwebstanfordedugroupnolanresourceshtml httpwebstanfordedugroupnolantechnologieshtml George McNamara ndash Cell Morphometry (41) Figure 1 right top two panels (55) The Chase (2016 temporal area maps lsquodynamic morphologyrsquo) (76) newsletter series on ldquoThe Chaserdquo (73) direct Vimeo movie of ldquoThe Chaserdquo Tiki_Goddess linkedin 10+plex blog httpsworksbepresscomgmcnamara41 httpsworksbepresscomgmcnamara55 httpsworksbepresscomgmcnamara76

httpsworksbepresscomgmcnamara73 httpsvimeocom175151196 httphomeearthlinknet~tiki_goddess httpswwwlinkedincomingeorgemcnamara httpswwwlinkedincompulsebd-biosciences-listed-tandems-horizon-brilliant-violets-mcnamara Gillian Griffiths - University of Cambridge - T-cell immunological synapse httpwwwcimrcamacukresearchprincipal-investigatorsprincipal-investigators-a-hgriffiths Hari Shroff NIBIB NIH httpswwwnibibnihgovlabs-at-nibibsection-high-resolution-optical-imaging-hroi HHMI Janelia Farm Research Campus (JFRC) - Advanced Imaging Center Open Science httpswwwjaneliaorgopen-scienceadvanced-imaging-center-aic httpswwwjaneliaorgopen-science Jeanne Lawrence University of Massachussetts Medical School httpwwwumassmededucellbiolabslawrencepersonnelprincipal-investigator Jennifer Lippincott-Schwartz ndash HHMI Janelia Farm httpswwwjaneliaorgpeoplejennifer-lippincott-schwartz Jin Zhang ndash UCSD httpprofilesucsdedujinzhang Joe DeRisi - UCSF - 3D printable lab stuff httpderisilabucsfeduindexphppage=3D John Russ Chris Russ Fovea Pro plugins for Adobe Photoshop httpwwwdrjohnrusscomindexhtml httpwwwdrjohnrusscombookshtml httpwwwreindeergraphicscomfoveaprotutorialhtml Julie Theriot httpcmgmstanfordedutheriot Karl Deisseroth ndash Stanford University ndash CLARITY optical tissue clearing Optogenetics httpclarityresourcecenterorg httpwebstanfordedugroupdlaboptogeneticsindexhtml Karsten Koumlnig (Koenig) - Saarland University and JenLab GmbH - biophotonics httpwwwbltuni-saarlanddeindex_ehtm httpwwwjenlabde httpwwwthelastescape-filmcom Karsten Rodenacker ndash image measurements httpkaro03bplacednetkaroMeMisc_WWWpdfMicrosoftWord-EQUAPATpdf Kevin Eliceiri ndash UW-Madison Open Source Photonics and Software Laboratory for Optical and Computational Instrumentation (LOCI) wwwlociwiscedu Klaus Kemp ndash Microlife Services ndash diatoms and other prepared microscope slides httpwwwdiatomscouk Kurt Thorn UCSF httpthornlabucsfedu httpsnicucsfedublog httpnicucsfeduFPvisualization httpgigapancomgigapans163370 Lihong Wang - WUSTL - Optical Imaging Laboratory photoacoustic tomography

httpoilabseaswustledu httpoilabseaswustleduresearch_0html Loren Looger - HHMI JFRC - iGluSnFr fluorescent protein biosensor httpswwwjaneliaorglablooger-lab Mary-Lou Pardue ndash MIT (first ever in situ hybridization with J Gall) httpsbiologymitedupeoplemary_lou_pardue httpsenwikipediaorgwikiMary-Lou_Pardue Nancy Allbritton - UNC - Chemical cytometry microraft arrays organ-on-a-chip httpswwwbmencsueduindexphpcomponentcomprofileruserprofilenlallbri httpwwwbmeuncedulabsallbritton Navin Varadarajan - UH - single-cell Lab httpwwwcheeuhedufacultyvaradarajan httpsinglecellcheeuheducontacthtml Nicholas Shaner - Scintillon Institute - mNeonGreen httpwwwscintillonorgshaner_lab Rebecca Richards-Kortum httpbioengineeringriceedufacultyrebecca_richards-kortumaspx Robert Campbell - Fluorescent proteins optogenetic proteins httpcampbellwebchemualbertaca httpcampbellwebchemualbertacaprojects-2 Robert Murphy ndash Cell measurements web services httpmurphylabwebcmueduservices Sabine Mai - University of Manitoba - Genomic Centre for Cancer Research and Diagnosis (GCCRD) - httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBPlatformsGCCRDhtml httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBScientistsMaiAwardshtml Sally Ward and Raimund Ober - Texas AampM University - httpwwwwardoberlabcom Simon Watkins - U Pittsburgh Center for Biologic Imaging httpwwwcbppittedufacultywatkinshtml httpwwwcbppittedufacultylabwatkinshtml httpwwwcbipittedu Stefan Hell ndash Deparment Hell NanoBiopohotonics httpwwwmpibpcmpgdehell httpsenwikipediaorgwikiStefan_Hell httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014hell-factshtml Sunney Xie Harvard httpsbernsteinharvardedu Susan Cox ndash 3B microscopy httpwwwcoxphysicscomindexhtml httpwwwcoxphysicscom3b Radim Chmeliacutek - Center for innovative microscopy Experimental biophotonics group httpswwwceiteceuceitec-butexperimental-biophotonicsrg3 httpwwwbiophotczhome Taekjip Ha ndash Johns Hopkins University ndash single molecules httphamedjhmiedu

Thomas Ried ndash NCI NIH SKYM-FISH and CGH Database httpsccrcancergovGenetics-Branchthomas-ried httpsccrcancergovGenetics-Branchthomas-riedqt-staff_profile_tabs=9qt-staff_profile_tabs ftpftpncbinlmnihgovsky-cghDATA httpswwwncbinlmnihgovdbvar Viviana Gradinaru ndash CalTech ndash CLARITYPACT Optogenetics httpwwwbbecaltecheducontentviviana-gradinaru httpglabcaltechedu Vladislav Verkhusha - near infrared fluorescent proteins httpwwweinsteinyuedulabsvlad-verkhushadefaultaspx httpwwweinsteinyueduresearchfacilitiesfluorescent WE Moerner ndash Stanford University httpwebstanfordedugroupmoerner Willard Wiggans ndash micro gallery httpwwwwillard-wigancomgallery Wolf Frommer ndash Molecular sensors httpbiosensordpbcarnegiescienceedu (fluorescent protein biosensors table) Xiaowei Zhuang = Harvard httpzhuangharvardedu Yuval Garini - Bar-Ilan University - Nano-Bio-Photonics laboratory httpgarinilabbiuacil Microscopy Magazines Imaging amp Microscopy httpwwwimaging-gitcommagazine Laser Focus World httpwwwlaserfocusworldcomindexhtml Microscopy amp Analysis httpwwwmicroscopy-analysiscom Microscopy Today httpwwwmicroscopy-todaycom Microscopy-UK httpwwwmicroscopy-ukorguk Photonics Spectra Biophotonics httpwwwphotonicscomPublicationsaspx The Microscope Journal httpmcriorgv72the-microscope-journal RMS Infocus Magazine httpwwwrmsorgukstudy-readinfocus-magazinehtml Nobel Prizes in Light Microscopy and Related Fields Chemistry 1925 colloids (light sheet) Zsigmondy (Siedentopf Zsigmondy 1902) httpswwwnobelprizeorgnobel_prizeschemistrylaureates1925

Chemistry 2000 conductive polymers Heeger MacDiarmid Shirakawa (Brilliant Violets Ultraviolets Blues) httpwwwnobelprizeorgnobel_prizeschemistrylaureates2000 Chemistry 2008 green fluorescent protein GFP Shimomura Chalfie Tsien httpwwwnobelprizeorgnobel_prizeschemistrylaureates2008 Chemistry 2014 super-resolved fluorescence microscopy Betzig Hell Moerner httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014 Physics 1953 Phase Contrast Zernike httpswwwnobelprizeorgnobel_prizesphysicslaureates1953 Physics 2009 invention of an imaging semiconductor circuit ndash the CCD sensor Kao Boyle Smith httpwwwnobelprizeorgnobel_prizesphysicslaureates2009 Physics 2014 efficient blue light emitting diodes Akasaki Amano Nakamura httpwwwnobelprizeorgnobel_prizesphysicslaureates2014 Physiology or Medicine 2006 Fire and Mello RNA interference ndash gene silencing by double stranded RNA httpwwwnobelprizeorgnobel_prizesmedicinelaureates2006 Physiology or Medicine 2006 Capecchi Evans Smithies specific gene modifications in mice by the use of embryonic stem cells httpwwwnobelprizeorgnobel_prizesmedicinelaureates2007 Physiology or Medicine 2009 Blackburn Greider Szostak how chromosomes are protected by telomeres and telomerase httpwwwnobelprizeorgnobel_prizesmedicinelaureates2009 Physiology or Medicine 2012 Gurdon Yamamanka matured cells can be reprogrammed to become pluripotent httpwwwnobelprizeorgnobel_prizesmedicinelaureates2012

Table 442 Fluorophores Photophysics Data

Fluorophore Abs or Ex max (nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Acridine orange 271 520 27000 020 5

Alexa Fluor 430 431 541 16000 055 9

Alexa Fluor 488 495 519 71000 094 67

Alexa Fluor 532 532 553 81000 080 65

Alexa Fluor 546 556 573 104000 096 100

Alexa Fluor 568 578 603 91300 075 69

Alexa Fluor 594 590 617 73000 064 47

Allophycocyanin (APC) 650 660 700000 068 476

Atto 390 390 479 24000 090 22

Atto 425 436 484 45000 065 29

Atto 430LS 433 547 32000 065 21

Atto 465 453 508 75000 075 56

Atto 490LS 496 661 40000 030 12

Atto 520 525 547 105000 095 100

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 4: McNamara 20161006 revised draft tables for CPHG Light ...

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http490biotechcomvectors-2 Abberior httpwwwabberiorcomshopLabels-by-FunctionFluorescent-Proteins7_14html httpwwwabberiorcomshopLabels-by-Application1html Addgeneorg wwwaddgeneorg httpswwwaddgeneorgfluorescent-proteins httpswwwaddgeneorgfluorescent-proteinsbiosensors httpswwwaddgeneorgfluorescent-proteinslocalization httpswwwaddgeneorgoptogenetics httpswwwaddgeneorgfluorescent-proteinsdavidson httpswwwaddgeneorgRoger_Tsien Allele Biotechnology httpwwwallelebiotechcomFluorescent-Proteins Bell Biosystems ndash Magnelle living MRI contrast agents (magnetotactic bacteria taken up by human cells in vitro) with fluorescent proteins ndash in vivo cell tracking httpwwwbellbiosystemscomProducts-and-ServicesCell-Tracking-Solutions BioBricks Foundation httpbiobricksorg BioPop (Intrexon) ndash Dinoflagellates bioluminescence luciferaseluciferin httpsbiopopcomproducts Chromotek GmbH - Chromobodies Nano-Boosters (llama nanobodies attached to or detecting FP) httpwwwchromotekcomproductschromobodies httpwwwchromotekcomproductschromobodiescell-cycle-chromobodyr httpwwwchromotekcomproductsnano-boosters DNA 20 chromogenic and fluorescent protein paintbox (not really IP-Free) httpswwwdna20comproductsprotein-paintbox Evrogen httpevrogencomproductsbasicFPsshtml httpevrogencomproductsBiosensorsshtml httpevrogencomproductsOrganelle-labelingshtml iGEM BioBricks ndash reporter proteins including fluorescent proteins httppartsigemorgProtein_coding_sequencesReporters iGEM Registry of Standard Biological Parts httppartsigemorgMain_Page InvivoGen ndash GFP Lucia luciferase reporters httpwwwinvivogencomdual-reporter MBL International Corp ndash fluorescent proteins httpswwwmblintlcomproductsfluorescent-proteins httpruomblcojpbioeproductflproteinfuccihtml Millipore-Sigma Sigma-Aldrich ndash firefly luciferase D-luciferin httpwwwsigmaaldrichcomlife-sciencemetabolomicsenzyme-exploreranalytical-enzymesluciferasehtml Molecular Probes Inc Invitrogen Thermo Fisher ndash Bacmam 20 fluorescent proteins biosensors FUCCI httpwwwprobescom httpwwwthermofishercomusenhomebrandsmolecular-probeshtml httpswwwthermofishercomusenhomeindustrialpharma-biopharmadrug-discovery-developmenttarget-and-lead-identification-and-validationpathway-biologycellular-pathway-analysisbacmam-systembacmam-reagentshtml

Montana Molecular LLC - genetically encoded fluorescent biosensors and probes for cell-based assays and live cell imaging httpmontanamolecularcomproductsproducts-overview NanoLight Technologies ndash Renilla GFP luciferases httpwwwnanolightcomNanoFluorsGFP_Expression_Vectorshtml httpswwwbiotoycomenlearn n3D Biosciences ndash generate 3D cell spheroids high throughput screening image changes using smartphone camera inside incubator httpwwwn3dbiocomproductsmagnetic-3d-bioprinting httpwwwn3dbiocomproductsassays New England BioLabs (NEB) ndash Cypridina Gaussia luciferases httpswwwnebcomapplicationscellular-analysisreporter-systems Promega ndash Monster GFP NanoLuc httpswwwpromegacomproductsreporter-assays-and-transfectionreporter-vectors-and-cell-linesmonster-green-fluorescent-protein-phmgfp-vector httpswwwpromegacomproductsreporter-assays-and-transfectionreporter-vectors-and-cell-linesnanoluc-luciferase-reportersnanoluc-genetic-reporter-vectors Fluorescence Products (reagents) Advanced Cell Diagnostics (Bio-Techne) - branched DNA probe sets for RNA FISH httpsacdbiocomproducts Affymetrix eBioscience Thermo Fisher - branched DNA probe sets for RNA FISH httpwwwaffymetrixcomestorepromotionsviewrnaishindexaffx Anaspec ndash HiLyte Fluorophores FRET probes httpswwwanaspeccomproductsproductcategoryaspid=10 Antibody Resource Page httpwwwantibodyresourcecom Biocompare ndash Antibodies httpwwwbiocomparecomAntibodies Cell Signaling Technology ndash fluorescence antibodies httpswwwcellsignalcombrowseimmunofluorescence-immunocytochemistryif-paraffinif-frozen Essen Biosciences ndash Bacmam 30 ready to use FP gene transfection reagents httpwwwessenbiosciencecomenproductsreagents-consumablesincucyte-nuclight-red-bacmam-30-reagent-nuclear-labeling-cat-no-4621 GE Healthcare Amersham Biosciences httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usbrandscydye Global Biological Standards Institute (GBSI) ndash Antibody Validation Initiative httpwwwgbsiorgworkantibodies Goryo Chemical httpwwwgoryochemicalcom Human Protein Atlas (academic) Atlas Antibodies (commercial arm) US distributor httpwwwproteinatlasorg httpsatlasantibodiescom httpwwwsigmaaldrichcomlife-sciencecell-biologyantibodiesprestige-antibodieshtml

Integrated DNA Technologies (IDT) httpwwwidtdnacomsiteCatalogmodificationsdyes httpwwwidtdnacompagesproductsmodificationsfluorophoresfreedom-dyes httpwwwidtdnacomsiteCatalogModificationsCategory4 Jackson ImmunoResearch httpswwwjacksonimmunocom KPL (formerly Kirkegaard amp Perry Laboratories Inc) SeraCare httpwwwkplcom LGC Biosearch Technologies ndash dyes for oligonucleotides single molecular RNA FISH image gallery httpswwwbiosearchtechcomsupporteducationfluorophores-and-quenchers httpstellarisfishsmugmugcom httpsinglemoleculefishcom httpswwwbiosearchtechcomproductsrna-fish (typically 48 20 base oligonucleotides) Marker Gene Technologies Inc (MGT) httpwwwmarkergenecomfluorescent-reagent Miltenyi Biotec ndash REAfinity recombinant engineered antibodies (no Fc Receptor binding) FASER fluorescence amplification kits NiraWave fluorophores (indocyanine green formulations) httpwwwmiltenyibioteccomenproducts-and-servicesmacs-flow-cytometryreagentsantibodies-and-dyesrecombinant-antibodiesaspx httpwwwmiltenyibioteccomenproducts-and-servicesmacs-flow-cytometryreagentssupport-reagentsfaser-kitsaspx httpwwwmiltenyibioteccomenproducts-and-servicesviscover-imagingoptical-imagingaspx Molecular Probes Inc Invitrogen Thermo Fisher ndash largest vendor of fluorophores Molecular Probes Handbook (web resource) Tyramide Signal Amplification kits httpwwwprobescom httpswwwthermofishercomusenhomereferencesmolecular-probes-the-handbookhtml httpswwwthermofishercomusenhomereferencesmolecular-probes-the-handbooktablestyramide-signal-amplification-tsa-kitshtml NIRvana Sciences httpnirvanasciencescom httpnirvanasciencescompage_id=3088 One World Lab ndash antibody search httponeworldlabcomantibodies CytoCell Oxford Gene Technologies ndash DNA FISH probes human mouse pig chicken httpwwwcytocell-uscom Perkin Elmer ndash nucleotides labeling kits Tyramide Signal Amplification Kits (TSA) Opal 7plex discovery panel kit based on sequential TSA httpwwwperkinelmercomcategoryfluorescent-hapten-nucleotides httpwwwperkinelmercomcategoryfluorescent-agents-labeling-kits-dyes httpwwwperkinelmercomlab-solutionsresourcesdocsBRO_TSAsignalamplificationpdf httpwwwperkinelmercomproductopal-7-immunology-discovery-kit-op7ds1001kt

Rockland Inc httpwwwrockland-inccomcommerceindexjsp

TEFLabs ndash fluorescent ion indicators (Ca++ Cl- K+ Mg++ Na+ pH Zn++) ionophores fluorophores httpwwwteflabscomion-indicators Vector Laboratories Inc httpwwwvectorlabscom

Live cell imaging dishes and multi-well plates (ldquoglass bottom dishesrdquo)

We recommend these for simplified handing and processing vs either thick plastic dishesplates or having to handle loose coverslips with your valuable cells

Leicester Imaging Technologies (LITE) - University of Leicester - table of dishes for live cell imaging (our table has current links and bad links left out) httpwww2leacukcollegesmedbiopsychfacilities-and-servicescbsliteaiftips-and-tricks-1dishes-for-live-cell-imaging Bellco Glass Inc - glass flat bottom plate httpwwwbellcoglasscomnode1046 Bioptechs - interchangable coverslip dish ($036 per experiment) httpwwwbioptechscomproductinterchangeable-coverslip-dish Brooks Automation Inc - clar bottom optical imaging microplates httpwwwbrookscomproductslife-scienceconsumablesmatrical-microplates-microtubes-racks-lidsglass-bottom-optical-imaging-microplates Cell EampG - glass bottom cell sulture dishes plates httpcellegcomproducthtml Cellvis - glass bottom dishes and plates httpwwwcellviscom_35-mm-glass-bottom-dishes_products_by_categoryphpcat_id=3 Corning - glass bottom microplates httpcatalog2corningcomLifeSciencesen-USShoppingCategoryaspxcategoryname=Microplates20-202015(Lifesciences)|Assay20Microplates20-202015(Lifesciences) Design 1 Solutions - Custom microplates and fabrication services httpwwwdesign1solutionscomcustom-microplateshtml Eppendorf - cell imaging dishes imaging plates httpsonline-shopeppendorfcomOC-enCell-Culture-and-Imaging-Consumables-110320Cell-Imaging-Consumables-120210Eppendorf-Cell-Imaging-Dishes-PF-19457html httpsonline-shopeppendorfcomOC-enCell-Culture-and-Imaging-Consumables-110320Cell-Imaging-Consumables-120210Eppendorf-Cell-Imaging-Plates-PF-19458html Greiner Bio-One International - CellView glass bottom dishes quadrant dishes httpsshopgbocomenrowarticlescataloguearticle0110_0110_0040_002027513 ibidi - u-Plates glass bottom dishes microfluidic slides httpibidicomxtproductsenibidi-Labwarem-Plates httpibidicomxtproductsenibidi-Labware Matsunami Glass Ind Ltd httpwwwmatsunami-glasscojpenglishlifebiodata01html Mattek - glass bottom dishes and SBS plates httpswwwmattekcomstore-categoryculturewareglass-bottom-dishes Nunc - glass bottom dishes httpswwwthermofishercomordercatalogproduct150680 NEST Biotechnology Co Ltd Wuxi Jiangsu PRChina httpwwwnestscientificusacomproducts_detailproductId=31html PerkinElmer - glass bottom plates httpwwwperkinelmercomSECatalogCategoryIDMicroplates

Porvair Sciences - clear bottom assay plates httpwwwporvair-sciencescomenservices-menulife-sciencesclear-bottom-assay-plates Ted Pella Inc - glass bottom dishes clear wall or black wall (manufactured by WillCo Wells) httpswwwtedpellacomsection_html706dishhtm Warner Instruments (Harvard Apparatus) - culture dishes perfusion systems httpswwwwarneronlinecomproduct_cat_infocfmid=1322 Willco Wells - glass bottom dishes wwwwillcowellscom World Precision Instruments - Fluorodish glass bottom dishes httpswwwwpiinccomproductslaboratory-suppliesfd35-100-fluorodish-cell-culture-dish-35mm-23mm-well-pkg-of-100 Microscopes Microscopy Accessories (accessorize) Reagents Resources 3scan ndash knife edge scanning microscope (images slices repeats through specimen) httpwww3scancomdata-2 89North (affiliated with Chroma Technology Corp) httpwww89northcom Abberior Instruments ndash STED RESOLFT precision localization super-resolution microscopes STEDYCON convert any fluorescence microscope to STED httpabberior-instrumentscom httpabberior-instrumentscomproductscompact-lineabberior-stedy-con Acquifer ndash HIVE imaging machine (computer hardware) for high content screening big data httpswwwacquiferde Adobe Systems Inc httpwwwAdobecom httpscreativeadobecomproductsdownloadphotoshop Affymetrix eBioscience (ThermoFisher) - microarrays httpwwwaffymetrixcomestorebrowselevel_one_category_template_onejspparent=35796ampcategory=35796 httpwwwaffymetrixcomestorecatalog131547AFFYGeneChip26231743B+System+3000Dx+v22623423B1_1 Agilent Technologies ndash SureScan microarray scanner (array CGH microRNA SNPs CNV) httpwwwgenomicsagilentcomenMicroarray-Scanner-Processing-HardwareSureScan-Microarray-Scannercid=AG-PT-144 Andor Technology (Oxford Instruments) ndash sCMOS cameras Dragonfly spinning disk confocal Revolution DSD2 differential spinning disk confocal photostimulation (fluorescence recovery after photobleaching optogenetics) Mosaic3 DMDDLP high speed light patterning (optogenetics structured illumination) MicroPoint pulsed UV laser for ablation DNA damage photobleachingactivation uncaging accessories httpwwwandorcomscientific-camerasneo-and-zyla-scmos-cameras httpwwwandorcommicroscopy-systemsdragonfly httpwwwandorcommicroscopy-systemsrevolution-dsd httpwwwandorcommicroscopy-systemsphotostimulation httpwwwandorcommicroscopy-systemsphotostimulationmosaic httpwwwandorcommicroscopy-systemsphotostimulationmicropoint httpwwwandorcommicroscopy-systemsmicroscopy-components Apogee Instruments Inc (Andor Technology) ndash CCD cameras and filter wheels (mostly marketed for astronomy) httpwwwccdcomandorhtml Applied Scientific Instrumentation Inc ndash light sheet imager (iSPIM diSPIM)

wwwasiimagingcom httpwwwasiimagingcomindexphpproductslight-sheet-microscopyselective-plane-illumination-microscopy-ispim-dispim Applied NanoFluorescence LLC ndash NS1 NanoSpectralyzer (Raman and UV-VISNIR) NS MiniTracer near infrared spectrometer NFM NanoFluorescence microscope multi-laser light source single wall carbon nanotubes (NIR II fluorophores) httpappliednanocomproductshtml httpappliednanocomproductsns1html httpappliednanocomproductsproduct-list77-ns-minitracerhtml httpappliednanocomproductsnfmhtml httpappliednanocomproductsls-nhtml httpwwwnanowerkcomnewsnewsid=24132php Applied Spectral Imaging Inc httpwwwspectral-imagingcom ArgoLight ndash fluorescence resolution test target slides httpargolightcom AttoCube - attoMICROSCOPY overview attoCFM - Multichannel cryogenic (low temperature) confocal fluorescence microscopes 08 NA objective lenses 400-1000 nm spectral range httpwwwattocubecom httpwwwattocubecomattomicroscopyintroductiontab-2 httpwwwattocubecomattodownloads AutoQuant (Media Cybernetics) spatial deconvolution httpwwwmediacycomautoquantx3 Becker amp Hickl GmbH httpwwwbecker-hicklcomproductshtm Berkeley Lights Inc ndash manueuver into nanowells incubate recover 4000 single cells per chip httpswwwberkeleylightscomtechnology Bioaxial ndash Codim imaging conical diffraction beam shaper for super-resolution (4 sub-images) httpwwwbioaxialcomcodim-imaging Bioptechs - Live-Cell Micro-Observation Products httpwwwbioptechscom Bionumbers - database of useful biological numbers httpbionumbershmsharvardeduKeyNumbersaspx Biostatus ndash DRAQ5 DRAQ7 ApopTRAK CyTRAK Orange CyGel HypoxiTRAK httpwwwbiostatuscomProducts Bio-Tek ndash Cytation 3 Cell Imaging Multi-Mode Reader Lionheart FX Automated Live Cell Imager httpwwwbiotekcomproductsimagingcytation3_cell_imaging_multi_mode_readerhtml httpwwwbiotekcomproductsimaginglionheartfx_automated_live_cell_imagerhtml Biovision Technologies ndash distributor for several imagers including VT-iSIM instant super-resolution microscope httpbiovision-technologiescom httpbiovision-technologiescomsystemshtml httpbiovision-technologiescomvtisimhtml Bitplane (Andor Oxford Instruments) ndash Imaris imaging software httpwwwbitplanecom BMV Optical - custom lens assemblies and optical filters wwwbmvopticalcom

Bruker (previously Prairie Technologies Vutara) ndash Opterra confocal Ultima Multiphoton Vutara 352 single molecule localization microscopes httpswwwbrukercomproductsfluorescence-microscopesopterra-confocal-microscopyoverviewhtml httpswwwbrukercomproductsfluorescence-microscopesultima-multiphoton-microscopyhtml httpswwwbrukercomproductsfluorescence-microscopesvutara-super-resolution-microscopyoverviewhtml Cairn Research ndash standard and custom accessories ex Light Sheet Illuminator MultiCam (4 cameras) custom design httpswwwcairn-researchcouk httpswwwcairn-researchcoukproductl-spi-single-plane-illuminator (dual L-SPI for 4 illumination directions) httpswwwcairn-researchcoukproductmulticam httpswwwcairn-researchcoukcustom-design Cameca ndash NanoSIMS 50L (7plex stable isotope imaging) httpwwwcamecacominstruments-for-researchnanosimsaspx CellMic (formerly Holomic) - blood analysis or fluorescence imaging cytometer on a cell phone httpwwwcellmiccomcontentadvanced-technologies httpwwwcellmiccomcontentfluorescent-imaging-cytometry-and-e-coli-detection-on-a-cell-phone CellOptic ndash FINCH (Fresnel INcoherence Correlation Holography) httpwwwcellopticcomindex2html CellProfiler ndash High content screening (HCS) image processing and analysis software httpcellprofilerorg ClearLight Diagnostics - CLARITY Optimized Light Sheet Microscopy (3D tissue optical clearing + light sheet imaging) httpwwwclearlightdxcomindexhtml Confocalnl ndash Rescan confocal microscopy to obtain 170 nm resolution with any pinhole diameter httpwwwconfocalnl CoolLED ndash LED light sources httpwwwcoolledcomproduct-detailpe-4000 Crest Optics SRL ndash X-Light confocal X-Light V2 + VCS (VideoConfocal super-resolution) httpwwwcrestoptcom httpwwwcrestoptcomhtmlx-light_v2_vcshtml Cytoskeleton Inc - live cell imaging reagents Spirochrome SiR bioimaging probes httpwwwcytoskeletoncomlive-cell-reagents httpwwwcytoskeletoncomlive-cell-reagentsspirochrome CytoViva ndash darkfield imaging hypspectral imaging httpwwwcytovivacomproducts3d-enhanced-darkfield-imaging httpwwwcytovivacomproductshyperspectral-imaging-2hyperspectral-imaging Data Translation Inc - digitizer cards httpwwwdatxcom Delmic BV - combined correlative scanning electron microscope with inverted fluorescence microscope httpwwwdelmiccomdelphi httpswwwdelphimicroscopecom httpwwwdelmiccomsecom-super-resolution Digital Light Innovations (DLi) - CELscope C-mount LED Microscope using Texas Instruments DLP illuminator with a simple stand httpswwwdlinnovationscomdli-deep-dives-celscope-c-mount-led-microscope Double Helix LLC ndash single molecule localization microscope (Piestun) httpdoublehelixopticscom Edinburgh Super-resolution Imaging Consortium (ESRIC)

httpwwwesricorg Energetiq ndash Deep ultraviolet (DUV high radiance 170-2100 nm) laser driven light source (LDLS) httpwwwenergetiqcom Epi Technology - CaliCube - Cube for fluorescence light path to inspect epi Illumination light source (lamp) fiber optic or liquid light guide httpwwwepitechnologycomepitechnology-1 Essen Biosciences ndash Incucyte Zoom (imager inside incubator) httpwwwessenbiosciencecomenproductsincucyte Estigen Tissue Science ndash manual and automated tissue arrayer (tissue microarray maker) httpwwwestigencom Euro-Bioimaging httpwwweurobioimagingeu Excelitas Technologies (formerly Lumen Dynamics) ndash X-Cite LEDs httpwwwexcelitascomPagesProductX-Cite-LED-Solutionsaspx Expansion Technologies Inc (extbio) ndash Expansion microscopy httpwwwextbiocombuycell FEI (formerly Till Photonics) (Thermo Fisher) ndash correlative LM-EM single molecule Cryo-EM httpswwwfeicomlife-sciencescellular-biology httpswwwfeicomlife-sciencescellular-biologycorrelative-microscopy httpswwwfeicomlife-sciencesstructural-biology Femtonics - Multi-phton microscopes software accessories caged glutamate reagents services httpfemtonicseuproducts First Light Imaging ndash C-Red NIR imaging (800-2500 nm NIR windows I II III 650-950 nm 1100-1350 nm 1600-1870 nm[Shi et al 2015]) high speed visible EMCCD (400-1000 nm) httpwwwfirst-lightfrcategoryrangesinfrared Fluidigm ndash Helios imaging CyTOF mass cytometer (42plex) Callisto (32 independent chambers dose with up to 16 independent factors for 1-1000 cell populations culture up to 3 week) Polaris functional genomics meets imaging (48 single cells up to 24 hours after single cell selection from a population) httpswwwfluidigmcomproductshelios httpswwwfluidigmcomproductscallisto httpswwwfluidigmcomproductspolaris GattaQuant - nanorulers for high resolution microscopes and super-resolution microscopes performance testing httpwwwgattaquantcomNanoruler GE Healthcare life Sciences Applied Precision ndash DeltaVision deconvolution OMX OMX SR httpwwwgelifesciencescomwebappwcsstoresservletproductByIdenGELifeSciences-us29065728 httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usproductsAlternativeProductStructure_2380729065721 httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usproductsAlternativeProductStructure_2380729115476 German BioImagingorg httpwwwgermanbioimagingorgwikiindexphpMain_Page httpwwwgermanbioimagingorgwikiindexphpWorkgroup6SoftwarePackages GIGAmacro ndash Magnify2 gigapixel imagery oof macroscopic and microscopic objects Terapixel macro image httpwwwgigamacrocomgigapixel-macro-imaging-system httpwwwgigamacrocomworlds-first-terapixel-macro-image

Glencoe Software ndash OMERO Plus enterprise data management for scientific images and any associated metadata (OME = Open Microscopy Environment) DataViewer PathViewer httpsglencoesoftwarecomomeroplushtml httpsglencoesoftwarecomdataviewerhtml httpsglencoesoftwarecompathviewerhtml Gooch amp Housego ndash spectral imager httpsgoochandhousegocomminiature-spectral-imaging-camera httpwwwghinstrumentscomproductsspectral-imaging-synthesishsi-440c-hyperspectral-imaging-system Hindsight Imaging ndash spectral imaging httphindsight-imagingcom Horiba Scientific - SWIFT ultra-fast Raman confocal imaging Raman spectroscopy httpwwwhoribacomscientificproductsraman-spectroscopyraman-imagingswift httpwwwhoribacomscientificproductsraman-spectroscopyraman-imaging httpwwwhoribacomscientificproductsraman-spectroscopy IATIA Ultima Capital ndash QPm (quantitative phase microscopy) httpwwwultimacapitalnetiatiaimagingPublicationsIatia20ImagingapplicationNotesqpmApplicationWithConfocalMicroscopespdf Ibidi - heating and incubation systems optical O2 measurement systems Nanolive 3D Cell Explorer pump system gas incubation system httpibidicomxtproductsenInstruments-AccessoriesHeating-Incubation-Systems httpibidicomxtproductsenInstruments-Accessoriesibidi-OPAL-Optical-O2-Measurement-System httpibidicomxtproductsenInstruments-AccessoriesNanolive-3D-Cell-Explorer httpibidicomxtproductsenInstruments-Accessoriesibidi-Pump-System httpibidicomxtproductsenInstruments-AccessoriesHeating-Incubation-Systemsibidi-Gas-Incubation-System iLAbSolutions (Agilent Technologies) - Instrument management and scheduling software (cores and labs) httpwwwilabsolutionscominstrument-access-control ImageJ - Fiji ImageJ NIH ImageJ ImageJ ndash Fiji (Fiji is just ImageJ) is the main download site httpfijisc httpsimagejnihgovij wwwimagejnet Inscopix ndash nVista in vivo mouse brain imaging miniature microscope httpswwwinscopixcomproducts Intelligent Imaging Innovations Inc (3i) ndash Slidebook imaging software Lattice light sheet (high speed gentle to cells high resolution imaging) Dual-view Inverted Selective Plane Illumination (diSPIM) VIVO 2-Photon (VIVO 2P) multiphoton microscopy Everest intravital imaging Marianas 3D real-time deconvolution timelapse spinning disk FRAP TIRF FLIM single molecule environmental control Phasor - optogenetic photostimulation using digital holography Yokogawa spinning disk confocal units wwwintelligent-imagingcom httpswwwintelligent-imagingcomslidebookphp httpswwwintelligent-imagingcomsystemsphplattice httpswwwintelligent-imagingcomsystemsphpdispim httpswwwintelligent-imagingcomsystemsphptwophoton httpswwwintelligent-imagingcomsystemsphpeverest httpswwwintelligent-imagingcomsystemsphpmarianas httpswwwintelligent-imagingcomoptogeneticsphp httpswwwintelligent-imagingcomsdcphp ISS Inc ndash fluorescence lifetime imaging microscopy fluorescence correlation spectroscopy (FCS) confocal imaging httpwwwisscommicroscopyindexhtml JenLab GmbH cyto-microscopy multiphoton tomography httpwwwjenlabdeproducts250html httpwwwjenlabde2PM-Cryo1330html

httpwwwjenlabdeMultiphoton-Tomography680html Jenoptik - microscope cameras httpswwwjenoptikcomproductscameras-and-imaging-modulesmicroscope-cameras JPK Instruments - integrated atomic force microscope (AFM) force sensing optical tweezers optical trapping single cell force spectroscopy (SCFS) httpwwwjpkcomindex2enhtml httpusajpkcomoptical-tweezers-optical-trapping29ushtml httpusajpkcomcellular-adhesion-cytomechanics30ushtml Keyence ndash VK-X confocal (upright) BZ-X700 widefield (inverted) httpwwwkeyencecomssproductsmicroscopevkx httpwwwkeyencecomssproductsmicroscopebz-x700indexjsp KK Technology - CapiScope HVCS Handheld Video Capillaroscopy System (CytoScan) httpwwwkktechnologycomhvcshtml LaVision BioTec ndash TriMscope Multiphoton TriM Scope II Adaptive Optics UltraMicroscope II light sheet httpwwwlavisionbiotecde httpwwwlavisionbiotecdetrim-scope-overviewhtml httpwwwlavisionbiotecdetrim-scope-ii-adaptive-opticshtml httpwwwlavisionbiotecdeultramicroscope-ii-introductionhtml Laxco ndash upright and inverted microscopes httpwwwlaxcoinccomMICROSCOPES Lego ndash Lego Idea Microscopes httpsideaslegocomprojects44370 httpwwwnico71frlego-working-microscope Li-Cor ndash near-infared fluorescent dyes and in vivo imaging agents in vivo and Western blot imaging systems httpswwwlicorcombioproductsreagents httpswwwlicorcombioproductsreagentsirdyebrightsite_imaging_agents httpswwwlicorcombioproductsimaging_systemsodyssey_familyhtml httpswwwlicorcombioproductsimaging_systemspearl httpswwwlicorcombioproductsimaging_systemscdigit Life Imaging Services - ldquothe Ludin chamberrsquo ldquothe cube amp the boxrdquo httpwwwlischthechamberhtml httpwwwlischtheboxhtml Lightform Inc ndash PARISS imaging spectrometer httplightforminccom LMU Bioimaging httpwwwbioimagingbmcmeduni-muenchendelinkswebsitesindexhtml httpwwwbioimagingbmcmeduni-muenchendelearneduwebsitesindexhtml Ludl Electronic Products Ltd ndash automated XY stages focus motors filter wheels httpwwwludlcom

LumaCyte ndash Laser force Cytology (laser trap meets microfluidics to suspend and manipulate single cells) httpwwwlumacytecomabouttechnology Lumencor ndash LEDs fluorescence light sources httplumencorcomproducts Luxcel ndash mitochondrial and cellular functions O2 sensor reagents httpluxcelcomproduct+list Luxendo GmbH ndash light sheet imager

wwwluxendoeu Lyncee tec - digital holography microscopy (DHM) high content screening by DHM httpwwwlynceeteccom httpwwwlynceeteccomhigh-content-screening Mad City Labs Inc - nanopositioning wwwmadcitylabscom Mauna Kea Technologies ndash CellVizio confocal laser endomicroscopy httpwwwmaunakeatechcomenhealthcare-professionalscellvizio-endomicroscopy-0 MBF Bioscience - stereology and neuron morphology quantitative imaging httpwwwmbfbiosciencecom McCrone Group wwwmccronecominstrument-sales Media Cybernetics Inc ndash Image Premier 3D AutoQuant X3 deconvolution httpwwwmediacycom Meiji Techno America wwwmeijitechnocom MesoLens Ltd httpwwwmesolenscomproducttechnical-specifications httpwwwmesolenscomimages httpswwwbiophotonicsstrathacukresearch_1htm Meyer Instruments ndash Pathscan Enabler GigaMacro digital pathology telepathology httpmeyerinstcom httpmeyerinstcompathscan-enabler-5 httpmeyerinstcomgigamacro-gigapixel-macro-imaging httpmeyerinstcomhomescanners httprealtimetelepathologycom Microarrays - Large-Scale Gene Expression and Microarray Links and Resources httpswwwebiacukarrayexpress Micro-Manager ndash Device Support ndash tabulates many microscope cameras and motorized accessories every new camera and accessory should have a uManager driver to enable simple use with Fiji ImageJ httpsmicro-managerorg httpsmicro-managerorgwikiDevice_Support httpsopen-imagingcom Microvolution ndash (near) instant gratification spatial deconvolution using NVidia GPU card(s) httpmicrovolutioncom Mightex Systems ndash optogenetics DMDDLP illuminator (digital micro-mirror device digital light processing) httpwwwmightexsystemscomindexphpcPath=245 Millipore-Sigma Merck KGaA (Amnis Corp CellASIC EMD Millipore) ndash ImageStreamX and FlowSight imaging flow cytometers ONIX2 Microperfusion System for microscopes httpswwwemdmilliporecom httpswwwemdmilliporecomUSenlife-science-researchcell-analysisamnis-imaging-flow-cytometersQ6ubqBm3UAAAFLCKIpygJnav httpwwwemdmilliporecomUSenlife-science-researchcell-culture-systemscellASIC-live-cell-analysisd1CbqBw58AAAE_0j13MnAnav Mitutoyo America Corp wwwmitutoyocom httpecatalogmitutoyocomMF-U-Series-176-High-power-Multi-function-Measuring-Microscopes-C1413aspx

Molecular Devices Corporation Universal Imaging Corporation (Danaher) ndash MetaMorph MetaFluor high content systems (HCS) httpswwwmoleculardevicescomsystemsmetamorph-research-imaging httpmdccusthelpcomappanswersdetaila_id19319 httpswwwmoleculardevicescomsystemshigh-content-imaging Molecular Machines amp Industries - laser microdissection and tweezer systems httpwwwmolecular-machinescomhome MUSE Microscopy Inc ndash Deep UV illumination for shallow depth of field imaging httpwwwmusemicrocom Micro Video Instruments Inc - DarkLite illuminator httpwwwmvi-inccom NanoEnTek ndash JuLI Stage (imager inside incubator or on lab bench) httpwwwjulistagecom National Instruments ndash LabView software httpwwwnicomen-ushtml Navitar - Hoffman Modulation Contrast (HMC alternative to differential interference contrast phase contrast) custom lens design UVDUVNUV imaging lenses httpsnavitarcommarketsmicroscopy httpsnavitarcomproductsimaging-opticscustom-microscope-objectivescustom-microscope-objectives httpsnavitarcomproductsimaging-opticsuv-imaging National Center for X-ray Tomography (NCXT) ndash soft X-ray tomography (CT of hydrated cells) XM-2 dedicated biological SXT microscope Prof Carolyn Larabell Director (see also SiriusXT) httpncxtlblgov httpncxtlblgovsxt httpncxtlblgovmanual httpncxtlblgovq=carolyn Neogenomics (Clarient) ndash MultiOmyx immunofluorescence or DNA FISH (ldquo60plexrdquo) httpneogenomicscomPharma-ServicesLab-ServicesMultiOmyxTechnologyMultiOmyx-IF-Assay-DNA-FISH-assay-NGS-from-ROI Nexcelom ndash Celigo imaging cytometer Cellometer cell counters httpwwwnexcelomcomCeligoindexphp httpwwwnexcelomcomProducts Nikon ndash Ti-LAPP modular illumination system (for Nikon Ti series microscopes) TIRF Optogenetics httpswwwnikoninstrumentscomProductsPhotostimulation-and-TIRFTi-LAPP Nirmidas Biotech httpwwwnirmidascomtechnologynir httpwwwnirmidascomproductsniriidye NVidia ndash Pascal 10+ Gbps GPU cards for instant gratification deconvolution (software from Microvolutioncom SVInl) httpwwwgeforcecomhardware10seriesgeforce-gtx-1080 httpwwwgeforcecomhardware10seriestitan-x-pascal httpwwwnvidiacomobjectquadro-graphics-with-pascalhtml Ocean Optics ndash spectrometers httpoceanopticscomproduct-categorymodular-spectrometers Oko-Lab stage top incubator httpwwwoko-labcomstage-top Open Microscopy Environment (OME) ndash OMERO (see also Glencoe Software) Bio-Formats LOCI

httpswwwopenmicroscopyorgsite httpswwwopenmicroscopyorgsiteproductsomero httpswwwopenmicroscopyorgsiteproductsbio-formats httpswwwopenmicroscopyorgsitesupportbio-formats52supported-formatshtml httpswwwopenmicroscopyorgsiteaboutdevelopment-teamskevin OpenSPIM ndash do-it-yourself selective plane illumination microscopy (light sheet imaging) httpopenspimorgWelcome_to_the_OpenSPIM_Wiki OpenSpinMicroscopy ndash do-it-yourself SPIMDSLMOPT microscopes httpssitesgooglecomsiteopenspinmicroscopy Ovizio ndash differential digital holography (similar to quantitative phase imaging) httpwwwoviziocomenHome httpwwwoviziocomenMicroscopesQMod Oxford Gene Technologies ndash microarrays ndash cytogenetics molecule genetics cancer research pre-implantation genetic diagnosis httpwwwogtcomclinical_genetics Oxford Nanoimaging ndash single molecule(s) localization fluorescence resonance energy transfer (FRET) (Kapanidis) wwwoxfordnicom Pathology Devices ndash LiveCell stage top incubator amp controller tissue microarrayers (TMA makers) httpwwwpathologydevicescomLiveCellhtm httpwwwpathologydevicescomTMArrayerhtm PeCon GmbH ndash microscope incubators httpwwwpeconbiz Pembroke Instruments ndash spectrometers mini-lasers httppembrokeinstrumentscomqmini-spectrometer httppembrokeinstrumentscommini-lasers PerkinElmer ndash in vivo imaging systems (bioluminescence NIR fluorescence) Vectra digital slide scanner httpwwwperkinelmercomcategoryin-vivo-imaging-instruments httpwwwperkinelmercomcategoryquantitative-pathology-imaging-instruments Phi Optics ndash CellVista SLIM Pro (quantitative phase microscopy) httpphiopticscom Photometrics (Roper Scientific) ndash DualView QuadView httpwwwphotometricscom httpwwwphotometricscomproductsmultichannel Photon Technology International httpwwwpti-njcomindexhtml

PicoQuant GmbH ndash fluorescence lifetime imaging microscopes (FLIM) STED 3D-EasySTED httpswwwpicoquantcomproductscategoryfluorescence-microscopes httpswwwpicoquantcomapplicationscategorylife-sciencested httpwwweasystedorg Physik Instrumente GmbH amp Co KG (PI) - Nanopositioning Applications for Microscopy Neuroscience and Metrology httpswwwphysikinstrumentecomen httpwwwpi-usausindexphp PreSens Prescision Sensing GmbH - VisiSens measure and visualize Oxygen pH or carbon dioxide distributions httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-biological-researchhtml httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-life-science-researchhtml Prior Scientific

httpwwwprior-uscom Profusa Inc - Lumee tissue-integrated biosensors scaffolds httpprofusacomtechnology Reindeer Graphics Inc ndash OptiPix Fovea Pro 9plugins for Adobe Photoshop 6 and CS series) httpwwwreindeergraphicscom Renishaw - StreamLine fast chemical imaging Raman spectroscopy httpwwwrenishawcomenstreamline-generate-chemical-images-rapidly--9449 httpwwwrenishawcomenraman-spectroscopy--6150 Sanford Burnham Prebys ndash High Content Screening httpwwwsbpdiscoveryorgtechnologysrPagesLaJolla_HighContentScreeningaspx ScopeM - Scientific Center for Optical and Electron Microscopy - ETH Zurich httpwwwscopemethzch SiriusXT - soft X-ray tomography (SXT) microscope (CT scan hydrated cell) httpsiriusxtcom SpectraGenetics - Fluorogen Activating Peptides (FAPs) new genetically encoded ldquobinaryrdquo reporters httpspectrageneticscomproductsvectors-for-expressing-fluorogen-activating-proteinsfap-technology-overview Spirochrome - Silicon Rhodamine (SiR) and other fluorescent reagents probes for bioimaging httpspirochromecom Stanford Photonics Inc httpwwwstanfordphotonicscom httpwwwstanfordphotonicscomLife20SciencesLifeScihtm

Stream Technologies Inc ndash ColorFlow lens (multi-wavelength emission onto a camera) httpwwwstreamtechinccomproducts Sutter Instrument Company httpwwwsuttercom httpwwwsuttercomMICROSCOPESindexhtml httpwwwsuttercomIMAGINGindexhtml SVI Huygens ndash Professional (general image analysis) deconvolution NVidia GPU deconvolution httpssvinlHuygensProfessional httpssvinlHuygensDeconvolution httpssvinlHuygensGPU Sysmex Partex ndash CyScope httpwwwsysmex-parteccomproductsmicroscopyhtml httpwwwsysmex-parteccomproductsprdouct-detailviewcyscopeR-malaria-3238html Technical Instruments httpwwwtechinstcomproductsphp TESCAN Brno sro - Tescan Q-PHASE multimodal holographic quantitative phase imaging system (QPi) optional fluorescence httpwwwtescancomenproductsq-phaseq-phase httpq-phasetescancom httpq-phasetescancomindexphptechnologyspecifications Ted Pella Inc ndash specialty light microscopy and electron microscopy supplies httpswwwtedpellacom Texas Instruments ndash DLP 4100 development kit (digital light processingrsquo DMD digital micromirror device) httpwwwticomtooldlpd4x00kit

ThorLabs ndash iCyte imaging cytometer multiphoton confocal EnVista digital slide scanning microscopes httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7473 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7494 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=5696 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=6570 TIRF Labs lightguide TIRF prism TIRF TIRF-Electrochemistry httpwwwtirf-labscom httpwwwtirf-labscomtechnologieshtml TissueVision - Serial Two Photon Tomography (image volume ablate imaged volume with multiphoton laser repeat) httpwwwtissuevisioncomtechnology Tokai Hit - stage top incubator httpwwwtokaihitcomenglishproduct_guidanceoptionhtml TopoNomos Ltd ndash Toponome Imaging Cycler ndash immunofluorescence (100plex) httpwwwtoposnomoscomtechnologyhtml Ultivue Inc ndash DNA-PAINT ndash reagents data processing service httpwwwultivuecom httpwwwultivuecomproducts UMech Technologies ndash Cytovar HCS up to 16 excitation wavelengths httpcloudumechcomproducts httpcloudumechcomproductsmodelC16 Visitech ndash vt-iSIM instant super-resolution microscopy up to 1000 frames per second confocal scanners and light engines httpwwwvisitechcoukvt-isimhtml httpwwwvisitechcoukproductshtml Visitron Systems GmbH - high speed imaging systems httpwwwvisitronde Visualsonics (Fujifilm) - photoacoustic imaging httpwwwvisualsonicscomproductstechnology-overview Wicked Lasers httpwwwwickedlaserscom httpwwwwickedlaserscomarctic WITec Wissenschaftliche Instrumente und Technologie GmbH - imaging systems for FLIM Raman AFM and SNOM analysis httpwitecdeproducts httpwwwwitec-instrumentscom WM Keck Center for Adaptive Optical Microscopy (CfAOM) at UC Santa Cruz httpscfaomsoeucscedu httpcfaoucolickorgpgallery Yokogawa Corp ndash spinning disk confocal scanner live cell imager high content screener confocal quantitative cytometer httpwwwyokogawacomsolutionsproducts-platformslife-science httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-scanner-unit-csu httpwwwyokogawacomsolutionsproducts-platformslife-scienceall-in-one-live-cell-imaging-solution httpwwwyokogawacomsolutionsproducts-platformslife-sciencehigh-throughput-cytological-discovery-system httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-quantitative-image-cytometer Zellkraftwerk (ChipCytometry) ndash immunofluorescence (80plex) httpwwwzellkraftwerkcomProducts2phtml httpwwwzellkraftwerkcomZKWOnephtmlSoftware

httpwwwchipcytometrycomtechnologyphtml Fluorescence Spectra Data and Graphing Sites PubSpectra ndash Excel file data download httpsworksbepresscomgmcnamara9 BD Biosciences ndash spectrum viewer Brilliant fluorophores httpwwwbdbiosciencescomussspectrumviewer httpwwwbdbiosciencescomusapplicationssspectrumguidepage BioLegend ndash spectra analyzer Brilliant Violet fluorophores httpwwwbiolegendcomspectraanalyzer httpwwwbiolegendcombrilliantviolet Chroma Technology httpswwwchromacomspectra-viewer eBioscience (Affymetrix ThermoFisher) ndash fluorPlan ndash a multi-laser spectra viewer httpwwwebiosciencecomresourcesfluorplan-spectra-viewerhtm Spectra Viewer (requires Java) Evrogen ndash Spectrum Viewer httpevrogencomspectra-viewerflashviewerhtml Fluorophoresorg ndash Fluorescent Substances httpwwwfluorophorestugrazatsubstance I Love GFP httpssitesgooglecomsiteilovegfpHomefps Lambert and Thorn UCSF Fluorescent protein properties httpnicucsfeduFPvisualization Leica Microsystem - ldquoFluoScoutrdquo httpwwwleica-microsystemscomfluoscout

Molecular Probes Invitrogen Thermo Fisher ndash Fluorescence SpectraViewer httpwwwthermofishercomusenhomelife-sciencecell-analysislabeling-chemistryfluorescence-spectraviewerhtml httpsitunesapplecomusappfluorescence-spectraviewerid421031826 (iTunes App) Nightsea - Compendium of spectra web sites httpwwwnightseacomsfa-sharingfluorescence-spectra-viewers Omega Optical ldquoCurvomatricrdquo httpswwwomegafilterscomcurvomatic

PhotoChemCAD 20 (Jonathan S Lindsey) dye spectra database and chemistry calculator NIRvana Sciences httpwwwphotochemcadcom httpnirvanasciencescompage_id=3088 UCSF (Lambert Thorn 2016) - Fluorescent protein properties httpnicucsfeduFPvisualization University of Arizona - Fluorescent Spectra Database httpwwwspectraarizonaedu Semrock - Searchlight httpssearchlightsemrockcom Spectroscopy Ninja ndash links to spectral and fluorescence data Spekwin32 spectroscopy software httpwwweffemm2deinfoinfo_specdatahtml

httpwwweffemm2deindexhtml Zeiss ndash interactive fluorescence dye and filter database overview dyes overview filter sets httpswwwmicro-shopzeisscoms=50479761ad21e5ampl=enampp=usampf=fampa=i httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=d httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=f Researcher Labs Alby Diaspro ndash IIT httpwwwlambsitindexphppage=People Alice Ting ndash MIT httpwwwtinglaborgresearch Allen Institute for Brain Science httpwwwalleninstituteorgwhat-we-dobrain-science Allen Institute for Cell Science httpwwwalleninstituteorgwhat-we-docell-science Amina Qutub - Rice University - How are human cells designed lab httpsqutublaborgqutub-lab Amy Herr UC Berkeley ndash Single cell Westerns httpherrlabberkeleyedu Amy Palmer ndash UC Boulder httpspalmerlabcoloradoedu Andrew York ndash Calico Life Sciences httpswwwcalicolabscomteam-memberandrew-york Anne Carpenter ndash Broad Institute CellProfiler httpspersonalbroadinstituteorganne Arjun Raj UPenn single molecule RNA FISH quantitative understanding cellular functions httprajlabseasupenneduindexhtml httpwwwpopscicomsciencearticle2013-09arjun-raj Atsuko Miyawaki - Laboratory for Cell Function Dynamics (CFDS) Fucci2 fluorescent proteins cell cycle indicator httpwwwbrainrikenjpenfacultydetails30 httpcfdsbrainrikenjp httpcfdsbrainrikenjpFuccihtml Aydogan Ozcan - UCLA - new imaging and sensing architectures httpinnovateeeuclaeduwelcomehtml httpwwwhhmiorgscientistsaydogan-ozcan Badri Roysam - UH - FARSIGHT Toolkit httpwwweeuhedufacultyroysam httpwwwfarsight-toolkitorgwikiMain_Page Brian J Ford ndash microscopist and popularizer httpsuklinkedincominprofbrianjford Carolyn Larabell ndashNational Center for X-ray Tomography (LBNL) UCSF httpncxtlblgovq=carolyn httpprofilesucsfeducarolynlarabell Clare Waterman ndash NHLBI NIH

httpswwwnhlbinihgovresearchintramuralresearcherspiwaterman-clare Dana Peer - Columbia University - Computational Systems Biology viSNE and more software httpwwwc2b2columbiaedudanapeerlabhtml httpwwwc2b2columbiaedudanapeerlabhtmlcythtml David Mayerich - UH - STIM Laboratory Scalable Tissue Imaging and Modeling httpwwweeuhedufacultymayerich httpstimeeuhedu David Piston WUSTL httpwwwcellbiologywustledufacultytenureddavid-w-piston-phd Diane Lidke and Keith Lidke - University of New Mexico httppathologyunmeduresearchfaculty-laboratoriesthe-lidke-laboratoryindexhtml httppanda3physunmedu~klidke Donna Arndt-Jovin and Thomas Jovin - Max Planck Institute for Biophysical Chemistry Laboratory of Cellular Dynamics httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsDonnaArdndt-JovinResearchAreasAndProjects httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsChairmanThomasJovinResearchAreasAndProjects Ed Boyden ndash MIT Media Lab ndash expansion microscopy (ExM) optogenetics httpsyntheticneurobiologyorg httpsyntheticneurobiologyorgprotocols httpsyntheticneurobiologyorgpublications httpwwwtedcomtalksed_boyden_baby_diapers_inspired_this_new_way_to_study_the_brain httpwwwextbiocombuycell Elizabeth Blackburn ndash Salk Institute - Telomeres httpswwwsalkeduscientistelizabeth-blackburn httpsenwikipediaorgwikiElizabeth_Blackburn httpswwwnobelprizeorgnobel_prizesmedicinelaureates2009blackburn-factshtml Elizabeth Hillman - Columbia university - SCAPE (Swept Confocally-Aligned Planar Excitation) high speed 3D microscopy DyCE (dynamic contrast enhancement to image and segment small animal organs live) Neuroimaging amp Neurovascular Coupling httporionbmecolumbiaedu~hillmanInstrumentationhtml httporionbmecolumbiaedu~hillmanSCAPEhtml httporionbmecolumbiaedu~hillmanMolecularhtml httporionbmecolumbiaedu~hillmanBrain_Imaginghtml Eric Betzig ndash UCSF (moving from HHMI Janelia Farm in 2016) httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014betzig-factshtml Eva Sevick-Muraca ndash UT Health Science Center at Houston molecular imaging clinical NIR fluoresceince imaging httpswwwutheduimmprofilehtmid=1005459 httpswwwutheduimmcentersmolecular-imaginghtm Evelin Schrock - Technische Universitaumlt Dresden spectral karyotyping cytogenetics httpswwwresearchgatenetprofileEvelin_Schrock Garry Nolan Stanford University ndash Mass cytometry MIBI-ToF high throughput imaging mass cytometry (42plex) httpwebstanfordedugroupnolanresourceshtml httpwebstanfordedugroupnolantechnologieshtml George McNamara ndash Cell Morphometry (41) Figure 1 right top two panels (55) The Chase (2016 temporal area maps lsquodynamic morphologyrsquo) (76) newsletter series on ldquoThe Chaserdquo (73) direct Vimeo movie of ldquoThe Chaserdquo Tiki_Goddess linkedin 10+plex blog httpsworksbepresscomgmcnamara41 httpsworksbepresscomgmcnamara55 httpsworksbepresscomgmcnamara76

httpsworksbepresscomgmcnamara73 httpsvimeocom175151196 httphomeearthlinknet~tiki_goddess httpswwwlinkedincomingeorgemcnamara httpswwwlinkedincompulsebd-biosciences-listed-tandems-horizon-brilliant-violets-mcnamara Gillian Griffiths - University of Cambridge - T-cell immunological synapse httpwwwcimrcamacukresearchprincipal-investigatorsprincipal-investigators-a-hgriffiths Hari Shroff NIBIB NIH httpswwwnibibnihgovlabs-at-nibibsection-high-resolution-optical-imaging-hroi HHMI Janelia Farm Research Campus (JFRC) - Advanced Imaging Center Open Science httpswwwjaneliaorgopen-scienceadvanced-imaging-center-aic httpswwwjaneliaorgopen-science Jeanne Lawrence University of Massachussetts Medical School httpwwwumassmededucellbiolabslawrencepersonnelprincipal-investigator Jennifer Lippincott-Schwartz ndash HHMI Janelia Farm httpswwwjaneliaorgpeoplejennifer-lippincott-schwartz Jin Zhang ndash UCSD httpprofilesucsdedujinzhang Joe DeRisi - UCSF - 3D printable lab stuff httpderisilabucsfeduindexphppage=3D John Russ Chris Russ Fovea Pro plugins for Adobe Photoshop httpwwwdrjohnrusscomindexhtml httpwwwdrjohnrusscombookshtml httpwwwreindeergraphicscomfoveaprotutorialhtml Julie Theriot httpcmgmstanfordedutheriot Karl Deisseroth ndash Stanford University ndash CLARITY optical tissue clearing Optogenetics httpclarityresourcecenterorg httpwebstanfordedugroupdlaboptogeneticsindexhtml Karsten Koumlnig (Koenig) - Saarland University and JenLab GmbH - biophotonics httpwwwbltuni-saarlanddeindex_ehtm httpwwwjenlabde httpwwwthelastescape-filmcom Karsten Rodenacker ndash image measurements httpkaro03bplacednetkaroMeMisc_WWWpdfMicrosoftWord-EQUAPATpdf Kevin Eliceiri ndash UW-Madison Open Source Photonics and Software Laboratory for Optical and Computational Instrumentation (LOCI) wwwlociwiscedu Klaus Kemp ndash Microlife Services ndash diatoms and other prepared microscope slides httpwwwdiatomscouk Kurt Thorn UCSF httpthornlabucsfedu httpsnicucsfedublog httpnicucsfeduFPvisualization httpgigapancomgigapans163370 Lihong Wang - WUSTL - Optical Imaging Laboratory photoacoustic tomography

httpoilabseaswustledu httpoilabseaswustleduresearch_0html Loren Looger - HHMI JFRC - iGluSnFr fluorescent protein biosensor httpswwwjaneliaorglablooger-lab Mary-Lou Pardue ndash MIT (first ever in situ hybridization with J Gall) httpsbiologymitedupeoplemary_lou_pardue httpsenwikipediaorgwikiMary-Lou_Pardue Nancy Allbritton - UNC - Chemical cytometry microraft arrays organ-on-a-chip httpswwwbmencsueduindexphpcomponentcomprofileruserprofilenlallbri httpwwwbmeuncedulabsallbritton Navin Varadarajan - UH - single-cell Lab httpwwwcheeuhedufacultyvaradarajan httpsinglecellcheeuheducontacthtml Nicholas Shaner - Scintillon Institute - mNeonGreen httpwwwscintillonorgshaner_lab Rebecca Richards-Kortum httpbioengineeringriceedufacultyrebecca_richards-kortumaspx Robert Campbell - Fluorescent proteins optogenetic proteins httpcampbellwebchemualbertaca httpcampbellwebchemualbertacaprojects-2 Robert Murphy ndash Cell measurements web services httpmurphylabwebcmueduservices Sabine Mai - University of Manitoba - Genomic Centre for Cancer Research and Diagnosis (GCCRD) - httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBPlatformsGCCRDhtml httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBScientistsMaiAwardshtml Sally Ward and Raimund Ober - Texas AampM University - httpwwwwardoberlabcom Simon Watkins - U Pittsburgh Center for Biologic Imaging httpwwwcbppittedufacultywatkinshtml httpwwwcbppittedufacultylabwatkinshtml httpwwwcbipittedu Stefan Hell ndash Deparment Hell NanoBiopohotonics httpwwwmpibpcmpgdehell httpsenwikipediaorgwikiStefan_Hell httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014hell-factshtml Sunney Xie Harvard httpsbernsteinharvardedu Susan Cox ndash 3B microscopy httpwwwcoxphysicscomindexhtml httpwwwcoxphysicscom3b Radim Chmeliacutek - Center for innovative microscopy Experimental biophotonics group httpswwwceiteceuceitec-butexperimental-biophotonicsrg3 httpwwwbiophotczhome Taekjip Ha ndash Johns Hopkins University ndash single molecules httphamedjhmiedu

Thomas Ried ndash NCI NIH SKYM-FISH and CGH Database httpsccrcancergovGenetics-Branchthomas-ried httpsccrcancergovGenetics-Branchthomas-riedqt-staff_profile_tabs=9qt-staff_profile_tabs ftpftpncbinlmnihgovsky-cghDATA httpswwwncbinlmnihgovdbvar Viviana Gradinaru ndash CalTech ndash CLARITYPACT Optogenetics httpwwwbbecaltecheducontentviviana-gradinaru httpglabcaltechedu Vladislav Verkhusha - near infrared fluorescent proteins httpwwweinsteinyuedulabsvlad-verkhushadefaultaspx httpwwweinsteinyueduresearchfacilitiesfluorescent WE Moerner ndash Stanford University httpwebstanfordedugroupmoerner Willard Wiggans ndash micro gallery httpwwwwillard-wigancomgallery Wolf Frommer ndash Molecular sensors httpbiosensordpbcarnegiescienceedu (fluorescent protein biosensors table) Xiaowei Zhuang = Harvard httpzhuangharvardedu Yuval Garini - Bar-Ilan University - Nano-Bio-Photonics laboratory httpgarinilabbiuacil Microscopy Magazines Imaging amp Microscopy httpwwwimaging-gitcommagazine Laser Focus World httpwwwlaserfocusworldcomindexhtml Microscopy amp Analysis httpwwwmicroscopy-analysiscom Microscopy Today httpwwwmicroscopy-todaycom Microscopy-UK httpwwwmicroscopy-ukorguk Photonics Spectra Biophotonics httpwwwphotonicscomPublicationsaspx The Microscope Journal httpmcriorgv72the-microscope-journal RMS Infocus Magazine httpwwwrmsorgukstudy-readinfocus-magazinehtml Nobel Prizes in Light Microscopy and Related Fields Chemistry 1925 colloids (light sheet) Zsigmondy (Siedentopf Zsigmondy 1902) httpswwwnobelprizeorgnobel_prizeschemistrylaureates1925

Chemistry 2000 conductive polymers Heeger MacDiarmid Shirakawa (Brilliant Violets Ultraviolets Blues) httpwwwnobelprizeorgnobel_prizeschemistrylaureates2000 Chemistry 2008 green fluorescent protein GFP Shimomura Chalfie Tsien httpwwwnobelprizeorgnobel_prizeschemistrylaureates2008 Chemistry 2014 super-resolved fluorescence microscopy Betzig Hell Moerner httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014 Physics 1953 Phase Contrast Zernike httpswwwnobelprizeorgnobel_prizesphysicslaureates1953 Physics 2009 invention of an imaging semiconductor circuit ndash the CCD sensor Kao Boyle Smith httpwwwnobelprizeorgnobel_prizesphysicslaureates2009 Physics 2014 efficient blue light emitting diodes Akasaki Amano Nakamura httpwwwnobelprizeorgnobel_prizesphysicslaureates2014 Physiology or Medicine 2006 Fire and Mello RNA interference ndash gene silencing by double stranded RNA httpwwwnobelprizeorgnobel_prizesmedicinelaureates2006 Physiology or Medicine 2006 Capecchi Evans Smithies specific gene modifications in mice by the use of embryonic stem cells httpwwwnobelprizeorgnobel_prizesmedicinelaureates2007 Physiology or Medicine 2009 Blackburn Greider Szostak how chromosomes are protected by telomeres and telomerase httpwwwnobelprizeorgnobel_prizesmedicinelaureates2009 Physiology or Medicine 2012 Gurdon Yamamanka matured cells can be reprogrammed to become pluripotent httpwwwnobelprizeorgnobel_prizesmedicinelaureates2012

Table 442 Fluorophores Photophysics Data

Fluorophore Abs or Ex max (nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Acridine orange 271 520 27000 020 5

Alexa Fluor 430 431 541 16000 055 9

Alexa Fluor 488 495 519 71000 094 67

Alexa Fluor 532 532 553 81000 080 65

Alexa Fluor 546 556 573 104000 096 100

Alexa Fluor 568 578 603 91300 075 69

Alexa Fluor 594 590 617 73000 064 47

Allophycocyanin (APC) 650 660 700000 068 476

Atto 390 390 479 24000 090 22

Atto 425 436 484 45000 065 29

Atto 430LS 433 547 32000 065 21

Atto 465 453 508 75000 075 56

Atto 490LS 496 661 40000 030 12

Atto 520 525 547 105000 095 100

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 5: McNamara 20161006 revised draft tables for CPHG Light ...

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Montana Molecular LLC - genetically encoded fluorescent biosensors and probes for cell-based assays and live cell imaging httpmontanamolecularcomproductsproducts-overview NanoLight Technologies ndash Renilla GFP luciferases httpwwwnanolightcomNanoFluorsGFP_Expression_Vectorshtml httpswwwbiotoycomenlearn n3D Biosciences ndash generate 3D cell spheroids high throughput screening image changes using smartphone camera inside incubator httpwwwn3dbiocomproductsmagnetic-3d-bioprinting httpwwwn3dbiocomproductsassays New England BioLabs (NEB) ndash Cypridina Gaussia luciferases httpswwwnebcomapplicationscellular-analysisreporter-systems Promega ndash Monster GFP NanoLuc httpswwwpromegacomproductsreporter-assays-and-transfectionreporter-vectors-and-cell-linesmonster-green-fluorescent-protein-phmgfp-vector httpswwwpromegacomproductsreporter-assays-and-transfectionreporter-vectors-and-cell-linesnanoluc-luciferase-reportersnanoluc-genetic-reporter-vectors Fluorescence Products (reagents) Advanced Cell Diagnostics (Bio-Techne) - branched DNA probe sets for RNA FISH httpsacdbiocomproducts Affymetrix eBioscience Thermo Fisher - branched DNA probe sets for RNA FISH httpwwwaffymetrixcomestorepromotionsviewrnaishindexaffx Anaspec ndash HiLyte Fluorophores FRET probes httpswwwanaspeccomproductsproductcategoryaspid=10 Antibody Resource Page httpwwwantibodyresourcecom Biocompare ndash Antibodies httpwwwbiocomparecomAntibodies Cell Signaling Technology ndash fluorescence antibodies httpswwwcellsignalcombrowseimmunofluorescence-immunocytochemistryif-paraffinif-frozen Essen Biosciences ndash Bacmam 30 ready to use FP gene transfection reagents httpwwwessenbiosciencecomenproductsreagents-consumablesincucyte-nuclight-red-bacmam-30-reagent-nuclear-labeling-cat-no-4621 GE Healthcare Amersham Biosciences httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usbrandscydye Global Biological Standards Institute (GBSI) ndash Antibody Validation Initiative httpwwwgbsiorgworkantibodies Goryo Chemical httpwwwgoryochemicalcom Human Protein Atlas (academic) Atlas Antibodies (commercial arm) US distributor httpwwwproteinatlasorg httpsatlasantibodiescom httpwwwsigmaaldrichcomlife-sciencecell-biologyantibodiesprestige-antibodieshtml

Integrated DNA Technologies (IDT) httpwwwidtdnacomsiteCatalogmodificationsdyes httpwwwidtdnacompagesproductsmodificationsfluorophoresfreedom-dyes httpwwwidtdnacomsiteCatalogModificationsCategory4 Jackson ImmunoResearch httpswwwjacksonimmunocom KPL (formerly Kirkegaard amp Perry Laboratories Inc) SeraCare httpwwwkplcom LGC Biosearch Technologies ndash dyes for oligonucleotides single molecular RNA FISH image gallery httpswwwbiosearchtechcomsupporteducationfluorophores-and-quenchers httpstellarisfishsmugmugcom httpsinglemoleculefishcom httpswwwbiosearchtechcomproductsrna-fish (typically 48 20 base oligonucleotides) Marker Gene Technologies Inc (MGT) httpwwwmarkergenecomfluorescent-reagent Miltenyi Biotec ndash REAfinity recombinant engineered antibodies (no Fc Receptor binding) FASER fluorescence amplification kits NiraWave fluorophores (indocyanine green formulations) httpwwwmiltenyibioteccomenproducts-and-servicesmacs-flow-cytometryreagentsantibodies-and-dyesrecombinant-antibodiesaspx httpwwwmiltenyibioteccomenproducts-and-servicesmacs-flow-cytometryreagentssupport-reagentsfaser-kitsaspx httpwwwmiltenyibioteccomenproducts-and-servicesviscover-imagingoptical-imagingaspx Molecular Probes Inc Invitrogen Thermo Fisher ndash largest vendor of fluorophores Molecular Probes Handbook (web resource) Tyramide Signal Amplification kits httpwwwprobescom httpswwwthermofishercomusenhomereferencesmolecular-probes-the-handbookhtml httpswwwthermofishercomusenhomereferencesmolecular-probes-the-handbooktablestyramide-signal-amplification-tsa-kitshtml NIRvana Sciences httpnirvanasciencescom httpnirvanasciencescompage_id=3088 One World Lab ndash antibody search httponeworldlabcomantibodies CytoCell Oxford Gene Technologies ndash DNA FISH probes human mouse pig chicken httpwwwcytocell-uscom Perkin Elmer ndash nucleotides labeling kits Tyramide Signal Amplification Kits (TSA) Opal 7plex discovery panel kit based on sequential TSA httpwwwperkinelmercomcategoryfluorescent-hapten-nucleotides httpwwwperkinelmercomcategoryfluorescent-agents-labeling-kits-dyes httpwwwperkinelmercomlab-solutionsresourcesdocsBRO_TSAsignalamplificationpdf httpwwwperkinelmercomproductopal-7-immunology-discovery-kit-op7ds1001kt

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TEFLabs ndash fluorescent ion indicators (Ca++ Cl- K+ Mg++ Na+ pH Zn++) ionophores fluorophores httpwwwteflabscomion-indicators Vector Laboratories Inc httpwwwvectorlabscom

Live cell imaging dishes and multi-well plates (ldquoglass bottom dishesrdquo)

We recommend these for simplified handing and processing vs either thick plastic dishesplates or having to handle loose coverslips with your valuable cells

Leicester Imaging Technologies (LITE) - University of Leicester - table of dishes for live cell imaging (our table has current links and bad links left out) httpwww2leacukcollegesmedbiopsychfacilities-and-servicescbsliteaiftips-and-tricks-1dishes-for-live-cell-imaging Bellco Glass Inc - glass flat bottom plate httpwwwbellcoglasscomnode1046 Bioptechs - interchangable coverslip dish ($036 per experiment) httpwwwbioptechscomproductinterchangeable-coverslip-dish Brooks Automation Inc - clar bottom optical imaging microplates httpwwwbrookscomproductslife-scienceconsumablesmatrical-microplates-microtubes-racks-lidsglass-bottom-optical-imaging-microplates Cell EampG - glass bottom cell sulture dishes plates httpcellegcomproducthtml Cellvis - glass bottom dishes and plates httpwwwcellviscom_35-mm-glass-bottom-dishes_products_by_categoryphpcat_id=3 Corning - glass bottom microplates httpcatalog2corningcomLifeSciencesen-USShoppingCategoryaspxcategoryname=Microplates20-202015(Lifesciences)|Assay20Microplates20-202015(Lifesciences) Design 1 Solutions - Custom microplates and fabrication services httpwwwdesign1solutionscomcustom-microplateshtml Eppendorf - cell imaging dishes imaging plates httpsonline-shopeppendorfcomOC-enCell-Culture-and-Imaging-Consumables-110320Cell-Imaging-Consumables-120210Eppendorf-Cell-Imaging-Dishes-PF-19457html httpsonline-shopeppendorfcomOC-enCell-Culture-and-Imaging-Consumables-110320Cell-Imaging-Consumables-120210Eppendorf-Cell-Imaging-Plates-PF-19458html Greiner Bio-One International - CellView glass bottom dishes quadrant dishes httpsshopgbocomenrowarticlescataloguearticle0110_0110_0040_002027513 ibidi - u-Plates glass bottom dishes microfluidic slides httpibidicomxtproductsenibidi-Labwarem-Plates httpibidicomxtproductsenibidi-Labware Matsunami Glass Ind Ltd httpwwwmatsunami-glasscojpenglishlifebiodata01html Mattek - glass bottom dishes and SBS plates httpswwwmattekcomstore-categoryculturewareglass-bottom-dishes Nunc - glass bottom dishes httpswwwthermofishercomordercatalogproduct150680 NEST Biotechnology Co Ltd Wuxi Jiangsu PRChina httpwwwnestscientificusacomproducts_detailproductId=31html PerkinElmer - glass bottom plates httpwwwperkinelmercomSECatalogCategoryIDMicroplates

Porvair Sciences - clear bottom assay plates httpwwwporvair-sciencescomenservices-menulife-sciencesclear-bottom-assay-plates Ted Pella Inc - glass bottom dishes clear wall or black wall (manufactured by WillCo Wells) httpswwwtedpellacomsection_html706dishhtm Warner Instruments (Harvard Apparatus) - culture dishes perfusion systems httpswwwwarneronlinecomproduct_cat_infocfmid=1322 Willco Wells - glass bottom dishes wwwwillcowellscom World Precision Instruments - Fluorodish glass bottom dishes httpswwwwpiinccomproductslaboratory-suppliesfd35-100-fluorodish-cell-culture-dish-35mm-23mm-well-pkg-of-100 Microscopes Microscopy Accessories (accessorize) Reagents Resources 3scan ndash knife edge scanning microscope (images slices repeats through specimen) httpwww3scancomdata-2 89North (affiliated with Chroma Technology Corp) httpwww89northcom Abberior Instruments ndash STED RESOLFT precision localization super-resolution microscopes STEDYCON convert any fluorescence microscope to STED httpabberior-instrumentscom httpabberior-instrumentscomproductscompact-lineabberior-stedy-con Acquifer ndash HIVE imaging machine (computer hardware) for high content screening big data httpswwwacquiferde Adobe Systems Inc httpwwwAdobecom httpscreativeadobecomproductsdownloadphotoshop Affymetrix eBioscience (ThermoFisher) - microarrays httpwwwaffymetrixcomestorebrowselevel_one_category_template_onejspparent=35796ampcategory=35796 httpwwwaffymetrixcomestorecatalog131547AFFYGeneChip26231743B+System+3000Dx+v22623423B1_1 Agilent Technologies ndash SureScan microarray scanner (array CGH microRNA SNPs CNV) httpwwwgenomicsagilentcomenMicroarray-Scanner-Processing-HardwareSureScan-Microarray-Scannercid=AG-PT-144 Andor Technology (Oxford Instruments) ndash sCMOS cameras Dragonfly spinning disk confocal Revolution DSD2 differential spinning disk confocal photostimulation (fluorescence recovery after photobleaching optogenetics) Mosaic3 DMDDLP high speed light patterning (optogenetics structured illumination) MicroPoint pulsed UV laser for ablation DNA damage photobleachingactivation uncaging accessories httpwwwandorcomscientific-camerasneo-and-zyla-scmos-cameras httpwwwandorcommicroscopy-systemsdragonfly httpwwwandorcommicroscopy-systemsrevolution-dsd httpwwwandorcommicroscopy-systemsphotostimulation httpwwwandorcommicroscopy-systemsphotostimulationmosaic httpwwwandorcommicroscopy-systemsphotostimulationmicropoint httpwwwandorcommicroscopy-systemsmicroscopy-components Apogee Instruments Inc (Andor Technology) ndash CCD cameras and filter wheels (mostly marketed for astronomy) httpwwwccdcomandorhtml Applied Scientific Instrumentation Inc ndash light sheet imager (iSPIM diSPIM)

wwwasiimagingcom httpwwwasiimagingcomindexphpproductslight-sheet-microscopyselective-plane-illumination-microscopy-ispim-dispim Applied NanoFluorescence LLC ndash NS1 NanoSpectralyzer (Raman and UV-VISNIR) NS MiniTracer near infrared spectrometer NFM NanoFluorescence microscope multi-laser light source single wall carbon nanotubes (NIR II fluorophores) httpappliednanocomproductshtml httpappliednanocomproductsns1html httpappliednanocomproductsproduct-list77-ns-minitracerhtml httpappliednanocomproductsnfmhtml httpappliednanocomproductsls-nhtml httpwwwnanowerkcomnewsnewsid=24132php Applied Spectral Imaging Inc httpwwwspectral-imagingcom ArgoLight ndash fluorescence resolution test target slides httpargolightcom AttoCube - attoMICROSCOPY overview attoCFM - Multichannel cryogenic (low temperature) confocal fluorescence microscopes 08 NA objective lenses 400-1000 nm spectral range httpwwwattocubecom httpwwwattocubecomattomicroscopyintroductiontab-2 httpwwwattocubecomattodownloads AutoQuant (Media Cybernetics) spatial deconvolution httpwwwmediacycomautoquantx3 Becker amp Hickl GmbH httpwwwbecker-hicklcomproductshtm Berkeley Lights Inc ndash manueuver into nanowells incubate recover 4000 single cells per chip httpswwwberkeleylightscomtechnology Bioaxial ndash Codim imaging conical diffraction beam shaper for super-resolution (4 sub-images) httpwwwbioaxialcomcodim-imaging Bioptechs - Live-Cell Micro-Observation Products httpwwwbioptechscom Bionumbers - database of useful biological numbers httpbionumbershmsharvardeduKeyNumbersaspx Biostatus ndash DRAQ5 DRAQ7 ApopTRAK CyTRAK Orange CyGel HypoxiTRAK httpwwwbiostatuscomProducts Bio-Tek ndash Cytation 3 Cell Imaging Multi-Mode Reader Lionheart FX Automated Live Cell Imager httpwwwbiotekcomproductsimagingcytation3_cell_imaging_multi_mode_readerhtml httpwwwbiotekcomproductsimaginglionheartfx_automated_live_cell_imagerhtml Biovision Technologies ndash distributor for several imagers including VT-iSIM instant super-resolution microscope httpbiovision-technologiescom httpbiovision-technologiescomsystemshtml httpbiovision-technologiescomvtisimhtml Bitplane (Andor Oxford Instruments) ndash Imaris imaging software httpwwwbitplanecom BMV Optical - custom lens assemblies and optical filters wwwbmvopticalcom

Bruker (previously Prairie Technologies Vutara) ndash Opterra confocal Ultima Multiphoton Vutara 352 single molecule localization microscopes httpswwwbrukercomproductsfluorescence-microscopesopterra-confocal-microscopyoverviewhtml httpswwwbrukercomproductsfluorescence-microscopesultima-multiphoton-microscopyhtml httpswwwbrukercomproductsfluorescence-microscopesvutara-super-resolution-microscopyoverviewhtml Cairn Research ndash standard and custom accessories ex Light Sheet Illuminator MultiCam (4 cameras) custom design httpswwwcairn-researchcouk httpswwwcairn-researchcoukproductl-spi-single-plane-illuminator (dual L-SPI for 4 illumination directions) httpswwwcairn-researchcoukproductmulticam httpswwwcairn-researchcoukcustom-design Cameca ndash NanoSIMS 50L (7plex stable isotope imaging) httpwwwcamecacominstruments-for-researchnanosimsaspx CellMic (formerly Holomic) - blood analysis or fluorescence imaging cytometer on a cell phone httpwwwcellmiccomcontentadvanced-technologies httpwwwcellmiccomcontentfluorescent-imaging-cytometry-and-e-coli-detection-on-a-cell-phone CellOptic ndash FINCH (Fresnel INcoherence Correlation Holography) httpwwwcellopticcomindex2html CellProfiler ndash High content screening (HCS) image processing and analysis software httpcellprofilerorg ClearLight Diagnostics - CLARITY Optimized Light Sheet Microscopy (3D tissue optical clearing + light sheet imaging) httpwwwclearlightdxcomindexhtml Confocalnl ndash Rescan confocal microscopy to obtain 170 nm resolution with any pinhole diameter httpwwwconfocalnl CoolLED ndash LED light sources httpwwwcoolledcomproduct-detailpe-4000 Crest Optics SRL ndash X-Light confocal X-Light V2 + VCS (VideoConfocal super-resolution) httpwwwcrestoptcom httpwwwcrestoptcomhtmlx-light_v2_vcshtml Cytoskeleton Inc - live cell imaging reagents Spirochrome SiR bioimaging probes httpwwwcytoskeletoncomlive-cell-reagents httpwwwcytoskeletoncomlive-cell-reagentsspirochrome CytoViva ndash darkfield imaging hypspectral imaging httpwwwcytovivacomproducts3d-enhanced-darkfield-imaging httpwwwcytovivacomproductshyperspectral-imaging-2hyperspectral-imaging Data Translation Inc - digitizer cards httpwwwdatxcom Delmic BV - combined correlative scanning electron microscope with inverted fluorescence microscope httpwwwdelmiccomdelphi httpswwwdelphimicroscopecom httpwwwdelmiccomsecom-super-resolution Digital Light Innovations (DLi) - CELscope C-mount LED Microscope using Texas Instruments DLP illuminator with a simple stand httpswwwdlinnovationscomdli-deep-dives-celscope-c-mount-led-microscope Double Helix LLC ndash single molecule localization microscope (Piestun) httpdoublehelixopticscom Edinburgh Super-resolution Imaging Consortium (ESRIC)

httpwwwesricorg Energetiq ndash Deep ultraviolet (DUV high radiance 170-2100 nm) laser driven light source (LDLS) httpwwwenergetiqcom Epi Technology - CaliCube - Cube for fluorescence light path to inspect epi Illumination light source (lamp) fiber optic or liquid light guide httpwwwepitechnologycomepitechnology-1 Essen Biosciences ndash Incucyte Zoom (imager inside incubator) httpwwwessenbiosciencecomenproductsincucyte Estigen Tissue Science ndash manual and automated tissue arrayer (tissue microarray maker) httpwwwestigencom Euro-Bioimaging httpwwweurobioimagingeu Excelitas Technologies (formerly Lumen Dynamics) ndash X-Cite LEDs httpwwwexcelitascomPagesProductX-Cite-LED-Solutionsaspx Expansion Technologies Inc (extbio) ndash Expansion microscopy httpwwwextbiocombuycell FEI (formerly Till Photonics) (Thermo Fisher) ndash correlative LM-EM single molecule Cryo-EM httpswwwfeicomlife-sciencescellular-biology httpswwwfeicomlife-sciencescellular-biologycorrelative-microscopy httpswwwfeicomlife-sciencesstructural-biology Femtonics - Multi-phton microscopes software accessories caged glutamate reagents services httpfemtonicseuproducts First Light Imaging ndash C-Red NIR imaging (800-2500 nm NIR windows I II III 650-950 nm 1100-1350 nm 1600-1870 nm[Shi et al 2015]) high speed visible EMCCD (400-1000 nm) httpwwwfirst-lightfrcategoryrangesinfrared Fluidigm ndash Helios imaging CyTOF mass cytometer (42plex) Callisto (32 independent chambers dose with up to 16 independent factors for 1-1000 cell populations culture up to 3 week) Polaris functional genomics meets imaging (48 single cells up to 24 hours after single cell selection from a population) httpswwwfluidigmcomproductshelios httpswwwfluidigmcomproductscallisto httpswwwfluidigmcomproductspolaris GattaQuant - nanorulers for high resolution microscopes and super-resolution microscopes performance testing httpwwwgattaquantcomNanoruler GE Healthcare life Sciences Applied Precision ndash DeltaVision deconvolution OMX OMX SR httpwwwgelifesciencescomwebappwcsstoresservletproductByIdenGELifeSciences-us29065728 httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usproductsAlternativeProductStructure_2380729065721 httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usproductsAlternativeProductStructure_2380729115476 German BioImagingorg httpwwwgermanbioimagingorgwikiindexphpMain_Page httpwwwgermanbioimagingorgwikiindexphpWorkgroup6SoftwarePackages GIGAmacro ndash Magnify2 gigapixel imagery oof macroscopic and microscopic objects Terapixel macro image httpwwwgigamacrocomgigapixel-macro-imaging-system httpwwwgigamacrocomworlds-first-terapixel-macro-image

Glencoe Software ndash OMERO Plus enterprise data management for scientific images and any associated metadata (OME = Open Microscopy Environment) DataViewer PathViewer httpsglencoesoftwarecomomeroplushtml httpsglencoesoftwarecomdataviewerhtml httpsglencoesoftwarecompathviewerhtml Gooch amp Housego ndash spectral imager httpsgoochandhousegocomminiature-spectral-imaging-camera httpwwwghinstrumentscomproductsspectral-imaging-synthesishsi-440c-hyperspectral-imaging-system Hindsight Imaging ndash spectral imaging httphindsight-imagingcom Horiba Scientific - SWIFT ultra-fast Raman confocal imaging Raman spectroscopy httpwwwhoribacomscientificproductsraman-spectroscopyraman-imagingswift httpwwwhoribacomscientificproductsraman-spectroscopyraman-imaging httpwwwhoribacomscientificproductsraman-spectroscopy IATIA Ultima Capital ndash QPm (quantitative phase microscopy) httpwwwultimacapitalnetiatiaimagingPublicationsIatia20ImagingapplicationNotesqpmApplicationWithConfocalMicroscopespdf Ibidi - heating and incubation systems optical O2 measurement systems Nanolive 3D Cell Explorer pump system gas incubation system httpibidicomxtproductsenInstruments-AccessoriesHeating-Incubation-Systems httpibidicomxtproductsenInstruments-Accessoriesibidi-OPAL-Optical-O2-Measurement-System httpibidicomxtproductsenInstruments-AccessoriesNanolive-3D-Cell-Explorer httpibidicomxtproductsenInstruments-Accessoriesibidi-Pump-System httpibidicomxtproductsenInstruments-AccessoriesHeating-Incubation-Systemsibidi-Gas-Incubation-System iLAbSolutions (Agilent Technologies) - Instrument management and scheduling software (cores and labs) httpwwwilabsolutionscominstrument-access-control ImageJ - Fiji ImageJ NIH ImageJ ImageJ ndash Fiji (Fiji is just ImageJ) is the main download site httpfijisc httpsimagejnihgovij wwwimagejnet Inscopix ndash nVista in vivo mouse brain imaging miniature microscope httpswwwinscopixcomproducts Intelligent Imaging Innovations Inc (3i) ndash Slidebook imaging software Lattice light sheet (high speed gentle to cells high resolution imaging) Dual-view Inverted Selective Plane Illumination (diSPIM) VIVO 2-Photon (VIVO 2P) multiphoton microscopy Everest intravital imaging Marianas 3D real-time deconvolution timelapse spinning disk FRAP TIRF FLIM single molecule environmental control Phasor - optogenetic photostimulation using digital holography Yokogawa spinning disk confocal units wwwintelligent-imagingcom httpswwwintelligent-imagingcomslidebookphp httpswwwintelligent-imagingcomsystemsphplattice httpswwwintelligent-imagingcomsystemsphpdispim httpswwwintelligent-imagingcomsystemsphptwophoton httpswwwintelligent-imagingcomsystemsphpeverest httpswwwintelligent-imagingcomsystemsphpmarianas httpswwwintelligent-imagingcomoptogeneticsphp httpswwwintelligent-imagingcomsdcphp ISS Inc ndash fluorescence lifetime imaging microscopy fluorescence correlation spectroscopy (FCS) confocal imaging httpwwwisscommicroscopyindexhtml JenLab GmbH cyto-microscopy multiphoton tomography httpwwwjenlabdeproducts250html httpwwwjenlabde2PM-Cryo1330html

httpwwwjenlabdeMultiphoton-Tomography680html Jenoptik - microscope cameras httpswwwjenoptikcomproductscameras-and-imaging-modulesmicroscope-cameras JPK Instruments - integrated atomic force microscope (AFM) force sensing optical tweezers optical trapping single cell force spectroscopy (SCFS) httpwwwjpkcomindex2enhtml httpusajpkcomoptical-tweezers-optical-trapping29ushtml httpusajpkcomcellular-adhesion-cytomechanics30ushtml Keyence ndash VK-X confocal (upright) BZ-X700 widefield (inverted) httpwwwkeyencecomssproductsmicroscopevkx httpwwwkeyencecomssproductsmicroscopebz-x700indexjsp KK Technology - CapiScope HVCS Handheld Video Capillaroscopy System (CytoScan) httpwwwkktechnologycomhvcshtml LaVision BioTec ndash TriMscope Multiphoton TriM Scope II Adaptive Optics UltraMicroscope II light sheet httpwwwlavisionbiotecde httpwwwlavisionbiotecdetrim-scope-overviewhtml httpwwwlavisionbiotecdetrim-scope-ii-adaptive-opticshtml httpwwwlavisionbiotecdeultramicroscope-ii-introductionhtml Laxco ndash upright and inverted microscopes httpwwwlaxcoinccomMICROSCOPES Lego ndash Lego Idea Microscopes httpsideaslegocomprojects44370 httpwwwnico71frlego-working-microscope Li-Cor ndash near-infared fluorescent dyes and in vivo imaging agents in vivo and Western blot imaging systems httpswwwlicorcombioproductsreagents httpswwwlicorcombioproductsreagentsirdyebrightsite_imaging_agents httpswwwlicorcombioproductsimaging_systemsodyssey_familyhtml httpswwwlicorcombioproductsimaging_systemspearl httpswwwlicorcombioproductsimaging_systemscdigit Life Imaging Services - ldquothe Ludin chamberrsquo ldquothe cube amp the boxrdquo httpwwwlischthechamberhtml httpwwwlischtheboxhtml Lightform Inc ndash PARISS imaging spectrometer httplightforminccom LMU Bioimaging httpwwwbioimagingbmcmeduni-muenchendelinkswebsitesindexhtml httpwwwbioimagingbmcmeduni-muenchendelearneduwebsitesindexhtml Ludl Electronic Products Ltd ndash automated XY stages focus motors filter wheels httpwwwludlcom

LumaCyte ndash Laser force Cytology (laser trap meets microfluidics to suspend and manipulate single cells) httpwwwlumacytecomabouttechnology Lumencor ndash LEDs fluorescence light sources httplumencorcomproducts Luxcel ndash mitochondrial and cellular functions O2 sensor reagents httpluxcelcomproduct+list Luxendo GmbH ndash light sheet imager

wwwluxendoeu Lyncee tec - digital holography microscopy (DHM) high content screening by DHM httpwwwlynceeteccom httpwwwlynceeteccomhigh-content-screening Mad City Labs Inc - nanopositioning wwwmadcitylabscom Mauna Kea Technologies ndash CellVizio confocal laser endomicroscopy httpwwwmaunakeatechcomenhealthcare-professionalscellvizio-endomicroscopy-0 MBF Bioscience - stereology and neuron morphology quantitative imaging httpwwwmbfbiosciencecom McCrone Group wwwmccronecominstrument-sales Media Cybernetics Inc ndash Image Premier 3D AutoQuant X3 deconvolution httpwwwmediacycom Meiji Techno America wwwmeijitechnocom MesoLens Ltd httpwwwmesolenscomproducttechnical-specifications httpwwwmesolenscomimages httpswwwbiophotonicsstrathacukresearch_1htm Meyer Instruments ndash Pathscan Enabler GigaMacro digital pathology telepathology httpmeyerinstcom httpmeyerinstcompathscan-enabler-5 httpmeyerinstcomgigamacro-gigapixel-macro-imaging httpmeyerinstcomhomescanners httprealtimetelepathologycom Microarrays - Large-Scale Gene Expression and Microarray Links and Resources httpswwwebiacukarrayexpress Micro-Manager ndash Device Support ndash tabulates many microscope cameras and motorized accessories every new camera and accessory should have a uManager driver to enable simple use with Fiji ImageJ httpsmicro-managerorg httpsmicro-managerorgwikiDevice_Support httpsopen-imagingcom Microvolution ndash (near) instant gratification spatial deconvolution using NVidia GPU card(s) httpmicrovolutioncom Mightex Systems ndash optogenetics DMDDLP illuminator (digital micro-mirror device digital light processing) httpwwwmightexsystemscomindexphpcPath=245 Millipore-Sigma Merck KGaA (Amnis Corp CellASIC EMD Millipore) ndash ImageStreamX and FlowSight imaging flow cytometers ONIX2 Microperfusion System for microscopes httpswwwemdmilliporecom httpswwwemdmilliporecomUSenlife-science-researchcell-analysisamnis-imaging-flow-cytometersQ6ubqBm3UAAAFLCKIpygJnav httpwwwemdmilliporecomUSenlife-science-researchcell-culture-systemscellASIC-live-cell-analysisd1CbqBw58AAAE_0j13MnAnav Mitutoyo America Corp wwwmitutoyocom httpecatalogmitutoyocomMF-U-Series-176-High-power-Multi-function-Measuring-Microscopes-C1413aspx

Molecular Devices Corporation Universal Imaging Corporation (Danaher) ndash MetaMorph MetaFluor high content systems (HCS) httpswwwmoleculardevicescomsystemsmetamorph-research-imaging httpmdccusthelpcomappanswersdetaila_id19319 httpswwwmoleculardevicescomsystemshigh-content-imaging Molecular Machines amp Industries - laser microdissection and tweezer systems httpwwwmolecular-machinescomhome MUSE Microscopy Inc ndash Deep UV illumination for shallow depth of field imaging httpwwwmusemicrocom Micro Video Instruments Inc - DarkLite illuminator httpwwwmvi-inccom NanoEnTek ndash JuLI Stage (imager inside incubator or on lab bench) httpwwwjulistagecom National Instruments ndash LabView software httpwwwnicomen-ushtml Navitar - Hoffman Modulation Contrast (HMC alternative to differential interference contrast phase contrast) custom lens design UVDUVNUV imaging lenses httpsnavitarcommarketsmicroscopy httpsnavitarcomproductsimaging-opticscustom-microscope-objectivescustom-microscope-objectives httpsnavitarcomproductsimaging-opticsuv-imaging National Center for X-ray Tomography (NCXT) ndash soft X-ray tomography (CT of hydrated cells) XM-2 dedicated biological SXT microscope Prof Carolyn Larabell Director (see also SiriusXT) httpncxtlblgov httpncxtlblgovsxt httpncxtlblgovmanual httpncxtlblgovq=carolyn Neogenomics (Clarient) ndash MultiOmyx immunofluorescence or DNA FISH (ldquo60plexrdquo) httpneogenomicscomPharma-ServicesLab-ServicesMultiOmyxTechnologyMultiOmyx-IF-Assay-DNA-FISH-assay-NGS-from-ROI Nexcelom ndash Celigo imaging cytometer Cellometer cell counters httpwwwnexcelomcomCeligoindexphp httpwwwnexcelomcomProducts Nikon ndash Ti-LAPP modular illumination system (for Nikon Ti series microscopes) TIRF Optogenetics httpswwwnikoninstrumentscomProductsPhotostimulation-and-TIRFTi-LAPP Nirmidas Biotech httpwwwnirmidascomtechnologynir httpwwwnirmidascomproductsniriidye NVidia ndash Pascal 10+ Gbps GPU cards for instant gratification deconvolution (software from Microvolutioncom SVInl) httpwwwgeforcecomhardware10seriesgeforce-gtx-1080 httpwwwgeforcecomhardware10seriestitan-x-pascal httpwwwnvidiacomobjectquadro-graphics-with-pascalhtml Ocean Optics ndash spectrometers httpoceanopticscomproduct-categorymodular-spectrometers Oko-Lab stage top incubator httpwwwoko-labcomstage-top Open Microscopy Environment (OME) ndash OMERO (see also Glencoe Software) Bio-Formats LOCI

httpswwwopenmicroscopyorgsite httpswwwopenmicroscopyorgsiteproductsomero httpswwwopenmicroscopyorgsiteproductsbio-formats httpswwwopenmicroscopyorgsitesupportbio-formats52supported-formatshtml httpswwwopenmicroscopyorgsiteaboutdevelopment-teamskevin OpenSPIM ndash do-it-yourself selective plane illumination microscopy (light sheet imaging) httpopenspimorgWelcome_to_the_OpenSPIM_Wiki OpenSpinMicroscopy ndash do-it-yourself SPIMDSLMOPT microscopes httpssitesgooglecomsiteopenspinmicroscopy Ovizio ndash differential digital holography (similar to quantitative phase imaging) httpwwwoviziocomenHome httpwwwoviziocomenMicroscopesQMod Oxford Gene Technologies ndash microarrays ndash cytogenetics molecule genetics cancer research pre-implantation genetic diagnosis httpwwwogtcomclinical_genetics Oxford Nanoimaging ndash single molecule(s) localization fluorescence resonance energy transfer (FRET) (Kapanidis) wwwoxfordnicom Pathology Devices ndash LiveCell stage top incubator amp controller tissue microarrayers (TMA makers) httpwwwpathologydevicescomLiveCellhtm httpwwwpathologydevicescomTMArrayerhtm PeCon GmbH ndash microscope incubators httpwwwpeconbiz Pembroke Instruments ndash spectrometers mini-lasers httppembrokeinstrumentscomqmini-spectrometer httppembrokeinstrumentscommini-lasers PerkinElmer ndash in vivo imaging systems (bioluminescence NIR fluorescence) Vectra digital slide scanner httpwwwperkinelmercomcategoryin-vivo-imaging-instruments httpwwwperkinelmercomcategoryquantitative-pathology-imaging-instruments Phi Optics ndash CellVista SLIM Pro (quantitative phase microscopy) httpphiopticscom Photometrics (Roper Scientific) ndash DualView QuadView httpwwwphotometricscom httpwwwphotometricscomproductsmultichannel Photon Technology International httpwwwpti-njcomindexhtml

PicoQuant GmbH ndash fluorescence lifetime imaging microscopes (FLIM) STED 3D-EasySTED httpswwwpicoquantcomproductscategoryfluorescence-microscopes httpswwwpicoquantcomapplicationscategorylife-sciencested httpwwweasystedorg Physik Instrumente GmbH amp Co KG (PI) - Nanopositioning Applications for Microscopy Neuroscience and Metrology httpswwwphysikinstrumentecomen httpwwwpi-usausindexphp PreSens Prescision Sensing GmbH - VisiSens measure and visualize Oxygen pH or carbon dioxide distributions httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-biological-researchhtml httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-life-science-researchhtml Prior Scientific

httpwwwprior-uscom Profusa Inc - Lumee tissue-integrated biosensors scaffolds httpprofusacomtechnology Reindeer Graphics Inc ndash OptiPix Fovea Pro 9plugins for Adobe Photoshop 6 and CS series) httpwwwreindeergraphicscom Renishaw - StreamLine fast chemical imaging Raman spectroscopy httpwwwrenishawcomenstreamline-generate-chemical-images-rapidly--9449 httpwwwrenishawcomenraman-spectroscopy--6150 Sanford Burnham Prebys ndash High Content Screening httpwwwsbpdiscoveryorgtechnologysrPagesLaJolla_HighContentScreeningaspx ScopeM - Scientific Center for Optical and Electron Microscopy - ETH Zurich httpwwwscopemethzch SiriusXT - soft X-ray tomography (SXT) microscope (CT scan hydrated cell) httpsiriusxtcom SpectraGenetics - Fluorogen Activating Peptides (FAPs) new genetically encoded ldquobinaryrdquo reporters httpspectrageneticscomproductsvectors-for-expressing-fluorogen-activating-proteinsfap-technology-overview Spirochrome - Silicon Rhodamine (SiR) and other fluorescent reagents probes for bioimaging httpspirochromecom Stanford Photonics Inc httpwwwstanfordphotonicscom httpwwwstanfordphotonicscomLife20SciencesLifeScihtm

Stream Technologies Inc ndash ColorFlow lens (multi-wavelength emission onto a camera) httpwwwstreamtechinccomproducts Sutter Instrument Company httpwwwsuttercom httpwwwsuttercomMICROSCOPESindexhtml httpwwwsuttercomIMAGINGindexhtml SVI Huygens ndash Professional (general image analysis) deconvolution NVidia GPU deconvolution httpssvinlHuygensProfessional httpssvinlHuygensDeconvolution httpssvinlHuygensGPU Sysmex Partex ndash CyScope httpwwwsysmex-parteccomproductsmicroscopyhtml httpwwwsysmex-parteccomproductsprdouct-detailviewcyscopeR-malaria-3238html Technical Instruments httpwwwtechinstcomproductsphp TESCAN Brno sro - Tescan Q-PHASE multimodal holographic quantitative phase imaging system (QPi) optional fluorescence httpwwwtescancomenproductsq-phaseq-phase httpq-phasetescancom httpq-phasetescancomindexphptechnologyspecifications Ted Pella Inc ndash specialty light microscopy and electron microscopy supplies httpswwwtedpellacom Texas Instruments ndash DLP 4100 development kit (digital light processingrsquo DMD digital micromirror device) httpwwwticomtooldlpd4x00kit

ThorLabs ndash iCyte imaging cytometer multiphoton confocal EnVista digital slide scanning microscopes httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7473 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7494 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=5696 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=6570 TIRF Labs lightguide TIRF prism TIRF TIRF-Electrochemistry httpwwwtirf-labscom httpwwwtirf-labscomtechnologieshtml TissueVision - Serial Two Photon Tomography (image volume ablate imaged volume with multiphoton laser repeat) httpwwwtissuevisioncomtechnology Tokai Hit - stage top incubator httpwwwtokaihitcomenglishproduct_guidanceoptionhtml TopoNomos Ltd ndash Toponome Imaging Cycler ndash immunofluorescence (100plex) httpwwwtoposnomoscomtechnologyhtml Ultivue Inc ndash DNA-PAINT ndash reagents data processing service httpwwwultivuecom httpwwwultivuecomproducts UMech Technologies ndash Cytovar HCS up to 16 excitation wavelengths httpcloudumechcomproducts httpcloudumechcomproductsmodelC16 Visitech ndash vt-iSIM instant super-resolution microscopy up to 1000 frames per second confocal scanners and light engines httpwwwvisitechcoukvt-isimhtml httpwwwvisitechcoukproductshtml Visitron Systems GmbH - high speed imaging systems httpwwwvisitronde Visualsonics (Fujifilm) - photoacoustic imaging httpwwwvisualsonicscomproductstechnology-overview Wicked Lasers httpwwwwickedlaserscom httpwwwwickedlaserscomarctic WITec Wissenschaftliche Instrumente und Technologie GmbH - imaging systems for FLIM Raman AFM and SNOM analysis httpwitecdeproducts httpwwwwitec-instrumentscom WM Keck Center for Adaptive Optical Microscopy (CfAOM) at UC Santa Cruz httpscfaomsoeucscedu httpcfaoucolickorgpgallery Yokogawa Corp ndash spinning disk confocal scanner live cell imager high content screener confocal quantitative cytometer httpwwwyokogawacomsolutionsproducts-platformslife-science httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-scanner-unit-csu httpwwwyokogawacomsolutionsproducts-platformslife-scienceall-in-one-live-cell-imaging-solution httpwwwyokogawacomsolutionsproducts-platformslife-sciencehigh-throughput-cytological-discovery-system httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-quantitative-image-cytometer Zellkraftwerk (ChipCytometry) ndash immunofluorescence (80plex) httpwwwzellkraftwerkcomProducts2phtml httpwwwzellkraftwerkcomZKWOnephtmlSoftware

httpwwwchipcytometrycomtechnologyphtml Fluorescence Spectra Data and Graphing Sites PubSpectra ndash Excel file data download httpsworksbepresscomgmcnamara9 BD Biosciences ndash spectrum viewer Brilliant fluorophores httpwwwbdbiosciencescomussspectrumviewer httpwwwbdbiosciencescomusapplicationssspectrumguidepage BioLegend ndash spectra analyzer Brilliant Violet fluorophores httpwwwbiolegendcomspectraanalyzer httpwwwbiolegendcombrilliantviolet Chroma Technology httpswwwchromacomspectra-viewer eBioscience (Affymetrix ThermoFisher) ndash fluorPlan ndash a multi-laser spectra viewer httpwwwebiosciencecomresourcesfluorplan-spectra-viewerhtm Spectra Viewer (requires Java) Evrogen ndash Spectrum Viewer httpevrogencomspectra-viewerflashviewerhtml Fluorophoresorg ndash Fluorescent Substances httpwwwfluorophorestugrazatsubstance I Love GFP httpssitesgooglecomsiteilovegfpHomefps Lambert and Thorn UCSF Fluorescent protein properties httpnicucsfeduFPvisualization Leica Microsystem - ldquoFluoScoutrdquo httpwwwleica-microsystemscomfluoscout

Molecular Probes Invitrogen Thermo Fisher ndash Fluorescence SpectraViewer httpwwwthermofishercomusenhomelife-sciencecell-analysislabeling-chemistryfluorescence-spectraviewerhtml httpsitunesapplecomusappfluorescence-spectraviewerid421031826 (iTunes App) Nightsea - Compendium of spectra web sites httpwwwnightseacomsfa-sharingfluorescence-spectra-viewers Omega Optical ldquoCurvomatricrdquo httpswwwomegafilterscomcurvomatic

PhotoChemCAD 20 (Jonathan S Lindsey) dye spectra database and chemistry calculator NIRvana Sciences httpwwwphotochemcadcom httpnirvanasciencescompage_id=3088 UCSF (Lambert Thorn 2016) - Fluorescent protein properties httpnicucsfeduFPvisualization University of Arizona - Fluorescent Spectra Database httpwwwspectraarizonaedu Semrock - Searchlight httpssearchlightsemrockcom Spectroscopy Ninja ndash links to spectral and fluorescence data Spekwin32 spectroscopy software httpwwweffemm2deinfoinfo_specdatahtml

httpwwweffemm2deindexhtml Zeiss ndash interactive fluorescence dye and filter database overview dyes overview filter sets httpswwwmicro-shopzeisscoms=50479761ad21e5ampl=enampp=usampf=fampa=i httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=d httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=f Researcher Labs Alby Diaspro ndash IIT httpwwwlambsitindexphppage=People Alice Ting ndash MIT httpwwwtinglaborgresearch Allen Institute for Brain Science httpwwwalleninstituteorgwhat-we-dobrain-science Allen Institute for Cell Science httpwwwalleninstituteorgwhat-we-docell-science Amina Qutub - Rice University - How are human cells designed lab httpsqutublaborgqutub-lab Amy Herr UC Berkeley ndash Single cell Westerns httpherrlabberkeleyedu Amy Palmer ndash UC Boulder httpspalmerlabcoloradoedu Andrew York ndash Calico Life Sciences httpswwwcalicolabscomteam-memberandrew-york Anne Carpenter ndash Broad Institute CellProfiler httpspersonalbroadinstituteorganne Arjun Raj UPenn single molecule RNA FISH quantitative understanding cellular functions httprajlabseasupenneduindexhtml httpwwwpopscicomsciencearticle2013-09arjun-raj Atsuko Miyawaki - Laboratory for Cell Function Dynamics (CFDS) Fucci2 fluorescent proteins cell cycle indicator httpwwwbrainrikenjpenfacultydetails30 httpcfdsbrainrikenjp httpcfdsbrainrikenjpFuccihtml Aydogan Ozcan - UCLA - new imaging and sensing architectures httpinnovateeeuclaeduwelcomehtml httpwwwhhmiorgscientistsaydogan-ozcan Badri Roysam - UH - FARSIGHT Toolkit httpwwweeuhedufacultyroysam httpwwwfarsight-toolkitorgwikiMain_Page Brian J Ford ndash microscopist and popularizer httpsuklinkedincominprofbrianjford Carolyn Larabell ndashNational Center for X-ray Tomography (LBNL) UCSF httpncxtlblgovq=carolyn httpprofilesucsfeducarolynlarabell Clare Waterman ndash NHLBI NIH

httpswwwnhlbinihgovresearchintramuralresearcherspiwaterman-clare Dana Peer - Columbia University - Computational Systems Biology viSNE and more software httpwwwc2b2columbiaedudanapeerlabhtml httpwwwc2b2columbiaedudanapeerlabhtmlcythtml David Mayerich - UH - STIM Laboratory Scalable Tissue Imaging and Modeling httpwwweeuhedufacultymayerich httpstimeeuhedu David Piston WUSTL httpwwwcellbiologywustledufacultytenureddavid-w-piston-phd Diane Lidke and Keith Lidke - University of New Mexico httppathologyunmeduresearchfaculty-laboratoriesthe-lidke-laboratoryindexhtml httppanda3physunmedu~klidke Donna Arndt-Jovin and Thomas Jovin - Max Planck Institute for Biophysical Chemistry Laboratory of Cellular Dynamics httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsDonnaArdndt-JovinResearchAreasAndProjects httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsChairmanThomasJovinResearchAreasAndProjects Ed Boyden ndash MIT Media Lab ndash expansion microscopy (ExM) optogenetics httpsyntheticneurobiologyorg httpsyntheticneurobiologyorgprotocols httpsyntheticneurobiologyorgpublications httpwwwtedcomtalksed_boyden_baby_diapers_inspired_this_new_way_to_study_the_brain httpwwwextbiocombuycell Elizabeth Blackburn ndash Salk Institute - Telomeres httpswwwsalkeduscientistelizabeth-blackburn httpsenwikipediaorgwikiElizabeth_Blackburn httpswwwnobelprizeorgnobel_prizesmedicinelaureates2009blackburn-factshtml Elizabeth Hillman - Columbia university - SCAPE (Swept Confocally-Aligned Planar Excitation) high speed 3D microscopy DyCE (dynamic contrast enhancement to image and segment small animal organs live) Neuroimaging amp Neurovascular Coupling httporionbmecolumbiaedu~hillmanInstrumentationhtml httporionbmecolumbiaedu~hillmanSCAPEhtml httporionbmecolumbiaedu~hillmanMolecularhtml httporionbmecolumbiaedu~hillmanBrain_Imaginghtml Eric Betzig ndash UCSF (moving from HHMI Janelia Farm in 2016) httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014betzig-factshtml Eva Sevick-Muraca ndash UT Health Science Center at Houston molecular imaging clinical NIR fluoresceince imaging httpswwwutheduimmprofilehtmid=1005459 httpswwwutheduimmcentersmolecular-imaginghtm Evelin Schrock - Technische Universitaumlt Dresden spectral karyotyping cytogenetics httpswwwresearchgatenetprofileEvelin_Schrock Garry Nolan Stanford University ndash Mass cytometry MIBI-ToF high throughput imaging mass cytometry (42plex) httpwebstanfordedugroupnolanresourceshtml httpwebstanfordedugroupnolantechnologieshtml George McNamara ndash Cell Morphometry (41) Figure 1 right top two panels (55) The Chase (2016 temporal area maps lsquodynamic morphologyrsquo) (76) newsletter series on ldquoThe Chaserdquo (73) direct Vimeo movie of ldquoThe Chaserdquo Tiki_Goddess linkedin 10+plex blog httpsworksbepresscomgmcnamara41 httpsworksbepresscomgmcnamara55 httpsworksbepresscomgmcnamara76

httpsworksbepresscomgmcnamara73 httpsvimeocom175151196 httphomeearthlinknet~tiki_goddess httpswwwlinkedincomingeorgemcnamara httpswwwlinkedincompulsebd-biosciences-listed-tandems-horizon-brilliant-violets-mcnamara Gillian Griffiths - University of Cambridge - T-cell immunological synapse httpwwwcimrcamacukresearchprincipal-investigatorsprincipal-investigators-a-hgriffiths Hari Shroff NIBIB NIH httpswwwnibibnihgovlabs-at-nibibsection-high-resolution-optical-imaging-hroi HHMI Janelia Farm Research Campus (JFRC) - Advanced Imaging Center Open Science httpswwwjaneliaorgopen-scienceadvanced-imaging-center-aic httpswwwjaneliaorgopen-science Jeanne Lawrence University of Massachussetts Medical School httpwwwumassmededucellbiolabslawrencepersonnelprincipal-investigator Jennifer Lippincott-Schwartz ndash HHMI Janelia Farm httpswwwjaneliaorgpeoplejennifer-lippincott-schwartz Jin Zhang ndash UCSD httpprofilesucsdedujinzhang Joe DeRisi - UCSF - 3D printable lab stuff httpderisilabucsfeduindexphppage=3D John Russ Chris Russ Fovea Pro plugins for Adobe Photoshop httpwwwdrjohnrusscomindexhtml httpwwwdrjohnrusscombookshtml httpwwwreindeergraphicscomfoveaprotutorialhtml Julie Theriot httpcmgmstanfordedutheriot Karl Deisseroth ndash Stanford University ndash CLARITY optical tissue clearing Optogenetics httpclarityresourcecenterorg httpwebstanfordedugroupdlaboptogeneticsindexhtml Karsten Koumlnig (Koenig) - Saarland University and JenLab GmbH - biophotonics httpwwwbltuni-saarlanddeindex_ehtm httpwwwjenlabde httpwwwthelastescape-filmcom Karsten Rodenacker ndash image measurements httpkaro03bplacednetkaroMeMisc_WWWpdfMicrosoftWord-EQUAPATpdf Kevin Eliceiri ndash UW-Madison Open Source Photonics and Software Laboratory for Optical and Computational Instrumentation (LOCI) wwwlociwiscedu Klaus Kemp ndash Microlife Services ndash diatoms and other prepared microscope slides httpwwwdiatomscouk Kurt Thorn UCSF httpthornlabucsfedu httpsnicucsfedublog httpnicucsfeduFPvisualization httpgigapancomgigapans163370 Lihong Wang - WUSTL - Optical Imaging Laboratory photoacoustic tomography

httpoilabseaswustledu httpoilabseaswustleduresearch_0html Loren Looger - HHMI JFRC - iGluSnFr fluorescent protein biosensor httpswwwjaneliaorglablooger-lab Mary-Lou Pardue ndash MIT (first ever in situ hybridization with J Gall) httpsbiologymitedupeoplemary_lou_pardue httpsenwikipediaorgwikiMary-Lou_Pardue Nancy Allbritton - UNC - Chemical cytometry microraft arrays organ-on-a-chip httpswwwbmencsueduindexphpcomponentcomprofileruserprofilenlallbri httpwwwbmeuncedulabsallbritton Navin Varadarajan - UH - single-cell Lab httpwwwcheeuhedufacultyvaradarajan httpsinglecellcheeuheducontacthtml Nicholas Shaner - Scintillon Institute - mNeonGreen httpwwwscintillonorgshaner_lab Rebecca Richards-Kortum httpbioengineeringriceedufacultyrebecca_richards-kortumaspx Robert Campbell - Fluorescent proteins optogenetic proteins httpcampbellwebchemualbertaca httpcampbellwebchemualbertacaprojects-2 Robert Murphy ndash Cell measurements web services httpmurphylabwebcmueduservices Sabine Mai - University of Manitoba - Genomic Centre for Cancer Research and Diagnosis (GCCRD) - httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBPlatformsGCCRDhtml httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBScientistsMaiAwardshtml Sally Ward and Raimund Ober - Texas AampM University - httpwwwwardoberlabcom Simon Watkins - U Pittsburgh Center for Biologic Imaging httpwwwcbppittedufacultywatkinshtml httpwwwcbppittedufacultylabwatkinshtml httpwwwcbipittedu Stefan Hell ndash Deparment Hell NanoBiopohotonics httpwwwmpibpcmpgdehell httpsenwikipediaorgwikiStefan_Hell httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014hell-factshtml Sunney Xie Harvard httpsbernsteinharvardedu Susan Cox ndash 3B microscopy httpwwwcoxphysicscomindexhtml httpwwwcoxphysicscom3b Radim Chmeliacutek - Center for innovative microscopy Experimental biophotonics group httpswwwceiteceuceitec-butexperimental-biophotonicsrg3 httpwwwbiophotczhome Taekjip Ha ndash Johns Hopkins University ndash single molecules httphamedjhmiedu

Thomas Ried ndash NCI NIH SKYM-FISH and CGH Database httpsccrcancergovGenetics-Branchthomas-ried httpsccrcancergovGenetics-Branchthomas-riedqt-staff_profile_tabs=9qt-staff_profile_tabs ftpftpncbinlmnihgovsky-cghDATA httpswwwncbinlmnihgovdbvar Viviana Gradinaru ndash CalTech ndash CLARITYPACT Optogenetics httpwwwbbecaltecheducontentviviana-gradinaru httpglabcaltechedu Vladislav Verkhusha - near infrared fluorescent proteins httpwwweinsteinyuedulabsvlad-verkhushadefaultaspx httpwwweinsteinyueduresearchfacilitiesfluorescent WE Moerner ndash Stanford University httpwebstanfordedugroupmoerner Willard Wiggans ndash micro gallery httpwwwwillard-wigancomgallery Wolf Frommer ndash Molecular sensors httpbiosensordpbcarnegiescienceedu (fluorescent protein biosensors table) Xiaowei Zhuang = Harvard httpzhuangharvardedu Yuval Garini - Bar-Ilan University - Nano-Bio-Photonics laboratory httpgarinilabbiuacil Microscopy Magazines Imaging amp Microscopy httpwwwimaging-gitcommagazine Laser Focus World httpwwwlaserfocusworldcomindexhtml Microscopy amp Analysis httpwwwmicroscopy-analysiscom Microscopy Today httpwwwmicroscopy-todaycom Microscopy-UK httpwwwmicroscopy-ukorguk Photonics Spectra Biophotonics httpwwwphotonicscomPublicationsaspx The Microscope Journal httpmcriorgv72the-microscope-journal RMS Infocus Magazine httpwwwrmsorgukstudy-readinfocus-magazinehtml Nobel Prizes in Light Microscopy and Related Fields Chemistry 1925 colloids (light sheet) Zsigmondy (Siedentopf Zsigmondy 1902) httpswwwnobelprizeorgnobel_prizeschemistrylaureates1925

Chemistry 2000 conductive polymers Heeger MacDiarmid Shirakawa (Brilliant Violets Ultraviolets Blues) httpwwwnobelprizeorgnobel_prizeschemistrylaureates2000 Chemistry 2008 green fluorescent protein GFP Shimomura Chalfie Tsien httpwwwnobelprizeorgnobel_prizeschemistrylaureates2008 Chemistry 2014 super-resolved fluorescence microscopy Betzig Hell Moerner httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014 Physics 1953 Phase Contrast Zernike httpswwwnobelprizeorgnobel_prizesphysicslaureates1953 Physics 2009 invention of an imaging semiconductor circuit ndash the CCD sensor Kao Boyle Smith httpwwwnobelprizeorgnobel_prizesphysicslaureates2009 Physics 2014 efficient blue light emitting diodes Akasaki Amano Nakamura httpwwwnobelprizeorgnobel_prizesphysicslaureates2014 Physiology or Medicine 2006 Fire and Mello RNA interference ndash gene silencing by double stranded RNA httpwwwnobelprizeorgnobel_prizesmedicinelaureates2006 Physiology or Medicine 2006 Capecchi Evans Smithies specific gene modifications in mice by the use of embryonic stem cells httpwwwnobelprizeorgnobel_prizesmedicinelaureates2007 Physiology or Medicine 2009 Blackburn Greider Szostak how chromosomes are protected by telomeres and telomerase httpwwwnobelprizeorgnobel_prizesmedicinelaureates2009 Physiology or Medicine 2012 Gurdon Yamamanka matured cells can be reprogrammed to become pluripotent httpwwwnobelprizeorgnobel_prizesmedicinelaureates2012

Table 442 Fluorophores Photophysics Data

Fluorophore Abs or Ex max (nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Acridine orange 271 520 27000 020 5

Alexa Fluor 430 431 541 16000 055 9

Alexa Fluor 488 495 519 71000 094 67

Alexa Fluor 532 532 553 81000 080 65

Alexa Fluor 546 556 573 104000 096 100

Alexa Fluor 568 578 603 91300 075 69

Alexa Fluor 594 590 617 73000 064 47

Allophycocyanin (APC) 650 660 700000 068 476

Atto 390 390 479 24000 090 22

Atto 425 436 484 45000 065 29

Atto 430LS 433 547 32000 065 21

Atto 465 453 508 75000 075 56

Atto 490LS 496 661 40000 030 12

Atto 520 525 547 105000 095 100

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 6: McNamara 20161006 revised draft tables for CPHG Light ...

Montana Molecular LLC - genetically encoded fluorescent biosensors and probes for cell-based assays and live cell imaging httpmontanamolecularcomproductsproducts-overview NanoLight Technologies ndash Renilla GFP luciferases httpwwwnanolightcomNanoFluorsGFP_Expression_Vectorshtml httpswwwbiotoycomenlearn n3D Biosciences ndash generate 3D cell spheroids high throughput screening image changes using smartphone camera inside incubator httpwwwn3dbiocomproductsmagnetic-3d-bioprinting httpwwwn3dbiocomproductsassays New England BioLabs (NEB) ndash Cypridina Gaussia luciferases httpswwwnebcomapplicationscellular-analysisreporter-systems Promega ndash Monster GFP NanoLuc httpswwwpromegacomproductsreporter-assays-and-transfectionreporter-vectors-and-cell-linesmonster-green-fluorescent-protein-phmgfp-vector httpswwwpromegacomproductsreporter-assays-and-transfectionreporter-vectors-and-cell-linesnanoluc-luciferase-reportersnanoluc-genetic-reporter-vectors Fluorescence Products (reagents) Advanced Cell Diagnostics (Bio-Techne) - branched DNA probe sets for RNA FISH httpsacdbiocomproducts Affymetrix eBioscience Thermo Fisher - branched DNA probe sets for RNA FISH httpwwwaffymetrixcomestorepromotionsviewrnaishindexaffx Anaspec ndash HiLyte Fluorophores FRET probes httpswwwanaspeccomproductsproductcategoryaspid=10 Antibody Resource Page httpwwwantibodyresourcecom Biocompare ndash Antibodies httpwwwbiocomparecomAntibodies Cell Signaling Technology ndash fluorescence antibodies httpswwwcellsignalcombrowseimmunofluorescence-immunocytochemistryif-paraffinif-frozen Essen Biosciences ndash Bacmam 30 ready to use FP gene transfection reagents httpwwwessenbiosciencecomenproductsreagents-consumablesincucyte-nuclight-red-bacmam-30-reagent-nuclear-labeling-cat-no-4621 GE Healthcare Amersham Biosciences httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usbrandscydye Global Biological Standards Institute (GBSI) ndash Antibody Validation Initiative httpwwwgbsiorgworkantibodies Goryo Chemical httpwwwgoryochemicalcom Human Protein Atlas (academic) Atlas Antibodies (commercial arm) US distributor httpwwwproteinatlasorg httpsatlasantibodiescom httpwwwsigmaaldrichcomlife-sciencecell-biologyantibodiesprestige-antibodieshtml

Integrated DNA Technologies (IDT) httpwwwidtdnacomsiteCatalogmodificationsdyes httpwwwidtdnacompagesproductsmodificationsfluorophoresfreedom-dyes httpwwwidtdnacomsiteCatalogModificationsCategory4 Jackson ImmunoResearch httpswwwjacksonimmunocom KPL (formerly Kirkegaard amp Perry Laboratories Inc) SeraCare httpwwwkplcom LGC Biosearch Technologies ndash dyes for oligonucleotides single molecular RNA FISH image gallery httpswwwbiosearchtechcomsupporteducationfluorophores-and-quenchers httpstellarisfishsmugmugcom httpsinglemoleculefishcom httpswwwbiosearchtechcomproductsrna-fish (typically 48 20 base oligonucleotides) Marker Gene Technologies Inc (MGT) httpwwwmarkergenecomfluorescent-reagent Miltenyi Biotec ndash REAfinity recombinant engineered antibodies (no Fc Receptor binding) FASER fluorescence amplification kits NiraWave fluorophores (indocyanine green formulations) httpwwwmiltenyibioteccomenproducts-and-servicesmacs-flow-cytometryreagentsantibodies-and-dyesrecombinant-antibodiesaspx httpwwwmiltenyibioteccomenproducts-and-servicesmacs-flow-cytometryreagentssupport-reagentsfaser-kitsaspx httpwwwmiltenyibioteccomenproducts-and-servicesviscover-imagingoptical-imagingaspx Molecular Probes Inc Invitrogen Thermo Fisher ndash largest vendor of fluorophores Molecular Probes Handbook (web resource) Tyramide Signal Amplification kits httpwwwprobescom httpswwwthermofishercomusenhomereferencesmolecular-probes-the-handbookhtml httpswwwthermofishercomusenhomereferencesmolecular-probes-the-handbooktablestyramide-signal-amplification-tsa-kitshtml NIRvana Sciences httpnirvanasciencescom httpnirvanasciencescompage_id=3088 One World Lab ndash antibody search httponeworldlabcomantibodies CytoCell Oxford Gene Technologies ndash DNA FISH probes human mouse pig chicken httpwwwcytocell-uscom Perkin Elmer ndash nucleotides labeling kits Tyramide Signal Amplification Kits (TSA) Opal 7plex discovery panel kit based on sequential TSA httpwwwperkinelmercomcategoryfluorescent-hapten-nucleotides httpwwwperkinelmercomcategoryfluorescent-agents-labeling-kits-dyes httpwwwperkinelmercomlab-solutionsresourcesdocsBRO_TSAsignalamplificationpdf httpwwwperkinelmercomproductopal-7-immunology-discovery-kit-op7ds1001kt

Rockland Inc httpwwwrockland-inccomcommerceindexjsp

TEFLabs ndash fluorescent ion indicators (Ca++ Cl- K+ Mg++ Na+ pH Zn++) ionophores fluorophores httpwwwteflabscomion-indicators Vector Laboratories Inc httpwwwvectorlabscom

Live cell imaging dishes and multi-well plates (ldquoglass bottom dishesrdquo)

We recommend these for simplified handing and processing vs either thick plastic dishesplates or having to handle loose coverslips with your valuable cells

Leicester Imaging Technologies (LITE) - University of Leicester - table of dishes for live cell imaging (our table has current links and bad links left out) httpwww2leacukcollegesmedbiopsychfacilities-and-servicescbsliteaiftips-and-tricks-1dishes-for-live-cell-imaging Bellco Glass Inc - glass flat bottom plate httpwwwbellcoglasscomnode1046 Bioptechs - interchangable coverslip dish ($036 per experiment) httpwwwbioptechscomproductinterchangeable-coverslip-dish Brooks Automation Inc - clar bottom optical imaging microplates httpwwwbrookscomproductslife-scienceconsumablesmatrical-microplates-microtubes-racks-lidsglass-bottom-optical-imaging-microplates Cell EampG - glass bottom cell sulture dishes plates httpcellegcomproducthtml Cellvis - glass bottom dishes and plates httpwwwcellviscom_35-mm-glass-bottom-dishes_products_by_categoryphpcat_id=3 Corning - glass bottom microplates httpcatalog2corningcomLifeSciencesen-USShoppingCategoryaspxcategoryname=Microplates20-202015(Lifesciences)|Assay20Microplates20-202015(Lifesciences) Design 1 Solutions - Custom microplates and fabrication services httpwwwdesign1solutionscomcustom-microplateshtml Eppendorf - cell imaging dishes imaging plates httpsonline-shopeppendorfcomOC-enCell-Culture-and-Imaging-Consumables-110320Cell-Imaging-Consumables-120210Eppendorf-Cell-Imaging-Dishes-PF-19457html httpsonline-shopeppendorfcomOC-enCell-Culture-and-Imaging-Consumables-110320Cell-Imaging-Consumables-120210Eppendorf-Cell-Imaging-Plates-PF-19458html Greiner Bio-One International - CellView glass bottom dishes quadrant dishes httpsshopgbocomenrowarticlescataloguearticle0110_0110_0040_002027513 ibidi - u-Plates glass bottom dishes microfluidic slides httpibidicomxtproductsenibidi-Labwarem-Plates httpibidicomxtproductsenibidi-Labware Matsunami Glass Ind Ltd httpwwwmatsunami-glasscojpenglishlifebiodata01html Mattek - glass bottom dishes and SBS plates httpswwwmattekcomstore-categoryculturewareglass-bottom-dishes Nunc - glass bottom dishes httpswwwthermofishercomordercatalogproduct150680 NEST Biotechnology Co Ltd Wuxi Jiangsu PRChina httpwwwnestscientificusacomproducts_detailproductId=31html PerkinElmer - glass bottom plates httpwwwperkinelmercomSECatalogCategoryIDMicroplates

Porvair Sciences - clear bottom assay plates httpwwwporvair-sciencescomenservices-menulife-sciencesclear-bottom-assay-plates Ted Pella Inc - glass bottom dishes clear wall or black wall (manufactured by WillCo Wells) httpswwwtedpellacomsection_html706dishhtm Warner Instruments (Harvard Apparatus) - culture dishes perfusion systems httpswwwwarneronlinecomproduct_cat_infocfmid=1322 Willco Wells - glass bottom dishes wwwwillcowellscom World Precision Instruments - Fluorodish glass bottom dishes httpswwwwpiinccomproductslaboratory-suppliesfd35-100-fluorodish-cell-culture-dish-35mm-23mm-well-pkg-of-100 Microscopes Microscopy Accessories (accessorize) Reagents Resources 3scan ndash knife edge scanning microscope (images slices repeats through specimen) httpwww3scancomdata-2 89North (affiliated with Chroma Technology Corp) httpwww89northcom Abberior Instruments ndash STED RESOLFT precision localization super-resolution microscopes STEDYCON convert any fluorescence microscope to STED httpabberior-instrumentscom httpabberior-instrumentscomproductscompact-lineabberior-stedy-con Acquifer ndash HIVE imaging machine (computer hardware) for high content screening big data httpswwwacquiferde Adobe Systems Inc httpwwwAdobecom httpscreativeadobecomproductsdownloadphotoshop Affymetrix eBioscience (ThermoFisher) - microarrays httpwwwaffymetrixcomestorebrowselevel_one_category_template_onejspparent=35796ampcategory=35796 httpwwwaffymetrixcomestorecatalog131547AFFYGeneChip26231743B+System+3000Dx+v22623423B1_1 Agilent Technologies ndash SureScan microarray scanner (array CGH microRNA SNPs CNV) httpwwwgenomicsagilentcomenMicroarray-Scanner-Processing-HardwareSureScan-Microarray-Scannercid=AG-PT-144 Andor Technology (Oxford Instruments) ndash sCMOS cameras Dragonfly spinning disk confocal Revolution DSD2 differential spinning disk confocal photostimulation (fluorescence recovery after photobleaching optogenetics) Mosaic3 DMDDLP high speed light patterning (optogenetics structured illumination) MicroPoint pulsed UV laser for ablation DNA damage photobleachingactivation uncaging accessories httpwwwandorcomscientific-camerasneo-and-zyla-scmos-cameras httpwwwandorcommicroscopy-systemsdragonfly httpwwwandorcommicroscopy-systemsrevolution-dsd httpwwwandorcommicroscopy-systemsphotostimulation httpwwwandorcommicroscopy-systemsphotostimulationmosaic httpwwwandorcommicroscopy-systemsphotostimulationmicropoint httpwwwandorcommicroscopy-systemsmicroscopy-components Apogee Instruments Inc (Andor Technology) ndash CCD cameras and filter wheels (mostly marketed for astronomy) httpwwwccdcomandorhtml Applied Scientific Instrumentation Inc ndash light sheet imager (iSPIM diSPIM)

wwwasiimagingcom httpwwwasiimagingcomindexphpproductslight-sheet-microscopyselective-plane-illumination-microscopy-ispim-dispim Applied NanoFluorescence LLC ndash NS1 NanoSpectralyzer (Raman and UV-VISNIR) NS MiniTracer near infrared spectrometer NFM NanoFluorescence microscope multi-laser light source single wall carbon nanotubes (NIR II fluorophores) httpappliednanocomproductshtml httpappliednanocomproductsns1html httpappliednanocomproductsproduct-list77-ns-minitracerhtml httpappliednanocomproductsnfmhtml httpappliednanocomproductsls-nhtml httpwwwnanowerkcomnewsnewsid=24132php Applied Spectral Imaging Inc httpwwwspectral-imagingcom ArgoLight ndash fluorescence resolution test target slides httpargolightcom AttoCube - attoMICROSCOPY overview attoCFM - Multichannel cryogenic (low temperature) confocal fluorescence microscopes 08 NA objective lenses 400-1000 nm spectral range httpwwwattocubecom httpwwwattocubecomattomicroscopyintroductiontab-2 httpwwwattocubecomattodownloads AutoQuant (Media Cybernetics) spatial deconvolution httpwwwmediacycomautoquantx3 Becker amp Hickl GmbH httpwwwbecker-hicklcomproductshtm Berkeley Lights Inc ndash manueuver into nanowells incubate recover 4000 single cells per chip httpswwwberkeleylightscomtechnology Bioaxial ndash Codim imaging conical diffraction beam shaper for super-resolution (4 sub-images) httpwwwbioaxialcomcodim-imaging Bioptechs - Live-Cell Micro-Observation Products httpwwwbioptechscom Bionumbers - database of useful biological numbers httpbionumbershmsharvardeduKeyNumbersaspx Biostatus ndash DRAQ5 DRAQ7 ApopTRAK CyTRAK Orange CyGel HypoxiTRAK httpwwwbiostatuscomProducts Bio-Tek ndash Cytation 3 Cell Imaging Multi-Mode Reader Lionheart FX Automated Live Cell Imager httpwwwbiotekcomproductsimagingcytation3_cell_imaging_multi_mode_readerhtml httpwwwbiotekcomproductsimaginglionheartfx_automated_live_cell_imagerhtml Biovision Technologies ndash distributor for several imagers including VT-iSIM instant super-resolution microscope httpbiovision-technologiescom httpbiovision-technologiescomsystemshtml httpbiovision-technologiescomvtisimhtml Bitplane (Andor Oxford Instruments) ndash Imaris imaging software httpwwwbitplanecom BMV Optical - custom lens assemblies and optical filters wwwbmvopticalcom

Bruker (previously Prairie Technologies Vutara) ndash Opterra confocal Ultima Multiphoton Vutara 352 single molecule localization microscopes httpswwwbrukercomproductsfluorescence-microscopesopterra-confocal-microscopyoverviewhtml httpswwwbrukercomproductsfluorescence-microscopesultima-multiphoton-microscopyhtml httpswwwbrukercomproductsfluorescence-microscopesvutara-super-resolution-microscopyoverviewhtml Cairn Research ndash standard and custom accessories ex Light Sheet Illuminator MultiCam (4 cameras) custom design httpswwwcairn-researchcouk httpswwwcairn-researchcoukproductl-spi-single-plane-illuminator (dual L-SPI for 4 illumination directions) httpswwwcairn-researchcoukproductmulticam httpswwwcairn-researchcoukcustom-design Cameca ndash NanoSIMS 50L (7plex stable isotope imaging) httpwwwcamecacominstruments-for-researchnanosimsaspx CellMic (formerly Holomic) - blood analysis or fluorescence imaging cytometer on a cell phone httpwwwcellmiccomcontentadvanced-technologies httpwwwcellmiccomcontentfluorescent-imaging-cytometry-and-e-coli-detection-on-a-cell-phone CellOptic ndash FINCH (Fresnel INcoherence Correlation Holography) httpwwwcellopticcomindex2html CellProfiler ndash High content screening (HCS) image processing and analysis software httpcellprofilerorg ClearLight Diagnostics - CLARITY Optimized Light Sheet Microscopy (3D tissue optical clearing + light sheet imaging) httpwwwclearlightdxcomindexhtml Confocalnl ndash Rescan confocal microscopy to obtain 170 nm resolution with any pinhole diameter httpwwwconfocalnl CoolLED ndash LED light sources httpwwwcoolledcomproduct-detailpe-4000 Crest Optics SRL ndash X-Light confocal X-Light V2 + VCS (VideoConfocal super-resolution) httpwwwcrestoptcom httpwwwcrestoptcomhtmlx-light_v2_vcshtml Cytoskeleton Inc - live cell imaging reagents Spirochrome SiR bioimaging probes httpwwwcytoskeletoncomlive-cell-reagents httpwwwcytoskeletoncomlive-cell-reagentsspirochrome CytoViva ndash darkfield imaging hypspectral imaging httpwwwcytovivacomproducts3d-enhanced-darkfield-imaging httpwwwcytovivacomproductshyperspectral-imaging-2hyperspectral-imaging Data Translation Inc - digitizer cards httpwwwdatxcom Delmic BV - combined correlative scanning electron microscope with inverted fluorescence microscope httpwwwdelmiccomdelphi httpswwwdelphimicroscopecom httpwwwdelmiccomsecom-super-resolution Digital Light Innovations (DLi) - CELscope C-mount LED Microscope using Texas Instruments DLP illuminator with a simple stand httpswwwdlinnovationscomdli-deep-dives-celscope-c-mount-led-microscope Double Helix LLC ndash single molecule localization microscope (Piestun) httpdoublehelixopticscom Edinburgh Super-resolution Imaging Consortium (ESRIC)

httpwwwesricorg Energetiq ndash Deep ultraviolet (DUV high radiance 170-2100 nm) laser driven light source (LDLS) httpwwwenergetiqcom Epi Technology - CaliCube - Cube for fluorescence light path to inspect epi Illumination light source (lamp) fiber optic or liquid light guide httpwwwepitechnologycomepitechnology-1 Essen Biosciences ndash Incucyte Zoom (imager inside incubator) httpwwwessenbiosciencecomenproductsincucyte Estigen Tissue Science ndash manual and automated tissue arrayer (tissue microarray maker) httpwwwestigencom Euro-Bioimaging httpwwweurobioimagingeu Excelitas Technologies (formerly Lumen Dynamics) ndash X-Cite LEDs httpwwwexcelitascomPagesProductX-Cite-LED-Solutionsaspx Expansion Technologies Inc (extbio) ndash Expansion microscopy httpwwwextbiocombuycell FEI (formerly Till Photonics) (Thermo Fisher) ndash correlative LM-EM single molecule Cryo-EM httpswwwfeicomlife-sciencescellular-biology httpswwwfeicomlife-sciencescellular-biologycorrelative-microscopy httpswwwfeicomlife-sciencesstructural-biology Femtonics - Multi-phton microscopes software accessories caged glutamate reagents services httpfemtonicseuproducts First Light Imaging ndash C-Red NIR imaging (800-2500 nm NIR windows I II III 650-950 nm 1100-1350 nm 1600-1870 nm[Shi et al 2015]) high speed visible EMCCD (400-1000 nm) httpwwwfirst-lightfrcategoryrangesinfrared Fluidigm ndash Helios imaging CyTOF mass cytometer (42plex) Callisto (32 independent chambers dose with up to 16 independent factors for 1-1000 cell populations culture up to 3 week) Polaris functional genomics meets imaging (48 single cells up to 24 hours after single cell selection from a population) httpswwwfluidigmcomproductshelios httpswwwfluidigmcomproductscallisto httpswwwfluidigmcomproductspolaris GattaQuant - nanorulers for high resolution microscopes and super-resolution microscopes performance testing httpwwwgattaquantcomNanoruler GE Healthcare life Sciences Applied Precision ndash DeltaVision deconvolution OMX OMX SR httpwwwgelifesciencescomwebappwcsstoresservletproductByIdenGELifeSciences-us29065728 httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usproductsAlternativeProductStructure_2380729065721 httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usproductsAlternativeProductStructure_2380729115476 German BioImagingorg httpwwwgermanbioimagingorgwikiindexphpMain_Page httpwwwgermanbioimagingorgwikiindexphpWorkgroup6SoftwarePackages GIGAmacro ndash Magnify2 gigapixel imagery oof macroscopic and microscopic objects Terapixel macro image httpwwwgigamacrocomgigapixel-macro-imaging-system httpwwwgigamacrocomworlds-first-terapixel-macro-image

Glencoe Software ndash OMERO Plus enterprise data management for scientific images and any associated metadata (OME = Open Microscopy Environment) DataViewer PathViewer httpsglencoesoftwarecomomeroplushtml httpsglencoesoftwarecomdataviewerhtml httpsglencoesoftwarecompathviewerhtml Gooch amp Housego ndash spectral imager httpsgoochandhousegocomminiature-spectral-imaging-camera httpwwwghinstrumentscomproductsspectral-imaging-synthesishsi-440c-hyperspectral-imaging-system Hindsight Imaging ndash spectral imaging httphindsight-imagingcom Horiba Scientific - SWIFT ultra-fast Raman confocal imaging Raman spectroscopy httpwwwhoribacomscientificproductsraman-spectroscopyraman-imagingswift httpwwwhoribacomscientificproductsraman-spectroscopyraman-imaging httpwwwhoribacomscientificproductsraman-spectroscopy IATIA Ultima Capital ndash QPm (quantitative phase microscopy) httpwwwultimacapitalnetiatiaimagingPublicationsIatia20ImagingapplicationNotesqpmApplicationWithConfocalMicroscopespdf Ibidi - heating and incubation systems optical O2 measurement systems Nanolive 3D Cell Explorer pump system gas incubation system httpibidicomxtproductsenInstruments-AccessoriesHeating-Incubation-Systems httpibidicomxtproductsenInstruments-Accessoriesibidi-OPAL-Optical-O2-Measurement-System httpibidicomxtproductsenInstruments-AccessoriesNanolive-3D-Cell-Explorer httpibidicomxtproductsenInstruments-Accessoriesibidi-Pump-System httpibidicomxtproductsenInstruments-AccessoriesHeating-Incubation-Systemsibidi-Gas-Incubation-System iLAbSolutions (Agilent Technologies) - Instrument management and scheduling software (cores and labs) httpwwwilabsolutionscominstrument-access-control ImageJ - Fiji ImageJ NIH ImageJ ImageJ ndash Fiji (Fiji is just ImageJ) is the main download site httpfijisc httpsimagejnihgovij wwwimagejnet Inscopix ndash nVista in vivo mouse brain imaging miniature microscope httpswwwinscopixcomproducts Intelligent Imaging Innovations Inc (3i) ndash Slidebook imaging software Lattice light sheet (high speed gentle to cells high resolution imaging) Dual-view Inverted Selective Plane Illumination (diSPIM) VIVO 2-Photon (VIVO 2P) multiphoton microscopy Everest intravital imaging Marianas 3D real-time deconvolution timelapse spinning disk FRAP TIRF FLIM single molecule environmental control Phasor - optogenetic photostimulation using digital holography Yokogawa spinning disk confocal units wwwintelligent-imagingcom httpswwwintelligent-imagingcomslidebookphp httpswwwintelligent-imagingcomsystemsphplattice httpswwwintelligent-imagingcomsystemsphpdispim httpswwwintelligent-imagingcomsystemsphptwophoton httpswwwintelligent-imagingcomsystemsphpeverest httpswwwintelligent-imagingcomsystemsphpmarianas httpswwwintelligent-imagingcomoptogeneticsphp httpswwwintelligent-imagingcomsdcphp ISS Inc ndash fluorescence lifetime imaging microscopy fluorescence correlation spectroscopy (FCS) confocal imaging httpwwwisscommicroscopyindexhtml JenLab GmbH cyto-microscopy multiphoton tomography httpwwwjenlabdeproducts250html httpwwwjenlabde2PM-Cryo1330html

httpwwwjenlabdeMultiphoton-Tomography680html Jenoptik - microscope cameras httpswwwjenoptikcomproductscameras-and-imaging-modulesmicroscope-cameras JPK Instruments - integrated atomic force microscope (AFM) force sensing optical tweezers optical trapping single cell force spectroscopy (SCFS) httpwwwjpkcomindex2enhtml httpusajpkcomoptical-tweezers-optical-trapping29ushtml httpusajpkcomcellular-adhesion-cytomechanics30ushtml Keyence ndash VK-X confocal (upright) BZ-X700 widefield (inverted) httpwwwkeyencecomssproductsmicroscopevkx httpwwwkeyencecomssproductsmicroscopebz-x700indexjsp KK Technology - CapiScope HVCS Handheld Video Capillaroscopy System (CytoScan) httpwwwkktechnologycomhvcshtml LaVision BioTec ndash TriMscope Multiphoton TriM Scope II Adaptive Optics UltraMicroscope II light sheet httpwwwlavisionbiotecde httpwwwlavisionbiotecdetrim-scope-overviewhtml httpwwwlavisionbiotecdetrim-scope-ii-adaptive-opticshtml httpwwwlavisionbiotecdeultramicroscope-ii-introductionhtml Laxco ndash upright and inverted microscopes httpwwwlaxcoinccomMICROSCOPES Lego ndash Lego Idea Microscopes httpsideaslegocomprojects44370 httpwwwnico71frlego-working-microscope Li-Cor ndash near-infared fluorescent dyes and in vivo imaging agents in vivo and Western blot imaging systems httpswwwlicorcombioproductsreagents httpswwwlicorcombioproductsreagentsirdyebrightsite_imaging_agents httpswwwlicorcombioproductsimaging_systemsodyssey_familyhtml httpswwwlicorcombioproductsimaging_systemspearl httpswwwlicorcombioproductsimaging_systemscdigit Life Imaging Services - ldquothe Ludin chamberrsquo ldquothe cube amp the boxrdquo httpwwwlischthechamberhtml httpwwwlischtheboxhtml Lightform Inc ndash PARISS imaging spectrometer httplightforminccom LMU Bioimaging httpwwwbioimagingbmcmeduni-muenchendelinkswebsitesindexhtml httpwwwbioimagingbmcmeduni-muenchendelearneduwebsitesindexhtml Ludl Electronic Products Ltd ndash automated XY stages focus motors filter wheels httpwwwludlcom

LumaCyte ndash Laser force Cytology (laser trap meets microfluidics to suspend and manipulate single cells) httpwwwlumacytecomabouttechnology Lumencor ndash LEDs fluorescence light sources httplumencorcomproducts Luxcel ndash mitochondrial and cellular functions O2 sensor reagents httpluxcelcomproduct+list Luxendo GmbH ndash light sheet imager

wwwluxendoeu Lyncee tec - digital holography microscopy (DHM) high content screening by DHM httpwwwlynceeteccom httpwwwlynceeteccomhigh-content-screening Mad City Labs Inc - nanopositioning wwwmadcitylabscom Mauna Kea Technologies ndash CellVizio confocal laser endomicroscopy httpwwwmaunakeatechcomenhealthcare-professionalscellvizio-endomicroscopy-0 MBF Bioscience - stereology and neuron morphology quantitative imaging httpwwwmbfbiosciencecom McCrone Group wwwmccronecominstrument-sales Media Cybernetics Inc ndash Image Premier 3D AutoQuant X3 deconvolution httpwwwmediacycom Meiji Techno America wwwmeijitechnocom MesoLens Ltd httpwwwmesolenscomproducttechnical-specifications httpwwwmesolenscomimages httpswwwbiophotonicsstrathacukresearch_1htm Meyer Instruments ndash Pathscan Enabler GigaMacro digital pathology telepathology httpmeyerinstcom httpmeyerinstcompathscan-enabler-5 httpmeyerinstcomgigamacro-gigapixel-macro-imaging httpmeyerinstcomhomescanners httprealtimetelepathologycom Microarrays - Large-Scale Gene Expression and Microarray Links and Resources httpswwwebiacukarrayexpress Micro-Manager ndash Device Support ndash tabulates many microscope cameras and motorized accessories every new camera and accessory should have a uManager driver to enable simple use with Fiji ImageJ httpsmicro-managerorg httpsmicro-managerorgwikiDevice_Support httpsopen-imagingcom Microvolution ndash (near) instant gratification spatial deconvolution using NVidia GPU card(s) httpmicrovolutioncom Mightex Systems ndash optogenetics DMDDLP illuminator (digital micro-mirror device digital light processing) httpwwwmightexsystemscomindexphpcPath=245 Millipore-Sigma Merck KGaA (Amnis Corp CellASIC EMD Millipore) ndash ImageStreamX and FlowSight imaging flow cytometers ONIX2 Microperfusion System for microscopes httpswwwemdmilliporecom httpswwwemdmilliporecomUSenlife-science-researchcell-analysisamnis-imaging-flow-cytometersQ6ubqBm3UAAAFLCKIpygJnav httpwwwemdmilliporecomUSenlife-science-researchcell-culture-systemscellASIC-live-cell-analysisd1CbqBw58AAAE_0j13MnAnav Mitutoyo America Corp wwwmitutoyocom httpecatalogmitutoyocomMF-U-Series-176-High-power-Multi-function-Measuring-Microscopes-C1413aspx

Molecular Devices Corporation Universal Imaging Corporation (Danaher) ndash MetaMorph MetaFluor high content systems (HCS) httpswwwmoleculardevicescomsystemsmetamorph-research-imaging httpmdccusthelpcomappanswersdetaila_id19319 httpswwwmoleculardevicescomsystemshigh-content-imaging Molecular Machines amp Industries - laser microdissection and tweezer systems httpwwwmolecular-machinescomhome MUSE Microscopy Inc ndash Deep UV illumination for shallow depth of field imaging httpwwwmusemicrocom Micro Video Instruments Inc - DarkLite illuminator httpwwwmvi-inccom NanoEnTek ndash JuLI Stage (imager inside incubator or on lab bench) httpwwwjulistagecom National Instruments ndash LabView software httpwwwnicomen-ushtml Navitar - Hoffman Modulation Contrast (HMC alternative to differential interference contrast phase contrast) custom lens design UVDUVNUV imaging lenses httpsnavitarcommarketsmicroscopy httpsnavitarcomproductsimaging-opticscustom-microscope-objectivescustom-microscope-objectives httpsnavitarcomproductsimaging-opticsuv-imaging National Center for X-ray Tomography (NCXT) ndash soft X-ray tomography (CT of hydrated cells) XM-2 dedicated biological SXT microscope Prof Carolyn Larabell Director (see also SiriusXT) httpncxtlblgov httpncxtlblgovsxt httpncxtlblgovmanual httpncxtlblgovq=carolyn Neogenomics (Clarient) ndash MultiOmyx immunofluorescence or DNA FISH (ldquo60plexrdquo) httpneogenomicscomPharma-ServicesLab-ServicesMultiOmyxTechnologyMultiOmyx-IF-Assay-DNA-FISH-assay-NGS-from-ROI Nexcelom ndash Celigo imaging cytometer Cellometer cell counters httpwwwnexcelomcomCeligoindexphp httpwwwnexcelomcomProducts Nikon ndash Ti-LAPP modular illumination system (for Nikon Ti series microscopes) TIRF Optogenetics httpswwwnikoninstrumentscomProductsPhotostimulation-and-TIRFTi-LAPP Nirmidas Biotech httpwwwnirmidascomtechnologynir httpwwwnirmidascomproductsniriidye NVidia ndash Pascal 10+ Gbps GPU cards for instant gratification deconvolution (software from Microvolutioncom SVInl) httpwwwgeforcecomhardware10seriesgeforce-gtx-1080 httpwwwgeforcecomhardware10seriestitan-x-pascal httpwwwnvidiacomobjectquadro-graphics-with-pascalhtml Ocean Optics ndash spectrometers httpoceanopticscomproduct-categorymodular-spectrometers Oko-Lab stage top incubator httpwwwoko-labcomstage-top Open Microscopy Environment (OME) ndash OMERO (see also Glencoe Software) Bio-Formats LOCI

httpswwwopenmicroscopyorgsite httpswwwopenmicroscopyorgsiteproductsomero httpswwwopenmicroscopyorgsiteproductsbio-formats httpswwwopenmicroscopyorgsitesupportbio-formats52supported-formatshtml httpswwwopenmicroscopyorgsiteaboutdevelopment-teamskevin OpenSPIM ndash do-it-yourself selective plane illumination microscopy (light sheet imaging) httpopenspimorgWelcome_to_the_OpenSPIM_Wiki OpenSpinMicroscopy ndash do-it-yourself SPIMDSLMOPT microscopes httpssitesgooglecomsiteopenspinmicroscopy Ovizio ndash differential digital holography (similar to quantitative phase imaging) httpwwwoviziocomenHome httpwwwoviziocomenMicroscopesQMod Oxford Gene Technologies ndash microarrays ndash cytogenetics molecule genetics cancer research pre-implantation genetic diagnosis httpwwwogtcomclinical_genetics Oxford Nanoimaging ndash single molecule(s) localization fluorescence resonance energy transfer (FRET) (Kapanidis) wwwoxfordnicom Pathology Devices ndash LiveCell stage top incubator amp controller tissue microarrayers (TMA makers) httpwwwpathologydevicescomLiveCellhtm httpwwwpathologydevicescomTMArrayerhtm PeCon GmbH ndash microscope incubators httpwwwpeconbiz Pembroke Instruments ndash spectrometers mini-lasers httppembrokeinstrumentscomqmini-spectrometer httppembrokeinstrumentscommini-lasers PerkinElmer ndash in vivo imaging systems (bioluminescence NIR fluorescence) Vectra digital slide scanner httpwwwperkinelmercomcategoryin-vivo-imaging-instruments httpwwwperkinelmercomcategoryquantitative-pathology-imaging-instruments Phi Optics ndash CellVista SLIM Pro (quantitative phase microscopy) httpphiopticscom Photometrics (Roper Scientific) ndash DualView QuadView httpwwwphotometricscom httpwwwphotometricscomproductsmultichannel Photon Technology International httpwwwpti-njcomindexhtml

PicoQuant GmbH ndash fluorescence lifetime imaging microscopes (FLIM) STED 3D-EasySTED httpswwwpicoquantcomproductscategoryfluorescence-microscopes httpswwwpicoquantcomapplicationscategorylife-sciencested httpwwweasystedorg Physik Instrumente GmbH amp Co KG (PI) - Nanopositioning Applications for Microscopy Neuroscience and Metrology httpswwwphysikinstrumentecomen httpwwwpi-usausindexphp PreSens Prescision Sensing GmbH - VisiSens measure and visualize Oxygen pH or carbon dioxide distributions httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-biological-researchhtml httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-life-science-researchhtml Prior Scientific

httpwwwprior-uscom Profusa Inc - Lumee tissue-integrated biosensors scaffolds httpprofusacomtechnology Reindeer Graphics Inc ndash OptiPix Fovea Pro 9plugins for Adobe Photoshop 6 and CS series) httpwwwreindeergraphicscom Renishaw - StreamLine fast chemical imaging Raman spectroscopy httpwwwrenishawcomenstreamline-generate-chemical-images-rapidly--9449 httpwwwrenishawcomenraman-spectroscopy--6150 Sanford Burnham Prebys ndash High Content Screening httpwwwsbpdiscoveryorgtechnologysrPagesLaJolla_HighContentScreeningaspx ScopeM - Scientific Center for Optical and Electron Microscopy - ETH Zurich httpwwwscopemethzch SiriusXT - soft X-ray tomography (SXT) microscope (CT scan hydrated cell) httpsiriusxtcom SpectraGenetics - Fluorogen Activating Peptides (FAPs) new genetically encoded ldquobinaryrdquo reporters httpspectrageneticscomproductsvectors-for-expressing-fluorogen-activating-proteinsfap-technology-overview Spirochrome - Silicon Rhodamine (SiR) and other fluorescent reagents probes for bioimaging httpspirochromecom Stanford Photonics Inc httpwwwstanfordphotonicscom httpwwwstanfordphotonicscomLife20SciencesLifeScihtm

Stream Technologies Inc ndash ColorFlow lens (multi-wavelength emission onto a camera) httpwwwstreamtechinccomproducts Sutter Instrument Company httpwwwsuttercom httpwwwsuttercomMICROSCOPESindexhtml httpwwwsuttercomIMAGINGindexhtml SVI Huygens ndash Professional (general image analysis) deconvolution NVidia GPU deconvolution httpssvinlHuygensProfessional httpssvinlHuygensDeconvolution httpssvinlHuygensGPU Sysmex Partex ndash CyScope httpwwwsysmex-parteccomproductsmicroscopyhtml httpwwwsysmex-parteccomproductsprdouct-detailviewcyscopeR-malaria-3238html Technical Instruments httpwwwtechinstcomproductsphp TESCAN Brno sro - Tescan Q-PHASE multimodal holographic quantitative phase imaging system (QPi) optional fluorescence httpwwwtescancomenproductsq-phaseq-phase httpq-phasetescancom httpq-phasetescancomindexphptechnologyspecifications Ted Pella Inc ndash specialty light microscopy and electron microscopy supplies httpswwwtedpellacom Texas Instruments ndash DLP 4100 development kit (digital light processingrsquo DMD digital micromirror device) httpwwwticomtooldlpd4x00kit

ThorLabs ndash iCyte imaging cytometer multiphoton confocal EnVista digital slide scanning microscopes httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7473 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7494 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=5696 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=6570 TIRF Labs lightguide TIRF prism TIRF TIRF-Electrochemistry httpwwwtirf-labscom httpwwwtirf-labscomtechnologieshtml TissueVision - Serial Two Photon Tomography (image volume ablate imaged volume with multiphoton laser repeat) httpwwwtissuevisioncomtechnology Tokai Hit - stage top incubator httpwwwtokaihitcomenglishproduct_guidanceoptionhtml TopoNomos Ltd ndash Toponome Imaging Cycler ndash immunofluorescence (100plex) httpwwwtoposnomoscomtechnologyhtml Ultivue Inc ndash DNA-PAINT ndash reagents data processing service httpwwwultivuecom httpwwwultivuecomproducts UMech Technologies ndash Cytovar HCS up to 16 excitation wavelengths httpcloudumechcomproducts httpcloudumechcomproductsmodelC16 Visitech ndash vt-iSIM instant super-resolution microscopy up to 1000 frames per second confocal scanners and light engines httpwwwvisitechcoukvt-isimhtml httpwwwvisitechcoukproductshtml Visitron Systems GmbH - high speed imaging systems httpwwwvisitronde Visualsonics (Fujifilm) - photoacoustic imaging httpwwwvisualsonicscomproductstechnology-overview Wicked Lasers httpwwwwickedlaserscom httpwwwwickedlaserscomarctic WITec Wissenschaftliche Instrumente und Technologie GmbH - imaging systems for FLIM Raman AFM and SNOM analysis httpwitecdeproducts httpwwwwitec-instrumentscom WM Keck Center for Adaptive Optical Microscopy (CfAOM) at UC Santa Cruz httpscfaomsoeucscedu httpcfaoucolickorgpgallery Yokogawa Corp ndash spinning disk confocal scanner live cell imager high content screener confocal quantitative cytometer httpwwwyokogawacomsolutionsproducts-platformslife-science httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-scanner-unit-csu httpwwwyokogawacomsolutionsproducts-platformslife-scienceall-in-one-live-cell-imaging-solution httpwwwyokogawacomsolutionsproducts-platformslife-sciencehigh-throughput-cytological-discovery-system httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-quantitative-image-cytometer Zellkraftwerk (ChipCytometry) ndash immunofluorescence (80plex) httpwwwzellkraftwerkcomProducts2phtml httpwwwzellkraftwerkcomZKWOnephtmlSoftware

httpwwwchipcytometrycomtechnologyphtml Fluorescence Spectra Data and Graphing Sites PubSpectra ndash Excel file data download httpsworksbepresscomgmcnamara9 BD Biosciences ndash spectrum viewer Brilliant fluorophores httpwwwbdbiosciencescomussspectrumviewer httpwwwbdbiosciencescomusapplicationssspectrumguidepage BioLegend ndash spectra analyzer Brilliant Violet fluorophores httpwwwbiolegendcomspectraanalyzer httpwwwbiolegendcombrilliantviolet Chroma Technology httpswwwchromacomspectra-viewer eBioscience (Affymetrix ThermoFisher) ndash fluorPlan ndash a multi-laser spectra viewer httpwwwebiosciencecomresourcesfluorplan-spectra-viewerhtm Spectra Viewer (requires Java) Evrogen ndash Spectrum Viewer httpevrogencomspectra-viewerflashviewerhtml Fluorophoresorg ndash Fluorescent Substances httpwwwfluorophorestugrazatsubstance I Love GFP httpssitesgooglecomsiteilovegfpHomefps Lambert and Thorn UCSF Fluorescent protein properties httpnicucsfeduFPvisualization Leica Microsystem - ldquoFluoScoutrdquo httpwwwleica-microsystemscomfluoscout

Molecular Probes Invitrogen Thermo Fisher ndash Fluorescence SpectraViewer httpwwwthermofishercomusenhomelife-sciencecell-analysislabeling-chemistryfluorescence-spectraviewerhtml httpsitunesapplecomusappfluorescence-spectraviewerid421031826 (iTunes App) Nightsea - Compendium of spectra web sites httpwwwnightseacomsfa-sharingfluorescence-spectra-viewers Omega Optical ldquoCurvomatricrdquo httpswwwomegafilterscomcurvomatic

PhotoChemCAD 20 (Jonathan S Lindsey) dye spectra database and chemistry calculator NIRvana Sciences httpwwwphotochemcadcom httpnirvanasciencescompage_id=3088 UCSF (Lambert Thorn 2016) - Fluorescent protein properties httpnicucsfeduFPvisualization University of Arizona - Fluorescent Spectra Database httpwwwspectraarizonaedu Semrock - Searchlight httpssearchlightsemrockcom Spectroscopy Ninja ndash links to spectral and fluorescence data Spekwin32 spectroscopy software httpwwweffemm2deinfoinfo_specdatahtml

httpwwweffemm2deindexhtml Zeiss ndash interactive fluorescence dye and filter database overview dyes overview filter sets httpswwwmicro-shopzeisscoms=50479761ad21e5ampl=enampp=usampf=fampa=i httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=d httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=f Researcher Labs Alby Diaspro ndash IIT httpwwwlambsitindexphppage=People Alice Ting ndash MIT httpwwwtinglaborgresearch Allen Institute for Brain Science httpwwwalleninstituteorgwhat-we-dobrain-science Allen Institute for Cell Science httpwwwalleninstituteorgwhat-we-docell-science Amina Qutub - Rice University - How are human cells designed lab httpsqutublaborgqutub-lab Amy Herr UC Berkeley ndash Single cell Westerns httpherrlabberkeleyedu Amy Palmer ndash UC Boulder httpspalmerlabcoloradoedu Andrew York ndash Calico Life Sciences httpswwwcalicolabscomteam-memberandrew-york Anne Carpenter ndash Broad Institute CellProfiler httpspersonalbroadinstituteorganne Arjun Raj UPenn single molecule RNA FISH quantitative understanding cellular functions httprajlabseasupenneduindexhtml httpwwwpopscicomsciencearticle2013-09arjun-raj Atsuko Miyawaki - Laboratory for Cell Function Dynamics (CFDS) Fucci2 fluorescent proteins cell cycle indicator httpwwwbrainrikenjpenfacultydetails30 httpcfdsbrainrikenjp httpcfdsbrainrikenjpFuccihtml Aydogan Ozcan - UCLA - new imaging and sensing architectures httpinnovateeeuclaeduwelcomehtml httpwwwhhmiorgscientistsaydogan-ozcan Badri Roysam - UH - FARSIGHT Toolkit httpwwweeuhedufacultyroysam httpwwwfarsight-toolkitorgwikiMain_Page Brian J Ford ndash microscopist and popularizer httpsuklinkedincominprofbrianjford Carolyn Larabell ndashNational Center for X-ray Tomography (LBNL) UCSF httpncxtlblgovq=carolyn httpprofilesucsfeducarolynlarabell Clare Waterman ndash NHLBI NIH

httpswwwnhlbinihgovresearchintramuralresearcherspiwaterman-clare Dana Peer - Columbia University - Computational Systems Biology viSNE and more software httpwwwc2b2columbiaedudanapeerlabhtml httpwwwc2b2columbiaedudanapeerlabhtmlcythtml David Mayerich - UH - STIM Laboratory Scalable Tissue Imaging and Modeling httpwwweeuhedufacultymayerich httpstimeeuhedu David Piston WUSTL httpwwwcellbiologywustledufacultytenureddavid-w-piston-phd Diane Lidke and Keith Lidke - University of New Mexico httppathologyunmeduresearchfaculty-laboratoriesthe-lidke-laboratoryindexhtml httppanda3physunmedu~klidke Donna Arndt-Jovin and Thomas Jovin - Max Planck Institute for Biophysical Chemistry Laboratory of Cellular Dynamics httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsDonnaArdndt-JovinResearchAreasAndProjects httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsChairmanThomasJovinResearchAreasAndProjects Ed Boyden ndash MIT Media Lab ndash expansion microscopy (ExM) optogenetics httpsyntheticneurobiologyorg httpsyntheticneurobiologyorgprotocols httpsyntheticneurobiologyorgpublications httpwwwtedcomtalksed_boyden_baby_diapers_inspired_this_new_way_to_study_the_brain httpwwwextbiocombuycell Elizabeth Blackburn ndash Salk Institute - Telomeres httpswwwsalkeduscientistelizabeth-blackburn httpsenwikipediaorgwikiElizabeth_Blackburn httpswwwnobelprizeorgnobel_prizesmedicinelaureates2009blackburn-factshtml Elizabeth Hillman - Columbia university - SCAPE (Swept Confocally-Aligned Planar Excitation) high speed 3D microscopy DyCE (dynamic contrast enhancement to image and segment small animal organs live) Neuroimaging amp Neurovascular Coupling httporionbmecolumbiaedu~hillmanInstrumentationhtml httporionbmecolumbiaedu~hillmanSCAPEhtml httporionbmecolumbiaedu~hillmanMolecularhtml httporionbmecolumbiaedu~hillmanBrain_Imaginghtml Eric Betzig ndash UCSF (moving from HHMI Janelia Farm in 2016) httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014betzig-factshtml Eva Sevick-Muraca ndash UT Health Science Center at Houston molecular imaging clinical NIR fluoresceince imaging httpswwwutheduimmprofilehtmid=1005459 httpswwwutheduimmcentersmolecular-imaginghtm Evelin Schrock - Technische Universitaumlt Dresden spectral karyotyping cytogenetics httpswwwresearchgatenetprofileEvelin_Schrock Garry Nolan Stanford University ndash Mass cytometry MIBI-ToF high throughput imaging mass cytometry (42plex) httpwebstanfordedugroupnolanresourceshtml httpwebstanfordedugroupnolantechnologieshtml George McNamara ndash Cell Morphometry (41) Figure 1 right top two panels (55) The Chase (2016 temporal area maps lsquodynamic morphologyrsquo) (76) newsletter series on ldquoThe Chaserdquo (73) direct Vimeo movie of ldquoThe Chaserdquo Tiki_Goddess linkedin 10+plex blog httpsworksbepresscomgmcnamara41 httpsworksbepresscomgmcnamara55 httpsworksbepresscomgmcnamara76

httpsworksbepresscomgmcnamara73 httpsvimeocom175151196 httphomeearthlinknet~tiki_goddess httpswwwlinkedincomingeorgemcnamara httpswwwlinkedincompulsebd-biosciences-listed-tandems-horizon-brilliant-violets-mcnamara Gillian Griffiths - University of Cambridge - T-cell immunological synapse httpwwwcimrcamacukresearchprincipal-investigatorsprincipal-investigators-a-hgriffiths Hari Shroff NIBIB NIH httpswwwnibibnihgovlabs-at-nibibsection-high-resolution-optical-imaging-hroi HHMI Janelia Farm Research Campus (JFRC) - Advanced Imaging Center Open Science httpswwwjaneliaorgopen-scienceadvanced-imaging-center-aic httpswwwjaneliaorgopen-science Jeanne Lawrence University of Massachussetts Medical School httpwwwumassmededucellbiolabslawrencepersonnelprincipal-investigator Jennifer Lippincott-Schwartz ndash HHMI Janelia Farm httpswwwjaneliaorgpeoplejennifer-lippincott-schwartz Jin Zhang ndash UCSD httpprofilesucsdedujinzhang Joe DeRisi - UCSF - 3D printable lab stuff httpderisilabucsfeduindexphppage=3D John Russ Chris Russ Fovea Pro plugins for Adobe Photoshop httpwwwdrjohnrusscomindexhtml httpwwwdrjohnrusscombookshtml httpwwwreindeergraphicscomfoveaprotutorialhtml Julie Theriot httpcmgmstanfordedutheriot Karl Deisseroth ndash Stanford University ndash CLARITY optical tissue clearing Optogenetics httpclarityresourcecenterorg httpwebstanfordedugroupdlaboptogeneticsindexhtml Karsten Koumlnig (Koenig) - Saarland University and JenLab GmbH - biophotonics httpwwwbltuni-saarlanddeindex_ehtm httpwwwjenlabde httpwwwthelastescape-filmcom Karsten Rodenacker ndash image measurements httpkaro03bplacednetkaroMeMisc_WWWpdfMicrosoftWord-EQUAPATpdf Kevin Eliceiri ndash UW-Madison Open Source Photonics and Software Laboratory for Optical and Computational Instrumentation (LOCI) wwwlociwiscedu Klaus Kemp ndash Microlife Services ndash diatoms and other prepared microscope slides httpwwwdiatomscouk Kurt Thorn UCSF httpthornlabucsfedu httpsnicucsfedublog httpnicucsfeduFPvisualization httpgigapancomgigapans163370 Lihong Wang - WUSTL - Optical Imaging Laboratory photoacoustic tomography

httpoilabseaswustledu httpoilabseaswustleduresearch_0html Loren Looger - HHMI JFRC - iGluSnFr fluorescent protein biosensor httpswwwjaneliaorglablooger-lab Mary-Lou Pardue ndash MIT (first ever in situ hybridization with J Gall) httpsbiologymitedupeoplemary_lou_pardue httpsenwikipediaorgwikiMary-Lou_Pardue Nancy Allbritton - UNC - Chemical cytometry microraft arrays organ-on-a-chip httpswwwbmencsueduindexphpcomponentcomprofileruserprofilenlallbri httpwwwbmeuncedulabsallbritton Navin Varadarajan - UH - single-cell Lab httpwwwcheeuhedufacultyvaradarajan httpsinglecellcheeuheducontacthtml Nicholas Shaner - Scintillon Institute - mNeonGreen httpwwwscintillonorgshaner_lab Rebecca Richards-Kortum httpbioengineeringriceedufacultyrebecca_richards-kortumaspx Robert Campbell - Fluorescent proteins optogenetic proteins httpcampbellwebchemualbertaca httpcampbellwebchemualbertacaprojects-2 Robert Murphy ndash Cell measurements web services httpmurphylabwebcmueduservices Sabine Mai - University of Manitoba - Genomic Centre for Cancer Research and Diagnosis (GCCRD) - httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBPlatformsGCCRDhtml httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBScientistsMaiAwardshtml Sally Ward and Raimund Ober - Texas AampM University - httpwwwwardoberlabcom Simon Watkins - U Pittsburgh Center for Biologic Imaging httpwwwcbppittedufacultywatkinshtml httpwwwcbppittedufacultylabwatkinshtml httpwwwcbipittedu Stefan Hell ndash Deparment Hell NanoBiopohotonics httpwwwmpibpcmpgdehell httpsenwikipediaorgwikiStefan_Hell httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014hell-factshtml Sunney Xie Harvard httpsbernsteinharvardedu Susan Cox ndash 3B microscopy httpwwwcoxphysicscomindexhtml httpwwwcoxphysicscom3b Radim Chmeliacutek - Center for innovative microscopy Experimental biophotonics group httpswwwceiteceuceitec-butexperimental-biophotonicsrg3 httpwwwbiophotczhome Taekjip Ha ndash Johns Hopkins University ndash single molecules httphamedjhmiedu

Thomas Ried ndash NCI NIH SKYM-FISH and CGH Database httpsccrcancergovGenetics-Branchthomas-ried httpsccrcancergovGenetics-Branchthomas-riedqt-staff_profile_tabs=9qt-staff_profile_tabs ftpftpncbinlmnihgovsky-cghDATA httpswwwncbinlmnihgovdbvar Viviana Gradinaru ndash CalTech ndash CLARITYPACT Optogenetics httpwwwbbecaltecheducontentviviana-gradinaru httpglabcaltechedu Vladislav Verkhusha - near infrared fluorescent proteins httpwwweinsteinyuedulabsvlad-verkhushadefaultaspx httpwwweinsteinyueduresearchfacilitiesfluorescent WE Moerner ndash Stanford University httpwebstanfordedugroupmoerner Willard Wiggans ndash micro gallery httpwwwwillard-wigancomgallery Wolf Frommer ndash Molecular sensors httpbiosensordpbcarnegiescienceedu (fluorescent protein biosensors table) Xiaowei Zhuang = Harvard httpzhuangharvardedu Yuval Garini - Bar-Ilan University - Nano-Bio-Photonics laboratory httpgarinilabbiuacil Microscopy Magazines Imaging amp Microscopy httpwwwimaging-gitcommagazine Laser Focus World httpwwwlaserfocusworldcomindexhtml Microscopy amp Analysis httpwwwmicroscopy-analysiscom Microscopy Today httpwwwmicroscopy-todaycom Microscopy-UK httpwwwmicroscopy-ukorguk Photonics Spectra Biophotonics httpwwwphotonicscomPublicationsaspx The Microscope Journal httpmcriorgv72the-microscope-journal RMS Infocus Magazine httpwwwrmsorgukstudy-readinfocus-magazinehtml Nobel Prizes in Light Microscopy and Related Fields Chemistry 1925 colloids (light sheet) Zsigmondy (Siedentopf Zsigmondy 1902) httpswwwnobelprizeorgnobel_prizeschemistrylaureates1925

Chemistry 2000 conductive polymers Heeger MacDiarmid Shirakawa (Brilliant Violets Ultraviolets Blues) httpwwwnobelprizeorgnobel_prizeschemistrylaureates2000 Chemistry 2008 green fluorescent protein GFP Shimomura Chalfie Tsien httpwwwnobelprizeorgnobel_prizeschemistrylaureates2008 Chemistry 2014 super-resolved fluorescence microscopy Betzig Hell Moerner httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014 Physics 1953 Phase Contrast Zernike httpswwwnobelprizeorgnobel_prizesphysicslaureates1953 Physics 2009 invention of an imaging semiconductor circuit ndash the CCD sensor Kao Boyle Smith httpwwwnobelprizeorgnobel_prizesphysicslaureates2009 Physics 2014 efficient blue light emitting diodes Akasaki Amano Nakamura httpwwwnobelprizeorgnobel_prizesphysicslaureates2014 Physiology or Medicine 2006 Fire and Mello RNA interference ndash gene silencing by double stranded RNA httpwwwnobelprizeorgnobel_prizesmedicinelaureates2006 Physiology or Medicine 2006 Capecchi Evans Smithies specific gene modifications in mice by the use of embryonic stem cells httpwwwnobelprizeorgnobel_prizesmedicinelaureates2007 Physiology or Medicine 2009 Blackburn Greider Szostak how chromosomes are protected by telomeres and telomerase httpwwwnobelprizeorgnobel_prizesmedicinelaureates2009 Physiology or Medicine 2012 Gurdon Yamamanka matured cells can be reprogrammed to become pluripotent httpwwwnobelprizeorgnobel_prizesmedicinelaureates2012

Table 442 Fluorophores Photophysics Data

Fluorophore Abs or Ex max (nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Acridine orange 271 520 27000 020 5

Alexa Fluor 430 431 541 16000 055 9

Alexa Fluor 488 495 519 71000 094 67

Alexa Fluor 532 532 553 81000 080 65

Alexa Fluor 546 556 573 104000 096 100

Alexa Fluor 568 578 603 91300 075 69

Alexa Fluor 594 590 617 73000 064 47

Allophycocyanin (APC) 650 660 700000 068 476

Atto 390 390 479 24000 090 22

Atto 425 436 484 45000 065 29

Atto 430LS 433 547 32000 065 21

Atto 465 453 508 75000 075 56

Atto 490LS 496 661 40000 030 12

Atto 520 525 547 105000 095 100

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 7: McNamara 20161006 revised draft tables for CPHG Light ...

Integrated DNA Technologies (IDT) httpwwwidtdnacomsiteCatalogmodificationsdyes httpwwwidtdnacompagesproductsmodificationsfluorophoresfreedom-dyes httpwwwidtdnacomsiteCatalogModificationsCategory4 Jackson ImmunoResearch httpswwwjacksonimmunocom KPL (formerly Kirkegaard amp Perry Laboratories Inc) SeraCare httpwwwkplcom LGC Biosearch Technologies ndash dyes for oligonucleotides single molecular RNA FISH image gallery httpswwwbiosearchtechcomsupporteducationfluorophores-and-quenchers httpstellarisfishsmugmugcom httpsinglemoleculefishcom httpswwwbiosearchtechcomproductsrna-fish (typically 48 20 base oligonucleotides) Marker Gene Technologies Inc (MGT) httpwwwmarkergenecomfluorescent-reagent Miltenyi Biotec ndash REAfinity recombinant engineered antibodies (no Fc Receptor binding) FASER fluorescence amplification kits NiraWave fluorophores (indocyanine green formulations) httpwwwmiltenyibioteccomenproducts-and-servicesmacs-flow-cytometryreagentsantibodies-and-dyesrecombinant-antibodiesaspx httpwwwmiltenyibioteccomenproducts-and-servicesmacs-flow-cytometryreagentssupport-reagentsfaser-kitsaspx httpwwwmiltenyibioteccomenproducts-and-servicesviscover-imagingoptical-imagingaspx Molecular Probes Inc Invitrogen Thermo Fisher ndash largest vendor of fluorophores Molecular Probes Handbook (web resource) Tyramide Signal Amplification kits httpwwwprobescom httpswwwthermofishercomusenhomereferencesmolecular-probes-the-handbookhtml httpswwwthermofishercomusenhomereferencesmolecular-probes-the-handbooktablestyramide-signal-amplification-tsa-kitshtml NIRvana Sciences httpnirvanasciencescom httpnirvanasciencescompage_id=3088 One World Lab ndash antibody search httponeworldlabcomantibodies CytoCell Oxford Gene Technologies ndash DNA FISH probes human mouse pig chicken httpwwwcytocell-uscom Perkin Elmer ndash nucleotides labeling kits Tyramide Signal Amplification Kits (TSA) Opal 7plex discovery panel kit based on sequential TSA httpwwwperkinelmercomcategoryfluorescent-hapten-nucleotides httpwwwperkinelmercomcategoryfluorescent-agents-labeling-kits-dyes httpwwwperkinelmercomlab-solutionsresourcesdocsBRO_TSAsignalamplificationpdf httpwwwperkinelmercomproductopal-7-immunology-discovery-kit-op7ds1001kt

Rockland Inc httpwwwrockland-inccomcommerceindexjsp

TEFLabs ndash fluorescent ion indicators (Ca++ Cl- K+ Mg++ Na+ pH Zn++) ionophores fluorophores httpwwwteflabscomion-indicators Vector Laboratories Inc httpwwwvectorlabscom

Live cell imaging dishes and multi-well plates (ldquoglass bottom dishesrdquo)

We recommend these for simplified handing and processing vs either thick plastic dishesplates or having to handle loose coverslips with your valuable cells

Leicester Imaging Technologies (LITE) - University of Leicester - table of dishes for live cell imaging (our table has current links and bad links left out) httpwww2leacukcollegesmedbiopsychfacilities-and-servicescbsliteaiftips-and-tricks-1dishes-for-live-cell-imaging Bellco Glass Inc - glass flat bottom plate httpwwwbellcoglasscomnode1046 Bioptechs - interchangable coverslip dish ($036 per experiment) httpwwwbioptechscomproductinterchangeable-coverslip-dish Brooks Automation Inc - clar bottom optical imaging microplates httpwwwbrookscomproductslife-scienceconsumablesmatrical-microplates-microtubes-racks-lidsglass-bottom-optical-imaging-microplates Cell EampG - glass bottom cell sulture dishes plates httpcellegcomproducthtml Cellvis - glass bottom dishes and plates httpwwwcellviscom_35-mm-glass-bottom-dishes_products_by_categoryphpcat_id=3 Corning - glass bottom microplates httpcatalog2corningcomLifeSciencesen-USShoppingCategoryaspxcategoryname=Microplates20-202015(Lifesciences)|Assay20Microplates20-202015(Lifesciences) Design 1 Solutions - Custom microplates and fabrication services httpwwwdesign1solutionscomcustom-microplateshtml Eppendorf - cell imaging dishes imaging plates httpsonline-shopeppendorfcomOC-enCell-Culture-and-Imaging-Consumables-110320Cell-Imaging-Consumables-120210Eppendorf-Cell-Imaging-Dishes-PF-19457html httpsonline-shopeppendorfcomOC-enCell-Culture-and-Imaging-Consumables-110320Cell-Imaging-Consumables-120210Eppendorf-Cell-Imaging-Plates-PF-19458html Greiner Bio-One International - CellView glass bottom dishes quadrant dishes httpsshopgbocomenrowarticlescataloguearticle0110_0110_0040_002027513 ibidi - u-Plates glass bottom dishes microfluidic slides httpibidicomxtproductsenibidi-Labwarem-Plates httpibidicomxtproductsenibidi-Labware Matsunami Glass Ind Ltd httpwwwmatsunami-glasscojpenglishlifebiodata01html Mattek - glass bottom dishes and SBS plates httpswwwmattekcomstore-categoryculturewareglass-bottom-dishes Nunc - glass bottom dishes httpswwwthermofishercomordercatalogproduct150680 NEST Biotechnology Co Ltd Wuxi Jiangsu PRChina httpwwwnestscientificusacomproducts_detailproductId=31html PerkinElmer - glass bottom plates httpwwwperkinelmercomSECatalogCategoryIDMicroplates

Porvair Sciences - clear bottom assay plates httpwwwporvair-sciencescomenservices-menulife-sciencesclear-bottom-assay-plates Ted Pella Inc - glass bottom dishes clear wall or black wall (manufactured by WillCo Wells) httpswwwtedpellacomsection_html706dishhtm Warner Instruments (Harvard Apparatus) - culture dishes perfusion systems httpswwwwarneronlinecomproduct_cat_infocfmid=1322 Willco Wells - glass bottom dishes wwwwillcowellscom World Precision Instruments - Fluorodish glass bottom dishes httpswwwwpiinccomproductslaboratory-suppliesfd35-100-fluorodish-cell-culture-dish-35mm-23mm-well-pkg-of-100 Microscopes Microscopy Accessories (accessorize) Reagents Resources 3scan ndash knife edge scanning microscope (images slices repeats through specimen) httpwww3scancomdata-2 89North (affiliated with Chroma Technology Corp) httpwww89northcom Abberior Instruments ndash STED RESOLFT precision localization super-resolution microscopes STEDYCON convert any fluorescence microscope to STED httpabberior-instrumentscom httpabberior-instrumentscomproductscompact-lineabberior-stedy-con Acquifer ndash HIVE imaging machine (computer hardware) for high content screening big data httpswwwacquiferde Adobe Systems Inc httpwwwAdobecom httpscreativeadobecomproductsdownloadphotoshop Affymetrix eBioscience (ThermoFisher) - microarrays httpwwwaffymetrixcomestorebrowselevel_one_category_template_onejspparent=35796ampcategory=35796 httpwwwaffymetrixcomestorecatalog131547AFFYGeneChip26231743B+System+3000Dx+v22623423B1_1 Agilent Technologies ndash SureScan microarray scanner (array CGH microRNA SNPs CNV) httpwwwgenomicsagilentcomenMicroarray-Scanner-Processing-HardwareSureScan-Microarray-Scannercid=AG-PT-144 Andor Technology (Oxford Instruments) ndash sCMOS cameras Dragonfly spinning disk confocal Revolution DSD2 differential spinning disk confocal photostimulation (fluorescence recovery after photobleaching optogenetics) Mosaic3 DMDDLP high speed light patterning (optogenetics structured illumination) MicroPoint pulsed UV laser for ablation DNA damage photobleachingactivation uncaging accessories httpwwwandorcomscientific-camerasneo-and-zyla-scmos-cameras httpwwwandorcommicroscopy-systemsdragonfly httpwwwandorcommicroscopy-systemsrevolution-dsd httpwwwandorcommicroscopy-systemsphotostimulation httpwwwandorcommicroscopy-systemsphotostimulationmosaic httpwwwandorcommicroscopy-systemsphotostimulationmicropoint httpwwwandorcommicroscopy-systemsmicroscopy-components Apogee Instruments Inc (Andor Technology) ndash CCD cameras and filter wheels (mostly marketed for astronomy) httpwwwccdcomandorhtml Applied Scientific Instrumentation Inc ndash light sheet imager (iSPIM diSPIM)

wwwasiimagingcom httpwwwasiimagingcomindexphpproductslight-sheet-microscopyselective-plane-illumination-microscopy-ispim-dispim Applied NanoFluorescence LLC ndash NS1 NanoSpectralyzer (Raman and UV-VISNIR) NS MiniTracer near infrared spectrometer NFM NanoFluorescence microscope multi-laser light source single wall carbon nanotubes (NIR II fluorophores) httpappliednanocomproductshtml httpappliednanocomproductsns1html httpappliednanocomproductsproduct-list77-ns-minitracerhtml httpappliednanocomproductsnfmhtml httpappliednanocomproductsls-nhtml httpwwwnanowerkcomnewsnewsid=24132php Applied Spectral Imaging Inc httpwwwspectral-imagingcom ArgoLight ndash fluorescence resolution test target slides httpargolightcom AttoCube - attoMICROSCOPY overview attoCFM - Multichannel cryogenic (low temperature) confocal fluorescence microscopes 08 NA objective lenses 400-1000 nm spectral range httpwwwattocubecom httpwwwattocubecomattomicroscopyintroductiontab-2 httpwwwattocubecomattodownloads AutoQuant (Media Cybernetics) spatial deconvolution httpwwwmediacycomautoquantx3 Becker amp Hickl GmbH httpwwwbecker-hicklcomproductshtm Berkeley Lights Inc ndash manueuver into nanowells incubate recover 4000 single cells per chip httpswwwberkeleylightscomtechnology Bioaxial ndash Codim imaging conical diffraction beam shaper for super-resolution (4 sub-images) httpwwwbioaxialcomcodim-imaging Bioptechs - Live-Cell Micro-Observation Products httpwwwbioptechscom Bionumbers - database of useful biological numbers httpbionumbershmsharvardeduKeyNumbersaspx Biostatus ndash DRAQ5 DRAQ7 ApopTRAK CyTRAK Orange CyGel HypoxiTRAK httpwwwbiostatuscomProducts Bio-Tek ndash Cytation 3 Cell Imaging Multi-Mode Reader Lionheart FX Automated Live Cell Imager httpwwwbiotekcomproductsimagingcytation3_cell_imaging_multi_mode_readerhtml httpwwwbiotekcomproductsimaginglionheartfx_automated_live_cell_imagerhtml Biovision Technologies ndash distributor for several imagers including VT-iSIM instant super-resolution microscope httpbiovision-technologiescom httpbiovision-technologiescomsystemshtml httpbiovision-technologiescomvtisimhtml Bitplane (Andor Oxford Instruments) ndash Imaris imaging software httpwwwbitplanecom BMV Optical - custom lens assemblies and optical filters wwwbmvopticalcom

Bruker (previously Prairie Technologies Vutara) ndash Opterra confocal Ultima Multiphoton Vutara 352 single molecule localization microscopes httpswwwbrukercomproductsfluorescence-microscopesopterra-confocal-microscopyoverviewhtml httpswwwbrukercomproductsfluorescence-microscopesultima-multiphoton-microscopyhtml httpswwwbrukercomproductsfluorescence-microscopesvutara-super-resolution-microscopyoverviewhtml Cairn Research ndash standard and custom accessories ex Light Sheet Illuminator MultiCam (4 cameras) custom design httpswwwcairn-researchcouk httpswwwcairn-researchcoukproductl-spi-single-plane-illuminator (dual L-SPI for 4 illumination directions) httpswwwcairn-researchcoukproductmulticam httpswwwcairn-researchcoukcustom-design Cameca ndash NanoSIMS 50L (7plex stable isotope imaging) httpwwwcamecacominstruments-for-researchnanosimsaspx CellMic (formerly Holomic) - blood analysis or fluorescence imaging cytometer on a cell phone httpwwwcellmiccomcontentadvanced-technologies httpwwwcellmiccomcontentfluorescent-imaging-cytometry-and-e-coli-detection-on-a-cell-phone CellOptic ndash FINCH (Fresnel INcoherence Correlation Holography) httpwwwcellopticcomindex2html CellProfiler ndash High content screening (HCS) image processing and analysis software httpcellprofilerorg ClearLight Diagnostics - CLARITY Optimized Light Sheet Microscopy (3D tissue optical clearing + light sheet imaging) httpwwwclearlightdxcomindexhtml Confocalnl ndash Rescan confocal microscopy to obtain 170 nm resolution with any pinhole diameter httpwwwconfocalnl CoolLED ndash LED light sources httpwwwcoolledcomproduct-detailpe-4000 Crest Optics SRL ndash X-Light confocal X-Light V2 + VCS (VideoConfocal super-resolution) httpwwwcrestoptcom httpwwwcrestoptcomhtmlx-light_v2_vcshtml Cytoskeleton Inc - live cell imaging reagents Spirochrome SiR bioimaging probes httpwwwcytoskeletoncomlive-cell-reagents httpwwwcytoskeletoncomlive-cell-reagentsspirochrome CytoViva ndash darkfield imaging hypspectral imaging httpwwwcytovivacomproducts3d-enhanced-darkfield-imaging httpwwwcytovivacomproductshyperspectral-imaging-2hyperspectral-imaging Data Translation Inc - digitizer cards httpwwwdatxcom Delmic BV - combined correlative scanning electron microscope with inverted fluorescence microscope httpwwwdelmiccomdelphi httpswwwdelphimicroscopecom httpwwwdelmiccomsecom-super-resolution Digital Light Innovations (DLi) - CELscope C-mount LED Microscope using Texas Instruments DLP illuminator with a simple stand httpswwwdlinnovationscomdli-deep-dives-celscope-c-mount-led-microscope Double Helix LLC ndash single molecule localization microscope (Piestun) httpdoublehelixopticscom Edinburgh Super-resolution Imaging Consortium (ESRIC)

httpwwwesricorg Energetiq ndash Deep ultraviolet (DUV high radiance 170-2100 nm) laser driven light source (LDLS) httpwwwenergetiqcom Epi Technology - CaliCube - Cube for fluorescence light path to inspect epi Illumination light source (lamp) fiber optic or liquid light guide httpwwwepitechnologycomepitechnology-1 Essen Biosciences ndash Incucyte Zoom (imager inside incubator) httpwwwessenbiosciencecomenproductsincucyte Estigen Tissue Science ndash manual and automated tissue arrayer (tissue microarray maker) httpwwwestigencom Euro-Bioimaging httpwwweurobioimagingeu Excelitas Technologies (formerly Lumen Dynamics) ndash X-Cite LEDs httpwwwexcelitascomPagesProductX-Cite-LED-Solutionsaspx Expansion Technologies Inc (extbio) ndash Expansion microscopy httpwwwextbiocombuycell FEI (formerly Till Photonics) (Thermo Fisher) ndash correlative LM-EM single molecule Cryo-EM httpswwwfeicomlife-sciencescellular-biology httpswwwfeicomlife-sciencescellular-biologycorrelative-microscopy httpswwwfeicomlife-sciencesstructural-biology Femtonics - Multi-phton microscopes software accessories caged glutamate reagents services httpfemtonicseuproducts First Light Imaging ndash C-Red NIR imaging (800-2500 nm NIR windows I II III 650-950 nm 1100-1350 nm 1600-1870 nm[Shi et al 2015]) high speed visible EMCCD (400-1000 nm) httpwwwfirst-lightfrcategoryrangesinfrared Fluidigm ndash Helios imaging CyTOF mass cytometer (42plex) Callisto (32 independent chambers dose with up to 16 independent factors for 1-1000 cell populations culture up to 3 week) Polaris functional genomics meets imaging (48 single cells up to 24 hours after single cell selection from a population) httpswwwfluidigmcomproductshelios httpswwwfluidigmcomproductscallisto httpswwwfluidigmcomproductspolaris GattaQuant - nanorulers for high resolution microscopes and super-resolution microscopes performance testing httpwwwgattaquantcomNanoruler GE Healthcare life Sciences Applied Precision ndash DeltaVision deconvolution OMX OMX SR httpwwwgelifesciencescomwebappwcsstoresservletproductByIdenGELifeSciences-us29065728 httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usproductsAlternativeProductStructure_2380729065721 httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usproductsAlternativeProductStructure_2380729115476 German BioImagingorg httpwwwgermanbioimagingorgwikiindexphpMain_Page httpwwwgermanbioimagingorgwikiindexphpWorkgroup6SoftwarePackages GIGAmacro ndash Magnify2 gigapixel imagery oof macroscopic and microscopic objects Terapixel macro image httpwwwgigamacrocomgigapixel-macro-imaging-system httpwwwgigamacrocomworlds-first-terapixel-macro-image

Glencoe Software ndash OMERO Plus enterprise data management for scientific images and any associated metadata (OME = Open Microscopy Environment) DataViewer PathViewer httpsglencoesoftwarecomomeroplushtml httpsglencoesoftwarecomdataviewerhtml httpsglencoesoftwarecompathviewerhtml Gooch amp Housego ndash spectral imager httpsgoochandhousegocomminiature-spectral-imaging-camera httpwwwghinstrumentscomproductsspectral-imaging-synthesishsi-440c-hyperspectral-imaging-system Hindsight Imaging ndash spectral imaging httphindsight-imagingcom Horiba Scientific - SWIFT ultra-fast Raman confocal imaging Raman spectroscopy httpwwwhoribacomscientificproductsraman-spectroscopyraman-imagingswift httpwwwhoribacomscientificproductsraman-spectroscopyraman-imaging httpwwwhoribacomscientificproductsraman-spectroscopy IATIA Ultima Capital ndash QPm (quantitative phase microscopy) httpwwwultimacapitalnetiatiaimagingPublicationsIatia20ImagingapplicationNotesqpmApplicationWithConfocalMicroscopespdf Ibidi - heating and incubation systems optical O2 measurement systems Nanolive 3D Cell Explorer pump system gas incubation system httpibidicomxtproductsenInstruments-AccessoriesHeating-Incubation-Systems httpibidicomxtproductsenInstruments-Accessoriesibidi-OPAL-Optical-O2-Measurement-System httpibidicomxtproductsenInstruments-AccessoriesNanolive-3D-Cell-Explorer httpibidicomxtproductsenInstruments-Accessoriesibidi-Pump-System httpibidicomxtproductsenInstruments-AccessoriesHeating-Incubation-Systemsibidi-Gas-Incubation-System iLAbSolutions (Agilent Technologies) - Instrument management and scheduling software (cores and labs) httpwwwilabsolutionscominstrument-access-control ImageJ - Fiji ImageJ NIH ImageJ ImageJ ndash Fiji (Fiji is just ImageJ) is the main download site httpfijisc httpsimagejnihgovij wwwimagejnet Inscopix ndash nVista in vivo mouse brain imaging miniature microscope httpswwwinscopixcomproducts Intelligent Imaging Innovations Inc (3i) ndash Slidebook imaging software Lattice light sheet (high speed gentle to cells high resolution imaging) Dual-view Inverted Selective Plane Illumination (diSPIM) VIVO 2-Photon (VIVO 2P) multiphoton microscopy Everest intravital imaging Marianas 3D real-time deconvolution timelapse spinning disk FRAP TIRF FLIM single molecule environmental control Phasor - optogenetic photostimulation using digital holography Yokogawa spinning disk confocal units wwwintelligent-imagingcom httpswwwintelligent-imagingcomslidebookphp httpswwwintelligent-imagingcomsystemsphplattice httpswwwintelligent-imagingcomsystemsphpdispim httpswwwintelligent-imagingcomsystemsphptwophoton httpswwwintelligent-imagingcomsystemsphpeverest httpswwwintelligent-imagingcomsystemsphpmarianas httpswwwintelligent-imagingcomoptogeneticsphp httpswwwintelligent-imagingcomsdcphp ISS Inc ndash fluorescence lifetime imaging microscopy fluorescence correlation spectroscopy (FCS) confocal imaging httpwwwisscommicroscopyindexhtml JenLab GmbH cyto-microscopy multiphoton tomography httpwwwjenlabdeproducts250html httpwwwjenlabde2PM-Cryo1330html

httpwwwjenlabdeMultiphoton-Tomography680html Jenoptik - microscope cameras httpswwwjenoptikcomproductscameras-and-imaging-modulesmicroscope-cameras JPK Instruments - integrated atomic force microscope (AFM) force sensing optical tweezers optical trapping single cell force spectroscopy (SCFS) httpwwwjpkcomindex2enhtml httpusajpkcomoptical-tweezers-optical-trapping29ushtml httpusajpkcomcellular-adhesion-cytomechanics30ushtml Keyence ndash VK-X confocal (upright) BZ-X700 widefield (inverted) httpwwwkeyencecomssproductsmicroscopevkx httpwwwkeyencecomssproductsmicroscopebz-x700indexjsp KK Technology - CapiScope HVCS Handheld Video Capillaroscopy System (CytoScan) httpwwwkktechnologycomhvcshtml LaVision BioTec ndash TriMscope Multiphoton TriM Scope II Adaptive Optics UltraMicroscope II light sheet httpwwwlavisionbiotecde httpwwwlavisionbiotecdetrim-scope-overviewhtml httpwwwlavisionbiotecdetrim-scope-ii-adaptive-opticshtml httpwwwlavisionbiotecdeultramicroscope-ii-introductionhtml Laxco ndash upright and inverted microscopes httpwwwlaxcoinccomMICROSCOPES Lego ndash Lego Idea Microscopes httpsideaslegocomprojects44370 httpwwwnico71frlego-working-microscope Li-Cor ndash near-infared fluorescent dyes and in vivo imaging agents in vivo and Western blot imaging systems httpswwwlicorcombioproductsreagents httpswwwlicorcombioproductsreagentsirdyebrightsite_imaging_agents httpswwwlicorcombioproductsimaging_systemsodyssey_familyhtml httpswwwlicorcombioproductsimaging_systemspearl httpswwwlicorcombioproductsimaging_systemscdigit Life Imaging Services - ldquothe Ludin chamberrsquo ldquothe cube amp the boxrdquo httpwwwlischthechamberhtml httpwwwlischtheboxhtml Lightform Inc ndash PARISS imaging spectrometer httplightforminccom LMU Bioimaging httpwwwbioimagingbmcmeduni-muenchendelinkswebsitesindexhtml httpwwwbioimagingbmcmeduni-muenchendelearneduwebsitesindexhtml Ludl Electronic Products Ltd ndash automated XY stages focus motors filter wheels httpwwwludlcom

LumaCyte ndash Laser force Cytology (laser trap meets microfluidics to suspend and manipulate single cells) httpwwwlumacytecomabouttechnology Lumencor ndash LEDs fluorescence light sources httplumencorcomproducts Luxcel ndash mitochondrial and cellular functions O2 sensor reagents httpluxcelcomproduct+list Luxendo GmbH ndash light sheet imager

wwwluxendoeu Lyncee tec - digital holography microscopy (DHM) high content screening by DHM httpwwwlynceeteccom httpwwwlynceeteccomhigh-content-screening Mad City Labs Inc - nanopositioning wwwmadcitylabscom Mauna Kea Technologies ndash CellVizio confocal laser endomicroscopy httpwwwmaunakeatechcomenhealthcare-professionalscellvizio-endomicroscopy-0 MBF Bioscience - stereology and neuron morphology quantitative imaging httpwwwmbfbiosciencecom McCrone Group wwwmccronecominstrument-sales Media Cybernetics Inc ndash Image Premier 3D AutoQuant X3 deconvolution httpwwwmediacycom Meiji Techno America wwwmeijitechnocom MesoLens Ltd httpwwwmesolenscomproducttechnical-specifications httpwwwmesolenscomimages httpswwwbiophotonicsstrathacukresearch_1htm Meyer Instruments ndash Pathscan Enabler GigaMacro digital pathology telepathology httpmeyerinstcom httpmeyerinstcompathscan-enabler-5 httpmeyerinstcomgigamacro-gigapixel-macro-imaging httpmeyerinstcomhomescanners httprealtimetelepathologycom Microarrays - Large-Scale Gene Expression and Microarray Links and Resources httpswwwebiacukarrayexpress Micro-Manager ndash Device Support ndash tabulates many microscope cameras and motorized accessories every new camera and accessory should have a uManager driver to enable simple use with Fiji ImageJ httpsmicro-managerorg httpsmicro-managerorgwikiDevice_Support httpsopen-imagingcom Microvolution ndash (near) instant gratification spatial deconvolution using NVidia GPU card(s) httpmicrovolutioncom Mightex Systems ndash optogenetics DMDDLP illuminator (digital micro-mirror device digital light processing) httpwwwmightexsystemscomindexphpcPath=245 Millipore-Sigma Merck KGaA (Amnis Corp CellASIC EMD Millipore) ndash ImageStreamX and FlowSight imaging flow cytometers ONIX2 Microperfusion System for microscopes httpswwwemdmilliporecom httpswwwemdmilliporecomUSenlife-science-researchcell-analysisamnis-imaging-flow-cytometersQ6ubqBm3UAAAFLCKIpygJnav httpwwwemdmilliporecomUSenlife-science-researchcell-culture-systemscellASIC-live-cell-analysisd1CbqBw58AAAE_0j13MnAnav Mitutoyo America Corp wwwmitutoyocom httpecatalogmitutoyocomMF-U-Series-176-High-power-Multi-function-Measuring-Microscopes-C1413aspx

Molecular Devices Corporation Universal Imaging Corporation (Danaher) ndash MetaMorph MetaFluor high content systems (HCS) httpswwwmoleculardevicescomsystemsmetamorph-research-imaging httpmdccusthelpcomappanswersdetaila_id19319 httpswwwmoleculardevicescomsystemshigh-content-imaging Molecular Machines amp Industries - laser microdissection and tweezer systems httpwwwmolecular-machinescomhome MUSE Microscopy Inc ndash Deep UV illumination for shallow depth of field imaging httpwwwmusemicrocom Micro Video Instruments Inc - DarkLite illuminator httpwwwmvi-inccom NanoEnTek ndash JuLI Stage (imager inside incubator or on lab bench) httpwwwjulistagecom National Instruments ndash LabView software httpwwwnicomen-ushtml Navitar - Hoffman Modulation Contrast (HMC alternative to differential interference contrast phase contrast) custom lens design UVDUVNUV imaging lenses httpsnavitarcommarketsmicroscopy httpsnavitarcomproductsimaging-opticscustom-microscope-objectivescustom-microscope-objectives httpsnavitarcomproductsimaging-opticsuv-imaging National Center for X-ray Tomography (NCXT) ndash soft X-ray tomography (CT of hydrated cells) XM-2 dedicated biological SXT microscope Prof Carolyn Larabell Director (see also SiriusXT) httpncxtlblgov httpncxtlblgovsxt httpncxtlblgovmanual httpncxtlblgovq=carolyn Neogenomics (Clarient) ndash MultiOmyx immunofluorescence or DNA FISH (ldquo60plexrdquo) httpneogenomicscomPharma-ServicesLab-ServicesMultiOmyxTechnologyMultiOmyx-IF-Assay-DNA-FISH-assay-NGS-from-ROI Nexcelom ndash Celigo imaging cytometer Cellometer cell counters httpwwwnexcelomcomCeligoindexphp httpwwwnexcelomcomProducts Nikon ndash Ti-LAPP modular illumination system (for Nikon Ti series microscopes) TIRF Optogenetics httpswwwnikoninstrumentscomProductsPhotostimulation-and-TIRFTi-LAPP Nirmidas Biotech httpwwwnirmidascomtechnologynir httpwwwnirmidascomproductsniriidye NVidia ndash Pascal 10+ Gbps GPU cards for instant gratification deconvolution (software from Microvolutioncom SVInl) httpwwwgeforcecomhardware10seriesgeforce-gtx-1080 httpwwwgeforcecomhardware10seriestitan-x-pascal httpwwwnvidiacomobjectquadro-graphics-with-pascalhtml Ocean Optics ndash spectrometers httpoceanopticscomproduct-categorymodular-spectrometers Oko-Lab stage top incubator httpwwwoko-labcomstage-top Open Microscopy Environment (OME) ndash OMERO (see also Glencoe Software) Bio-Formats LOCI

httpswwwopenmicroscopyorgsite httpswwwopenmicroscopyorgsiteproductsomero httpswwwopenmicroscopyorgsiteproductsbio-formats httpswwwopenmicroscopyorgsitesupportbio-formats52supported-formatshtml httpswwwopenmicroscopyorgsiteaboutdevelopment-teamskevin OpenSPIM ndash do-it-yourself selective plane illumination microscopy (light sheet imaging) httpopenspimorgWelcome_to_the_OpenSPIM_Wiki OpenSpinMicroscopy ndash do-it-yourself SPIMDSLMOPT microscopes httpssitesgooglecomsiteopenspinmicroscopy Ovizio ndash differential digital holography (similar to quantitative phase imaging) httpwwwoviziocomenHome httpwwwoviziocomenMicroscopesQMod Oxford Gene Technologies ndash microarrays ndash cytogenetics molecule genetics cancer research pre-implantation genetic diagnosis httpwwwogtcomclinical_genetics Oxford Nanoimaging ndash single molecule(s) localization fluorescence resonance energy transfer (FRET) (Kapanidis) wwwoxfordnicom Pathology Devices ndash LiveCell stage top incubator amp controller tissue microarrayers (TMA makers) httpwwwpathologydevicescomLiveCellhtm httpwwwpathologydevicescomTMArrayerhtm PeCon GmbH ndash microscope incubators httpwwwpeconbiz Pembroke Instruments ndash spectrometers mini-lasers httppembrokeinstrumentscomqmini-spectrometer httppembrokeinstrumentscommini-lasers PerkinElmer ndash in vivo imaging systems (bioluminescence NIR fluorescence) Vectra digital slide scanner httpwwwperkinelmercomcategoryin-vivo-imaging-instruments httpwwwperkinelmercomcategoryquantitative-pathology-imaging-instruments Phi Optics ndash CellVista SLIM Pro (quantitative phase microscopy) httpphiopticscom Photometrics (Roper Scientific) ndash DualView QuadView httpwwwphotometricscom httpwwwphotometricscomproductsmultichannel Photon Technology International httpwwwpti-njcomindexhtml

PicoQuant GmbH ndash fluorescence lifetime imaging microscopes (FLIM) STED 3D-EasySTED httpswwwpicoquantcomproductscategoryfluorescence-microscopes httpswwwpicoquantcomapplicationscategorylife-sciencested httpwwweasystedorg Physik Instrumente GmbH amp Co KG (PI) - Nanopositioning Applications for Microscopy Neuroscience and Metrology httpswwwphysikinstrumentecomen httpwwwpi-usausindexphp PreSens Prescision Sensing GmbH - VisiSens measure and visualize Oxygen pH or carbon dioxide distributions httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-biological-researchhtml httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-life-science-researchhtml Prior Scientific

httpwwwprior-uscom Profusa Inc - Lumee tissue-integrated biosensors scaffolds httpprofusacomtechnology Reindeer Graphics Inc ndash OptiPix Fovea Pro 9plugins for Adobe Photoshop 6 and CS series) httpwwwreindeergraphicscom Renishaw - StreamLine fast chemical imaging Raman spectroscopy httpwwwrenishawcomenstreamline-generate-chemical-images-rapidly--9449 httpwwwrenishawcomenraman-spectroscopy--6150 Sanford Burnham Prebys ndash High Content Screening httpwwwsbpdiscoveryorgtechnologysrPagesLaJolla_HighContentScreeningaspx ScopeM - Scientific Center for Optical and Electron Microscopy - ETH Zurich httpwwwscopemethzch SiriusXT - soft X-ray tomography (SXT) microscope (CT scan hydrated cell) httpsiriusxtcom SpectraGenetics - Fluorogen Activating Peptides (FAPs) new genetically encoded ldquobinaryrdquo reporters httpspectrageneticscomproductsvectors-for-expressing-fluorogen-activating-proteinsfap-technology-overview Spirochrome - Silicon Rhodamine (SiR) and other fluorescent reagents probes for bioimaging httpspirochromecom Stanford Photonics Inc httpwwwstanfordphotonicscom httpwwwstanfordphotonicscomLife20SciencesLifeScihtm

Stream Technologies Inc ndash ColorFlow lens (multi-wavelength emission onto a camera) httpwwwstreamtechinccomproducts Sutter Instrument Company httpwwwsuttercom httpwwwsuttercomMICROSCOPESindexhtml httpwwwsuttercomIMAGINGindexhtml SVI Huygens ndash Professional (general image analysis) deconvolution NVidia GPU deconvolution httpssvinlHuygensProfessional httpssvinlHuygensDeconvolution httpssvinlHuygensGPU Sysmex Partex ndash CyScope httpwwwsysmex-parteccomproductsmicroscopyhtml httpwwwsysmex-parteccomproductsprdouct-detailviewcyscopeR-malaria-3238html Technical Instruments httpwwwtechinstcomproductsphp TESCAN Brno sro - Tescan Q-PHASE multimodal holographic quantitative phase imaging system (QPi) optional fluorescence httpwwwtescancomenproductsq-phaseq-phase httpq-phasetescancom httpq-phasetescancomindexphptechnologyspecifications Ted Pella Inc ndash specialty light microscopy and electron microscopy supplies httpswwwtedpellacom Texas Instruments ndash DLP 4100 development kit (digital light processingrsquo DMD digital micromirror device) httpwwwticomtooldlpd4x00kit

ThorLabs ndash iCyte imaging cytometer multiphoton confocal EnVista digital slide scanning microscopes httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7473 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7494 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=5696 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=6570 TIRF Labs lightguide TIRF prism TIRF TIRF-Electrochemistry httpwwwtirf-labscom httpwwwtirf-labscomtechnologieshtml TissueVision - Serial Two Photon Tomography (image volume ablate imaged volume with multiphoton laser repeat) httpwwwtissuevisioncomtechnology Tokai Hit - stage top incubator httpwwwtokaihitcomenglishproduct_guidanceoptionhtml TopoNomos Ltd ndash Toponome Imaging Cycler ndash immunofluorescence (100plex) httpwwwtoposnomoscomtechnologyhtml Ultivue Inc ndash DNA-PAINT ndash reagents data processing service httpwwwultivuecom httpwwwultivuecomproducts UMech Technologies ndash Cytovar HCS up to 16 excitation wavelengths httpcloudumechcomproducts httpcloudumechcomproductsmodelC16 Visitech ndash vt-iSIM instant super-resolution microscopy up to 1000 frames per second confocal scanners and light engines httpwwwvisitechcoukvt-isimhtml httpwwwvisitechcoukproductshtml Visitron Systems GmbH - high speed imaging systems httpwwwvisitronde Visualsonics (Fujifilm) - photoacoustic imaging httpwwwvisualsonicscomproductstechnology-overview Wicked Lasers httpwwwwickedlaserscom httpwwwwickedlaserscomarctic WITec Wissenschaftliche Instrumente und Technologie GmbH - imaging systems for FLIM Raman AFM and SNOM analysis httpwitecdeproducts httpwwwwitec-instrumentscom WM Keck Center for Adaptive Optical Microscopy (CfAOM) at UC Santa Cruz httpscfaomsoeucscedu httpcfaoucolickorgpgallery Yokogawa Corp ndash spinning disk confocal scanner live cell imager high content screener confocal quantitative cytometer httpwwwyokogawacomsolutionsproducts-platformslife-science httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-scanner-unit-csu httpwwwyokogawacomsolutionsproducts-platformslife-scienceall-in-one-live-cell-imaging-solution httpwwwyokogawacomsolutionsproducts-platformslife-sciencehigh-throughput-cytological-discovery-system httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-quantitative-image-cytometer Zellkraftwerk (ChipCytometry) ndash immunofluorescence (80plex) httpwwwzellkraftwerkcomProducts2phtml httpwwwzellkraftwerkcomZKWOnephtmlSoftware

httpwwwchipcytometrycomtechnologyphtml Fluorescence Spectra Data and Graphing Sites PubSpectra ndash Excel file data download httpsworksbepresscomgmcnamara9 BD Biosciences ndash spectrum viewer Brilliant fluorophores httpwwwbdbiosciencescomussspectrumviewer httpwwwbdbiosciencescomusapplicationssspectrumguidepage BioLegend ndash spectra analyzer Brilliant Violet fluorophores httpwwwbiolegendcomspectraanalyzer httpwwwbiolegendcombrilliantviolet Chroma Technology httpswwwchromacomspectra-viewer eBioscience (Affymetrix ThermoFisher) ndash fluorPlan ndash a multi-laser spectra viewer httpwwwebiosciencecomresourcesfluorplan-spectra-viewerhtm Spectra Viewer (requires Java) Evrogen ndash Spectrum Viewer httpevrogencomspectra-viewerflashviewerhtml Fluorophoresorg ndash Fluorescent Substances httpwwwfluorophorestugrazatsubstance I Love GFP httpssitesgooglecomsiteilovegfpHomefps Lambert and Thorn UCSF Fluorescent protein properties httpnicucsfeduFPvisualization Leica Microsystem - ldquoFluoScoutrdquo httpwwwleica-microsystemscomfluoscout

Molecular Probes Invitrogen Thermo Fisher ndash Fluorescence SpectraViewer httpwwwthermofishercomusenhomelife-sciencecell-analysislabeling-chemistryfluorescence-spectraviewerhtml httpsitunesapplecomusappfluorescence-spectraviewerid421031826 (iTunes App) Nightsea - Compendium of spectra web sites httpwwwnightseacomsfa-sharingfluorescence-spectra-viewers Omega Optical ldquoCurvomatricrdquo httpswwwomegafilterscomcurvomatic

PhotoChemCAD 20 (Jonathan S Lindsey) dye spectra database and chemistry calculator NIRvana Sciences httpwwwphotochemcadcom httpnirvanasciencescompage_id=3088 UCSF (Lambert Thorn 2016) - Fluorescent protein properties httpnicucsfeduFPvisualization University of Arizona - Fluorescent Spectra Database httpwwwspectraarizonaedu Semrock - Searchlight httpssearchlightsemrockcom Spectroscopy Ninja ndash links to spectral and fluorescence data Spekwin32 spectroscopy software httpwwweffemm2deinfoinfo_specdatahtml

httpwwweffemm2deindexhtml Zeiss ndash interactive fluorescence dye and filter database overview dyes overview filter sets httpswwwmicro-shopzeisscoms=50479761ad21e5ampl=enampp=usampf=fampa=i httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=d httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=f Researcher Labs Alby Diaspro ndash IIT httpwwwlambsitindexphppage=People Alice Ting ndash MIT httpwwwtinglaborgresearch Allen Institute for Brain Science httpwwwalleninstituteorgwhat-we-dobrain-science Allen Institute for Cell Science httpwwwalleninstituteorgwhat-we-docell-science Amina Qutub - Rice University - How are human cells designed lab httpsqutublaborgqutub-lab Amy Herr UC Berkeley ndash Single cell Westerns httpherrlabberkeleyedu Amy Palmer ndash UC Boulder httpspalmerlabcoloradoedu Andrew York ndash Calico Life Sciences httpswwwcalicolabscomteam-memberandrew-york Anne Carpenter ndash Broad Institute CellProfiler httpspersonalbroadinstituteorganne Arjun Raj UPenn single molecule RNA FISH quantitative understanding cellular functions httprajlabseasupenneduindexhtml httpwwwpopscicomsciencearticle2013-09arjun-raj Atsuko Miyawaki - Laboratory for Cell Function Dynamics (CFDS) Fucci2 fluorescent proteins cell cycle indicator httpwwwbrainrikenjpenfacultydetails30 httpcfdsbrainrikenjp httpcfdsbrainrikenjpFuccihtml Aydogan Ozcan - UCLA - new imaging and sensing architectures httpinnovateeeuclaeduwelcomehtml httpwwwhhmiorgscientistsaydogan-ozcan Badri Roysam - UH - FARSIGHT Toolkit httpwwweeuhedufacultyroysam httpwwwfarsight-toolkitorgwikiMain_Page Brian J Ford ndash microscopist and popularizer httpsuklinkedincominprofbrianjford Carolyn Larabell ndashNational Center for X-ray Tomography (LBNL) UCSF httpncxtlblgovq=carolyn httpprofilesucsfeducarolynlarabell Clare Waterman ndash NHLBI NIH

httpswwwnhlbinihgovresearchintramuralresearcherspiwaterman-clare Dana Peer - Columbia University - Computational Systems Biology viSNE and more software httpwwwc2b2columbiaedudanapeerlabhtml httpwwwc2b2columbiaedudanapeerlabhtmlcythtml David Mayerich - UH - STIM Laboratory Scalable Tissue Imaging and Modeling httpwwweeuhedufacultymayerich httpstimeeuhedu David Piston WUSTL httpwwwcellbiologywustledufacultytenureddavid-w-piston-phd Diane Lidke and Keith Lidke - University of New Mexico httppathologyunmeduresearchfaculty-laboratoriesthe-lidke-laboratoryindexhtml httppanda3physunmedu~klidke Donna Arndt-Jovin and Thomas Jovin - Max Planck Institute for Biophysical Chemistry Laboratory of Cellular Dynamics httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsDonnaArdndt-JovinResearchAreasAndProjects httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsChairmanThomasJovinResearchAreasAndProjects Ed Boyden ndash MIT Media Lab ndash expansion microscopy (ExM) optogenetics httpsyntheticneurobiologyorg httpsyntheticneurobiologyorgprotocols httpsyntheticneurobiologyorgpublications httpwwwtedcomtalksed_boyden_baby_diapers_inspired_this_new_way_to_study_the_brain httpwwwextbiocombuycell Elizabeth Blackburn ndash Salk Institute - Telomeres httpswwwsalkeduscientistelizabeth-blackburn httpsenwikipediaorgwikiElizabeth_Blackburn httpswwwnobelprizeorgnobel_prizesmedicinelaureates2009blackburn-factshtml Elizabeth Hillman - Columbia university - SCAPE (Swept Confocally-Aligned Planar Excitation) high speed 3D microscopy DyCE (dynamic contrast enhancement to image and segment small animal organs live) Neuroimaging amp Neurovascular Coupling httporionbmecolumbiaedu~hillmanInstrumentationhtml httporionbmecolumbiaedu~hillmanSCAPEhtml httporionbmecolumbiaedu~hillmanMolecularhtml httporionbmecolumbiaedu~hillmanBrain_Imaginghtml Eric Betzig ndash UCSF (moving from HHMI Janelia Farm in 2016) httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014betzig-factshtml Eva Sevick-Muraca ndash UT Health Science Center at Houston molecular imaging clinical NIR fluoresceince imaging httpswwwutheduimmprofilehtmid=1005459 httpswwwutheduimmcentersmolecular-imaginghtm Evelin Schrock - Technische Universitaumlt Dresden spectral karyotyping cytogenetics httpswwwresearchgatenetprofileEvelin_Schrock Garry Nolan Stanford University ndash Mass cytometry MIBI-ToF high throughput imaging mass cytometry (42plex) httpwebstanfordedugroupnolanresourceshtml httpwebstanfordedugroupnolantechnologieshtml George McNamara ndash Cell Morphometry (41) Figure 1 right top two panels (55) The Chase (2016 temporal area maps lsquodynamic morphologyrsquo) (76) newsletter series on ldquoThe Chaserdquo (73) direct Vimeo movie of ldquoThe Chaserdquo Tiki_Goddess linkedin 10+plex blog httpsworksbepresscomgmcnamara41 httpsworksbepresscomgmcnamara55 httpsworksbepresscomgmcnamara76

httpsworksbepresscomgmcnamara73 httpsvimeocom175151196 httphomeearthlinknet~tiki_goddess httpswwwlinkedincomingeorgemcnamara httpswwwlinkedincompulsebd-biosciences-listed-tandems-horizon-brilliant-violets-mcnamara Gillian Griffiths - University of Cambridge - T-cell immunological synapse httpwwwcimrcamacukresearchprincipal-investigatorsprincipal-investigators-a-hgriffiths Hari Shroff NIBIB NIH httpswwwnibibnihgovlabs-at-nibibsection-high-resolution-optical-imaging-hroi HHMI Janelia Farm Research Campus (JFRC) - Advanced Imaging Center Open Science httpswwwjaneliaorgopen-scienceadvanced-imaging-center-aic httpswwwjaneliaorgopen-science Jeanne Lawrence University of Massachussetts Medical School httpwwwumassmededucellbiolabslawrencepersonnelprincipal-investigator Jennifer Lippincott-Schwartz ndash HHMI Janelia Farm httpswwwjaneliaorgpeoplejennifer-lippincott-schwartz Jin Zhang ndash UCSD httpprofilesucsdedujinzhang Joe DeRisi - UCSF - 3D printable lab stuff httpderisilabucsfeduindexphppage=3D John Russ Chris Russ Fovea Pro plugins for Adobe Photoshop httpwwwdrjohnrusscomindexhtml httpwwwdrjohnrusscombookshtml httpwwwreindeergraphicscomfoveaprotutorialhtml Julie Theriot httpcmgmstanfordedutheriot Karl Deisseroth ndash Stanford University ndash CLARITY optical tissue clearing Optogenetics httpclarityresourcecenterorg httpwebstanfordedugroupdlaboptogeneticsindexhtml Karsten Koumlnig (Koenig) - Saarland University and JenLab GmbH - biophotonics httpwwwbltuni-saarlanddeindex_ehtm httpwwwjenlabde httpwwwthelastescape-filmcom Karsten Rodenacker ndash image measurements httpkaro03bplacednetkaroMeMisc_WWWpdfMicrosoftWord-EQUAPATpdf Kevin Eliceiri ndash UW-Madison Open Source Photonics and Software Laboratory for Optical and Computational Instrumentation (LOCI) wwwlociwiscedu Klaus Kemp ndash Microlife Services ndash diatoms and other prepared microscope slides httpwwwdiatomscouk Kurt Thorn UCSF httpthornlabucsfedu httpsnicucsfedublog httpnicucsfeduFPvisualization httpgigapancomgigapans163370 Lihong Wang - WUSTL - Optical Imaging Laboratory photoacoustic tomography

httpoilabseaswustledu httpoilabseaswustleduresearch_0html Loren Looger - HHMI JFRC - iGluSnFr fluorescent protein biosensor httpswwwjaneliaorglablooger-lab Mary-Lou Pardue ndash MIT (first ever in situ hybridization with J Gall) httpsbiologymitedupeoplemary_lou_pardue httpsenwikipediaorgwikiMary-Lou_Pardue Nancy Allbritton - UNC - Chemical cytometry microraft arrays organ-on-a-chip httpswwwbmencsueduindexphpcomponentcomprofileruserprofilenlallbri httpwwwbmeuncedulabsallbritton Navin Varadarajan - UH - single-cell Lab httpwwwcheeuhedufacultyvaradarajan httpsinglecellcheeuheducontacthtml Nicholas Shaner - Scintillon Institute - mNeonGreen httpwwwscintillonorgshaner_lab Rebecca Richards-Kortum httpbioengineeringriceedufacultyrebecca_richards-kortumaspx Robert Campbell - Fluorescent proteins optogenetic proteins httpcampbellwebchemualbertaca httpcampbellwebchemualbertacaprojects-2 Robert Murphy ndash Cell measurements web services httpmurphylabwebcmueduservices Sabine Mai - University of Manitoba - Genomic Centre for Cancer Research and Diagnosis (GCCRD) - httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBPlatformsGCCRDhtml httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBScientistsMaiAwardshtml Sally Ward and Raimund Ober - Texas AampM University - httpwwwwardoberlabcom Simon Watkins - U Pittsburgh Center for Biologic Imaging httpwwwcbppittedufacultywatkinshtml httpwwwcbppittedufacultylabwatkinshtml httpwwwcbipittedu Stefan Hell ndash Deparment Hell NanoBiopohotonics httpwwwmpibpcmpgdehell httpsenwikipediaorgwikiStefan_Hell httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014hell-factshtml Sunney Xie Harvard httpsbernsteinharvardedu Susan Cox ndash 3B microscopy httpwwwcoxphysicscomindexhtml httpwwwcoxphysicscom3b Radim Chmeliacutek - Center for innovative microscopy Experimental biophotonics group httpswwwceiteceuceitec-butexperimental-biophotonicsrg3 httpwwwbiophotczhome Taekjip Ha ndash Johns Hopkins University ndash single molecules httphamedjhmiedu

Thomas Ried ndash NCI NIH SKYM-FISH and CGH Database httpsccrcancergovGenetics-Branchthomas-ried httpsccrcancergovGenetics-Branchthomas-riedqt-staff_profile_tabs=9qt-staff_profile_tabs ftpftpncbinlmnihgovsky-cghDATA httpswwwncbinlmnihgovdbvar Viviana Gradinaru ndash CalTech ndash CLARITYPACT Optogenetics httpwwwbbecaltecheducontentviviana-gradinaru httpglabcaltechedu Vladislav Verkhusha - near infrared fluorescent proteins httpwwweinsteinyuedulabsvlad-verkhushadefaultaspx httpwwweinsteinyueduresearchfacilitiesfluorescent WE Moerner ndash Stanford University httpwebstanfordedugroupmoerner Willard Wiggans ndash micro gallery httpwwwwillard-wigancomgallery Wolf Frommer ndash Molecular sensors httpbiosensordpbcarnegiescienceedu (fluorescent protein biosensors table) Xiaowei Zhuang = Harvard httpzhuangharvardedu Yuval Garini - Bar-Ilan University - Nano-Bio-Photonics laboratory httpgarinilabbiuacil Microscopy Magazines Imaging amp Microscopy httpwwwimaging-gitcommagazine Laser Focus World httpwwwlaserfocusworldcomindexhtml Microscopy amp Analysis httpwwwmicroscopy-analysiscom Microscopy Today httpwwwmicroscopy-todaycom Microscopy-UK httpwwwmicroscopy-ukorguk Photonics Spectra Biophotonics httpwwwphotonicscomPublicationsaspx The Microscope Journal httpmcriorgv72the-microscope-journal RMS Infocus Magazine httpwwwrmsorgukstudy-readinfocus-magazinehtml Nobel Prizes in Light Microscopy and Related Fields Chemistry 1925 colloids (light sheet) Zsigmondy (Siedentopf Zsigmondy 1902) httpswwwnobelprizeorgnobel_prizeschemistrylaureates1925

Chemistry 2000 conductive polymers Heeger MacDiarmid Shirakawa (Brilliant Violets Ultraviolets Blues) httpwwwnobelprizeorgnobel_prizeschemistrylaureates2000 Chemistry 2008 green fluorescent protein GFP Shimomura Chalfie Tsien httpwwwnobelprizeorgnobel_prizeschemistrylaureates2008 Chemistry 2014 super-resolved fluorescence microscopy Betzig Hell Moerner httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014 Physics 1953 Phase Contrast Zernike httpswwwnobelprizeorgnobel_prizesphysicslaureates1953 Physics 2009 invention of an imaging semiconductor circuit ndash the CCD sensor Kao Boyle Smith httpwwwnobelprizeorgnobel_prizesphysicslaureates2009 Physics 2014 efficient blue light emitting diodes Akasaki Amano Nakamura httpwwwnobelprizeorgnobel_prizesphysicslaureates2014 Physiology or Medicine 2006 Fire and Mello RNA interference ndash gene silencing by double stranded RNA httpwwwnobelprizeorgnobel_prizesmedicinelaureates2006 Physiology or Medicine 2006 Capecchi Evans Smithies specific gene modifications in mice by the use of embryonic stem cells httpwwwnobelprizeorgnobel_prizesmedicinelaureates2007 Physiology or Medicine 2009 Blackburn Greider Szostak how chromosomes are protected by telomeres and telomerase httpwwwnobelprizeorgnobel_prizesmedicinelaureates2009 Physiology or Medicine 2012 Gurdon Yamamanka matured cells can be reprogrammed to become pluripotent httpwwwnobelprizeorgnobel_prizesmedicinelaureates2012

Table 442 Fluorophores Photophysics Data

Fluorophore Abs or Ex max (nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Acridine orange 271 520 27000 020 5

Alexa Fluor 430 431 541 16000 055 9

Alexa Fluor 488 495 519 71000 094 67

Alexa Fluor 532 532 553 81000 080 65

Alexa Fluor 546 556 573 104000 096 100

Alexa Fluor 568 578 603 91300 075 69

Alexa Fluor 594 590 617 73000 064 47

Allophycocyanin (APC) 650 660 700000 068 476

Atto 390 390 479 24000 090 22

Atto 425 436 484 45000 065 29

Atto 430LS 433 547 32000 065 21

Atto 465 453 508 75000 075 56

Atto 490LS 496 661 40000 030 12

Atto 520 525 547 105000 095 100

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 8: McNamara 20161006 revised draft tables for CPHG Light ...

Live cell imaging dishes and multi-well plates (ldquoglass bottom dishesrdquo)

We recommend these for simplified handing and processing vs either thick plastic dishesplates or having to handle loose coverslips with your valuable cells

Leicester Imaging Technologies (LITE) - University of Leicester - table of dishes for live cell imaging (our table has current links and bad links left out) httpwww2leacukcollegesmedbiopsychfacilities-and-servicescbsliteaiftips-and-tricks-1dishes-for-live-cell-imaging Bellco Glass Inc - glass flat bottom plate httpwwwbellcoglasscomnode1046 Bioptechs - interchangable coverslip dish ($036 per experiment) httpwwwbioptechscomproductinterchangeable-coverslip-dish Brooks Automation Inc - clar bottom optical imaging microplates httpwwwbrookscomproductslife-scienceconsumablesmatrical-microplates-microtubes-racks-lidsglass-bottom-optical-imaging-microplates Cell EampG - glass bottom cell sulture dishes plates httpcellegcomproducthtml Cellvis - glass bottom dishes and plates httpwwwcellviscom_35-mm-glass-bottom-dishes_products_by_categoryphpcat_id=3 Corning - glass bottom microplates httpcatalog2corningcomLifeSciencesen-USShoppingCategoryaspxcategoryname=Microplates20-202015(Lifesciences)|Assay20Microplates20-202015(Lifesciences) Design 1 Solutions - Custom microplates and fabrication services httpwwwdesign1solutionscomcustom-microplateshtml Eppendorf - cell imaging dishes imaging plates httpsonline-shopeppendorfcomOC-enCell-Culture-and-Imaging-Consumables-110320Cell-Imaging-Consumables-120210Eppendorf-Cell-Imaging-Dishes-PF-19457html httpsonline-shopeppendorfcomOC-enCell-Culture-and-Imaging-Consumables-110320Cell-Imaging-Consumables-120210Eppendorf-Cell-Imaging-Plates-PF-19458html Greiner Bio-One International - CellView glass bottom dishes quadrant dishes httpsshopgbocomenrowarticlescataloguearticle0110_0110_0040_002027513 ibidi - u-Plates glass bottom dishes microfluidic slides httpibidicomxtproductsenibidi-Labwarem-Plates httpibidicomxtproductsenibidi-Labware Matsunami Glass Ind Ltd httpwwwmatsunami-glasscojpenglishlifebiodata01html Mattek - glass bottom dishes and SBS plates httpswwwmattekcomstore-categoryculturewareglass-bottom-dishes Nunc - glass bottom dishes httpswwwthermofishercomordercatalogproduct150680 NEST Biotechnology Co Ltd Wuxi Jiangsu PRChina httpwwwnestscientificusacomproducts_detailproductId=31html PerkinElmer - glass bottom plates httpwwwperkinelmercomSECatalogCategoryIDMicroplates

Porvair Sciences - clear bottom assay plates httpwwwporvair-sciencescomenservices-menulife-sciencesclear-bottom-assay-plates Ted Pella Inc - glass bottom dishes clear wall or black wall (manufactured by WillCo Wells) httpswwwtedpellacomsection_html706dishhtm Warner Instruments (Harvard Apparatus) - culture dishes perfusion systems httpswwwwarneronlinecomproduct_cat_infocfmid=1322 Willco Wells - glass bottom dishes wwwwillcowellscom World Precision Instruments - Fluorodish glass bottom dishes httpswwwwpiinccomproductslaboratory-suppliesfd35-100-fluorodish-cell-culture-dish-35mm-23mm-well-pkg-of-100 Microscopes Microscopy Accessories (accessorize) Reagents Resources 3scan ndash knife edge scanning microscope (images slices repeats through specimen) httpwww3scancomdata-2 89North (affiliated with Chroma Technology Corp) httpwww89northcom Abberior Instruments ndash STED RESOLFT precision localization super-resolution microscopes STEDYCON convert any fluorescence microscope to STED httpabberior-instrumentscom httpabberior-instrumentscomproductscompact-lineabberior-stedy-con Acquifer ndash HIVE imaging machine (computer hardware) for high content screening big data httpswwwacquiferde Adobe Systems Inc httpwwwAdobecom httpscreativeadobecomproductsdownloadphotoshop Affymetrix eBioscience (ThermoFisher) - microarrays httpwwwaffymetrixcomestorebrowselevel_one_category_template_onejspparent=35796ampcategory=35796 httpwwwaffymetrixcomestorecatalog131547AFFYGeneChip26231743B+System+3000Dx+v22623423B1_1 Agilent Technologies ndash SureScan microarray scanner (array CGH microRNA SNPs CNV) httpwwwgenomicsagilentcomenMicroarray-Scanner-Processing-HardwareSureScan-Microarray-Scannercid=AG-PT-144 Andor Technology (Oxford Instruments) ndash sCMOS cameras Dragonfly spinning disk confocal Revolution DSD2 differential spinning disk confocal photostimulation (fluorescence recovery after photobleaching optogenetics) Mosaic3 DMDDLP high speed light patterning (optogenetics structured illumination) MicroPoint pulsed UV laser for ablation DNA damage photobleachingactivation uncaging accessories httpwwwandorcomscientific-camerasneo-and-zyla-scmos-cameras httpwwwandorcommicroscopy-systemsdragonfly httpwwwandorcommicroscopy-systemsrevolution-dsd httpwwwandorcommicroscopy-systemsphotostimulation httpwwwandorcommicroscopy-systemsphotostimulationmosaic httpwwwandorcommicroscopy-systemsphotostimulationmicropoint httpwwwandorcommicroscopy-systemsmicroscopy-components Apogee Instruments Inc (Andor Technology) ndash CCD cameras and filter wheels (mostly marketed for astronomy) httpwwwccdcomandorhtml Applied Scientific Instrumentation Inc ndash light sheet imager (iSPIM diSPIM)

wwwasiimagingcom httpwwwasiimagingcomindexphpproductslight-sheet-microscopyselective-plane-illumination-microscopy-ispim-dispim Applied NanoFluorescence LLC ndash NS1 NanoSpectralyzer (Raman and UV-VISNIR) NS MiniTracer near infrared spectrometer NFM NanoFluorescence microscope multi-laser light source single wall carbon nanotubes (NIR II fluorophores) httpappliednanocomproductshtml httpappliednanocomproductsns1html httpappliednanocomproductsproduct-list77-ns-minitracerhtml httpappliednanocomproductsnfmhtml httpappliednanocomproductsls-nhtml httpwwwnanowerkcomnewsnewsid=24132php Applied Spectral Imaging Inc httpwwwspectral-imagingcom ArgoLight ndash fluorescence resolution test target slides httpargolightcom AttoCube - attoMICROSCOPY overview attoCFM - Multichannel cryogenic (low temperature) confocal fluorescence microscopes 08 NA objective lenses 400-1000 nm spectral range httpwwwattocubecom httpwwwattocubecomattomicroscopyintroductiontab-2 httpwwwattocubecomattodownloads AutoQuant (Media Cybernetics) spatial deconvolution httpwwwmediacycomautoquantx3 Becker amp Hickl GmbH httpwwwbecker-hicklcomproductshtm Berkeley Lights Inc ndash manueuver into nanowells incubate recover 4000 single cells per chip httpswwwberkeleylightscomtechnology Bioaxial ndash Codim imaging conical diffraction beam shaper for super-resolution (4 sub-images) httpwwwbioaxialcomcodim-imaging Bioptechs - Live-Cell Micro-Observation Products httpwwwbioptechscom Bionumbers - database of useful biological numbers httpbionumbershmsharvardeduKeyNumbersaspx Biostatus ndash DRAQ5 DRAQ7 ApopTRAK CyTRAK Orange CyGel HypoxiTRAK httpwwwbiostatuscomProducts Bio-Tek ndash Cytation 3 Cell Imaging Multi-Mode Reader Lionheart FX Automated Live Cell Imager httpwwwbiotekcomproductsimagingcytation3_cell_imaging_multi_mode_readerhtml httpwwwbiotekcomproductsimaginglionheartfx_automated_live_cell_imagerhtml Biovision Technologies ndash distributor for several imagers including VT-iSIM instant super-resolution microscope httpbiovision-technologiescom httpbiovision-technologiescomsystemshtml httpbiovision-technologiescomvtisimhtml Bitplane (Andor Oxford Instruments) ndash Imaris imaging software httpwwwbitplanecom BMV Optical - custom lens assemblies and optical filters wwwbmvopticalcom

Bruker (previously Prairie Technologies Vutara) ndash Opterra confocal Ultima Multiphoton Vutara 352 single molecule localization microscopes httpswwwbrukercomproductsfluorescence-microscopesopterra-confocal-microscopyoverviewhtml httpswwwbrukercomproductsfluorescence-microscopesultima-multiphoton-microscopyhtml httpswwwbrukercomproductsfluorescence-microscopesvutara-super-resolution-microscopyoverviewhtml Cairn Research ndash standard and custom accessories ex Light Sheet Illuminator MultiCam (4 cameras) custom design httpswwwcairn-researchcouk httpswwwcairn-researchcoukproductl-spi-single-plane-illuminator (dual L-SPI for 4 illumination directions) httpswwwcairn-researchcoukproductmulticam httpswwwcairn-researchcoukcustom-design Cameca ndash NanoSIMS 50L (7plex stable isotope imaging) httpwwwcamecacominstruments-for-researchnanosimsaspx CellMic (formerly Holomic) - blood analysis or fluorescence imaging cytometer on a cell phone httpwwwcellmiccomcontentadvanced-technologies httpwwwcellmiccomcontentfluorescent-imaging-cytometry-and-e-coli-detection-on-a-cell-phone CellOptic ndash FINCH (Fresnel INcoherence Correlation Holography) httpwwwcellopticcomindex2html CellProfiler ndash High content screening (HCS) image processing and analysis software httpcellprofilerorg ClearLight Diagnostics - CLARITY Optimized Light Sheet Microscopy (3D tissue optical clearing + light sheet imaging) httpwwwclearlightdxcomindexhtml Confocalnl ndash Rescan confocal microscopy to obtain 170 nm resolution with any pinhole diameter httpwwwconfocalnl CoolLED ndash LED light sources httpwwwcoolledcomproduct-detailpe-4000 Crest Optics SRL ndash X-Light confocal X-Light V2 + VCS (VideoConfocal super-resolution) httpwwwcrestoptcom httpwwwcrestoptcomhtmlx-light_v2_vcshtml Cytoskeleton Inc - live cell imaging reagents Spirochrome SiR bioimaging probes httpwwwcytoskeletoncomlive-cell-reagents httpwwwcytoskeletoncomlive-cell-reagentsspirochrome CytoViva ndash darkfield imaging hypspectral imaging httpwwwcytovivacomproducts3d-enhanced-darkfield-imaging httpwwwcytovivacomproductshyperspectral-imaging-2hyperspectral-imaging Data Translation Inc - digitizer cards httpwwwdatxcom Delmic BV - combined correlative scanning electron microscope with inverted fluorescence microscope httpwwwdelmiccomdelphi httpswwwdelphimicroscopecom httpwwwdelmiccomsecom-super-resolution Digital Light Innovations (DLi) - CELscope C-mount LED Microscope using Texas Instruments DLP illuminator with a simple stand httpswwwdlinnovationscomdli-deep-dives-celscope-c-mount-led-microscope Double Helix LLC ndash single molecule localization microscope (Piestun) httpdoublehelixopticscom Edinburgh Super-resolution Imaging Consortium (ESRIC)

httpwwwesricorg Energetiq ndash Deep ultraviolet (DUV high radiance 170-2100 nm) laser driven light source (LDLS) httpwwwenergetiqcom Epi Technology - CaliCube - Cube for fluorescence light path to inspect epi Illumination light source (lamp) fiber optic or liquid light guide httpwwwepitechnologycomepitechnology-1 Essen Biosciences ndash Incucyte Zoom (imager inside incubator) httpwwwessenbiosciencecomenproductsincucyte Estigen Tissue Science ndash manual and automated tissue arrayer (tissue microarray maker) httpwwwestigencom Euro-Bioimaging httpwwweurobioimagingeu Excelitas Technologies (formerly Lumen Dynamics) ndash X-Cite LEDs httpwwwexcelitascomPagesProductX-Cite-LED-Solutionsaspx Expansion Technologies Inc (extbio) ndash Expansion microscopy httpwwwextbiocombuycell FEI (formerly Till Photonics) (Thermo Fisher) ndash correlative LM-EM single molecule Cryo-EM httpswwwfeicomlife-sciencescellular-biology httpswwwfeicomlife-sciencescellular-biologycorrelative-microscopy httpswwwfeicomlife-sciencesstructural-biology Femtonics - Multi-phton microscopes software accessories caged glutamate reagents services httpfemtonicseuproducts First Light Imaging ndash C-Red NIR imaging (800-2500 nm NIR windows I II III 650-950 nm 1100-1350 nm 1600-1870 nm[Shi et al 2015]) high speed visible EMCCD (400-1000 nm) httpwwwfirst-lightfrcategoryrangesinfrared Fluidigm ndash Helios imaging CyTOF mass cytometer (42plex) Callisto (32 independent chambers dose with up to 16 independent factors for 1-1000 cell populations culture up to 3 week) Polaris functional genomics meets imaging (48 single cells up to 24 hours after single cell selection from a population) httpswwwfluidigmcomproductshelios httpswwwfluidigmcomproductscallisto httpswwwfluidigmcomproductspolaris GattaQuant - nanorulers for high resolution microscopes and super-resolution microscopes performance testing httpwwwgattaquantcomNanoruler GE Healthcare life Sciences Applied Precision ndash DeltaVision deconvolution OMX OMX SR httpwwwgelifesciencescomwebappwcsstoresservletproductByIdenGELifeSciences-us29065728 httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usproductsAlternativeProductStructure_2380729065721 httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usproductsAlternativeProductStructure_2380729115476 German BioImagingorg httpwwwgermanbioimagingorgwikiindexphpMain_Page httpwwwgermanbioimagingorgwikiindexphpWorkgroup6SoftwarePackages GIGAmacro ndash Magnify2 gigapixel imagery oof macroscopic and microscopic objects Terapixel macro image httpwwwgigamacrocomgigapixel-macro-imaging-system httpwwwgigamacrocomworlds-first-terapixel-macro-image

Glencoe Software ndash OMERO Plus enterprise data management for scientific images and any associated metadata (OME = Open Microscopy Environment) DataViewer PathViewer httpsglencoesoftwarecomomeroplushtml httpsglencoesoftwarecomdataviewerhtml httpsglencoesoftwarecompathviewerhtml Gooch amp Housego ndash spectral imager httpsgoochandhousegocomminiature-spectral-imaging-camera httpwwwghinstrumentscomproductsspectral-imaging-synthesishsi-440c-hyperspectral-imaging-system Hindsight Imaging ndash spectral imaging httphindsight-imagingcom Horiba Scientific - SWIFT ultra-fast Raman confocal imaging Raman spectroscopy httpwwwhoribacomscientificproductsraman-spectroscopyraman-imagingswift httpwwwhoribacomscientificproductsraman-spectroscopyraman-imaging httpwwwhoribacomscientificproductsraman-spectroscopy IATIA Ultima Capital ndash QPm (quantitative phase microscopy) httpwwwultimacapitalnetiatiaimagingPublicationsIatia20ImagingapplicationNotesqpmApplicationWithConfocalMicroscopespdf Ibidi - heating and incubation systems optical O2 measurement systems Nanolive 3D Cell Explorer pump system gas incubation system httpibidicomxtproductsenInstruments-AccessoriesHeating-Incubation-Systems httpibidicomxtproductsenInstruments-Accessoriesibidi-OPAL-Optical-O2-Measurement-System httpibidicomxtproductsenInstruments-AccessoriesNanolive-3D-Cell-Explorer httpibidicomxtproductsenInstruments-Accessoriesibidi-Pump-System httpibidicomxtproductsenInstruments-AccessoriesHeating-Incubation-Systemsibidi-Gas-Incubation-System iLAbSolutions (Agilent Technologies) - Instrument management and scheduling software (cores and labs) httpwwwilabsolutionscominstrument-access-control ImageJ - Fiji ImageJ NIH ImageJ ImageJ ndash Fiji (Fiji is just ImageJ) is the main download site httpfijisc httpsimagejnihgovij wwwimagejnet Inscopix ndash nVista in vivo mouse brain imaging miniature microscope httpswwwinscopixcomproducts Intelligent Imaging Innovations Inc (3i) ndash Slidebook imaging software Lattice light sheet (high speed gentle to cells high resolution imaging) Dual-view Inverted Selective Plane Illumination (diSPIM) VIVO 2-Photon (VIVO 2P) multiphoton microscopy Everest intravital imaging Marianas 3D real-time deconvolution timelapse spinning disk FRAP TIRF FLIM single molecule environmental control Phasor - optogenetic photostimulation using digital holography Yokogawa spinning disk confocal units wwwintelligent-imagingcom httpswwwintelligent-imagingcomslidebookphp httpswwwintelligent-imagingcomsystemsphplattice httpswwwintelligent-imagingcomsystemsphpdispim httpswwwintelligent-imagingcomsystemsphptwophoton httpswwwintelligent-imagingcomsystemsphpeverest httpswwwintelligent-imagingcomsystemsphpmarianas httpswwwintelligent-imagingcomoptogeneticsphp httpswwwintelligent-imagingcomsdcphp ISS Inc ndash fluorescence lifetime imaging microscopy fluorescence correlation spectroscopy (FCS) confocal imaging httpwwwisscommicroscopyindexhtml JenLab GmbH cyto-microscopy multiphoton tomography httpwwwjenlabdeproducts250html httpwwwjenlabde2PM-Cryo1330html

httpwwwjenlabdeMultiphoton-Tomography680html Jenoptik - microscope cameras httpswwwjenoptikcomproductscameras-and-imaging-modulesmicroscope-cameras JPK Instruments - integrated atomic force microscope (AFM) force sensing optical tweezers optical trapping single cell force spectroscopy (SCFS) httpwwwjpkcomindex2enhtml httpusajpkcomoptical-tweezers-optical-trapping29ushtml httpusajpkcomcellular-adhesion-cytomechanics30ushtml Keyence ndash VK-X confocal (upright) BZ-X700 widefield (inverted) httpwwwkeyencecomssproductsmicroscopevkx httpwwwkeyencecomssproductsmicroscopebz-x700indexjsp KK Technology - CapiScope HVCS Handheld Video Capillaroscopy System (CytoScan) httpwwwkktechnologycomhvcshtml LaVision BioTec ndash TriMscope Multiphoton TriM Scope II Adaptive Optics UltraMicroscope II light sheet httpwwwlavisionbiotecde httpwwwlavisionbiotecdetrim-scope-overviewhtml httpwwwlavisionbiotecdetrim-scope-ii-adaptive-opticshtml httpwwwlavisionbiotecdeultramicroscope-ii-introductionhtml Laxco ndash upright and inverted microscopes httpwwwlaxcoinccomMICROSCOPES Lego ndash Lego Idea Microscopes httpsideaslegocomprojects44370 httpwwwnico71frlego-working-microscope Li-Cor ndash near-infared fluorescent dyes and in vivo imaging agents in vivo and Western blot imaging systems httpswwwlicorcombioproductsreagents httpswwwlicorcombioproductsreagentsirdyebrightsite_imaging_agents httpswwwlicorcombioproductsimaging_systemsodyssey_familyhtml httpswwwlicorcombioproductsimaging_systemspearl httpswwwlicorcombioproductsimaging_systemscdigit Life Imaging Services - ldquothe Ludin chamberrsquo ldquothe cube amp the boxrdquo httpwwwlischthechamberhtml httpwwwlischtheboxhtml Lightform Inc ndash PARISS imaging spectrometer httplightforminccom LMU Bioimaging httpwwwbioimagingbmcmeduni-muenchendelinkswebsitesindexhtml httpwwwbioimagingbmcmeduni-muenchendelearneduwebsitesindexhtml Ludl Electronic Products Ltd ndash automated XY stages focus motors filter wheels httpwwwludlcom

LumaCyte ndash Laser force Cytology (laser trap meets microfluidics to suspend and manipulate single cells) httpwwwlumacytecomabouttechnology Lumencor ndash LEDs fluorescence light sources httplumencorcomproducts Luxcel ndash mitochondrial and cellular functions O2 sensor reagents httpluxcelcomproduct+list Luxendo GmbH ndash light sheet imager

wwwluxendoeu Lyncee tec - digital holography microscopy (DHM) high content screening by DHM httpwwwlynceeteccom httpwwwlynceeteccomhigh-content-screening Mad City Labs Inc - nanopositioning wwwmadcitylabscom Mauna Kea Technologies ndash CellVizio confocal laser endomicroscopy httpwwwmaunakeatechcomenhealthcare-professionalscellvizio-endomicroscopy-0 MBF Bioscience - stereology and neuron morphology quantitative imaging httpwwwmbfbiosciencecom McCrone Group wwwmccronecominstrument-sales Media Cybernetics Inc ndash Image Premier 3D AutoQuant X3 deconvolution httpwwwmediacycom Meiji Techno America wwwmeijitechnocom MesoLens Ltd httpwwwmesolenscomproducttechnical-specifications httpwwwmesolenscomimages httpswwwbiophotonicsstrathacukresearch_1htm Meyer Instruments ndash Pathscan Enabler GigaMacro digital pathology telepathology httpmeyerinstcom httpmeyerinstcompathscan-enabler-5 httpmeyerinstcomgigamacro-gigapixel-macro-imaging httpmeyerinstcomhomescanners httprealtimetelepathologycom Microarrays - Large-Scale Gene Expression and Microarray Links and Resources httpswwwebiacukarrayexpress Micro-Manager ndash Device Support ndash tabulates many microscope cameras and motorized accessories every new camera and accessory should have a uManager driver to enable simple use with Fiji ImageJ httpsmicro-managerorg httpsmicro-managerorgwikiDevice_Support httpsopen-imagingcom Microvolution ndash (near) instant gratification spatial deconvolution using NVidia GPU card(s) httpmicrovolutioncom Mightex Systems ndash optogenetics DMDDLP illuminator (digital micro-mirror device digital light processing) httpwwwmightexsystemscomindexphpcPath=245 Millipore-Sigma Merck KGaA (Amnis Corp CellASIC EMD Millipore) ndash ImageStreamX and FlowSight imaging flow cytometers ONIX2 Microperfusion System for microscopes httpswwwemdmilliporecom httpswwwemdmilliporecomUSenlife-science-researchcell-analysisamnis-imaging-flow-cytometersQ6ubqBm3UAAAFLCKIpygJnav httpwwwemdmilliporecomUSenlife-science-researchcell-culture-systemscellASIC-live-cell-analysisd1CbqBw58AAAE_0j13MnAnav Mitutoyo America Corp wwwmitutoyocom httpecatalogmitutoyocomMF-U-Series-176-High-power-Multi-function-Measuring-Microscopes-C1413aspx

Molecular Devices Corporation Universal Imaging Corporation (Danaher) ndash MetaMorph MetaFluor high content systems (HCS) httpswwwmoleculardevicescomsystemsmetamorph-research-imaging httpmdccusthelpcomappanswersdetaila_id19319 httpswwwmoleculardevicescomsystemshigh-content-imaging Molecular Machines amp Industries - laser microdissection and tweezer systems httpwwwmolecular-machinescomhome MUSE Microscopy Inc ndash Deep UV illumination for shallow depth of field imaging httpwwwmusemicrocom Micro Video Instruments Inc - DarkLite illuminator httpwwwmvi-inccom NanoEnTek ndash JuLI Stage (imager inside incubator or on lab bench) httpwwwjulistagecom National Instruments ndash LabView software httpwwwnicomen-ushtml Navitar - Hoffman Modulation Contrast (HMC alternative to differential interference contrast phase contrast) custom lens design UVDUVNUV imaging lenses httpsnavitarcommarketsmicroscopy httpsnavitarcomproductsimaging-opticscustom-microscope-objectivescustom-microscope-objectives httpsnavitarcomproductsimaging-opticsuv-imaging National Center for X-ray Tomography (NCXT) ndash soft X-ray tomography (CT of hydrated cells) XM-2 dedicated biological SXT microscope Prof Carolyn Larabell Director (see also SiriusXT) httpncxtlblgov httpncxtlblgovsxt httpncxtlblgovmanual httpncxtlblgovq=carolyn Neogenomics (Clarient) ndash MultiOmyx immunofluorescence or DNA FISH (ldquo60plexrdquo) httpneogenomicscomPharma-ServicesLab-ServicesMultiOmyxTechnologyMultiOmyx-IF-Assay-DNA-FISH-assay-NGS-from-ROI Nexcelom ndash Celigo imaging cytometer Cellometer cell counters httpwwwnexcelomcomCeligoindexphp httpwwwnexcelomcomProducts Nikon ndash Ti-LAPP modular illumination system (for Nikon Ti series microscopes) TIRF Optogenetics httpswwwnikoninstrumentscomProductsPhotostimulation-and-TIRFTi-LAPP Nirmidas Biotech httpwwwnirmidascomtechnologynir httpwwwnirmidascomproductsniriidye NVidia ndash Pascal 10+ Gbps GPU cards for instant gratification deconvolution (software from Microvolutioncom SVInl) httpwwwgeforcecomhardware10seriesgeforce-gtx-1080 httpwwwgeforcecomhardware10seriestitan-x-pascal httpwwwnvidiacomobjectquadro-graphics-with-pascalhtml Ocean Optics ndash spectrometers httpoceanopticscomproduct-categorymodular-spectrometers Oko-Lab stage top incubator httpwwwoko-labcomstage-top Open Microscopy Environment (OME) ndash OMERO (see also Glencoe Software) Bio-Formats LOCI

httpswwwopenmicroscopyorgsite httpswwwopenmicroscopyorgsiteproductsomero httpswwwopenmicroscopyorgsiteproductsbio-formats httpswwwopenmicroscopyorgsitesupportbio-formats52supported-formatshtml httpswwwopenmicroscopyorgsiteaboutdevelopment-teamskevin OpenSPIM ndash do-it-yourself selective plane illumination microscopy (light sheet imaging) httpopenspimorgWelcome_to_the_OpenSPIM_Wiki OpenSpinMicroscopy ndash do-it-yourself SPIMDSLMOPT microscopes httpssitesgooglecomsiteopenspinmicroscopy Ovizio ndash differential digital holography (similar to quantitative phase imaging) httpwwwoviziocomenHome httpwwwoviziocomenMicroscopesQMod Oxford Gene Technologies ndash microarrays ndash cytogenetics molecule genetics cancer research pre-implantation genetic diagnosis httpwwwogtcomclinical_genetics Oxford Nanoimaging ndash single molecule(s) localization fluorescence resonance energy transfer (FRET) (Kapanidis) wwwoxfordnicom Pathology Devices ndash LiveCell stage top incubator amp controller tissue microarrayers (TMA makers) httpwwwpathologydevicescomLiveCellhtm httpwwwpathologydevicescomTMArrayerhtm PeCon GmbH ndash microscope incubators httpwwwpeconbiz Pembroke Instruments ndash spectrometers mini-lasers httppembrokeinstrumentscomqmini-spectrometer httppembrokeinstrumentscommini-lasers PerkinElmer ndash in vivo imaging systems (bioluminescence NIR fluorescence) Vectra digital slide scanner httpwwwperkinelmercomcategoryin-vivo-imaging-instruments httpwwwperkinelmercomcategoryquantitative-pathology-imaging-instruments Phi Optics ndash CellVista SLIM Pro (quantitative phase microscopy) httpphiopticscom Photometrics (Roper Scientific) ndash DualView QuadView httpwwwphotometricscom httpwwwphotometricscomproductsmultichannel Photon Technology International httpwwwpti-njcomindexhtml

PicoQuant GmbH ndash fluorescence lifetime imaging microscopes (FLIM) STED 3D-EasySTED httpswwwpicoquantcomproductscategoryfluorescence-microscopes httpswwwpicoquantcomapplicationscategorylife-sciencested httpwwweasystedorg Physik Instrumente GmbH amp Co KG (PI) - Nanopositioning Applications for Microscopy Neuroscience and Metrology httpswwwphysikinstrumentecomen httpwwwpi-usausindexphp PreSens Prescision Sensing GmbH - VisiSens measure and visualize Oxygen pH or carbon dioxide distributions httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-biological-researchhtml httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-life-science-researchhtml Prior Scientific

httpwwwprior-uscom Profusa Inc - Lumee tissue-integrated biosensors scaffolds httpprofusacomtechnology Reindeer Graphics Inc ndash OptiPix Fovea Pro 9plugins for Adobe Photoshop 6 and CS series) httpwwwreindeergraphicscom Renishaw - StreamLine fast chemical imaging Raman spectroscopy httpwwwrenishawcomenstreamline-generate-chemical-images-rapidly--9449 httpwwwrenishawcomenraman-spectroscopy--6150 Sanford Burnham Prebys ndash High Content Screening httpwwwsbpdiscoveryorgtechnologysrPagesLaJolla_HighContentScreeningaspx ScopeM - Scientific Center for Optical and Electron Microscopy - ETH Zurich httpwwwscopemethzch SiriusXT - soft X-ray tomography (SXT) microscope (CT scan hydrated cell) httpsiriusxtcom SpectraGenetics - Fluorogen Activating Peptides (FAPs) new genetically encoded ldquobinaryrdquo reporters httpspectrageneticscomproductsvectors-for-expressing-fluorogen-activating-proteinsfap-technology-overview Spirochrome - Silicon Rhodamine (SiR) and other fluorescent reagents probes for bioimaging httpspirochromecom Stanford Photonics Inc httpwwwstanfordphotonicscom httpwwwstanfordphotonicscomLife20SciencesLifeScihtm

Stream Technologies Inc ndash ColorFlow lens (multi-wavelength emission onto a camera) httpwwwstreamtechinccomproducts Sutter Instrument Company httpwwwsuttercom httpwwwsuttercomMICROSCOPESindexhtml httpwwwsuttercomIMAGINGindexhtml SVI Huygens ndash Professional (general image analysis) deconvolution NVidia GPU deconvolution httpssvinlHuygensProfessional httpssvinlHuygensDeconvolution httpssvinlHuygensGPU Sysmex Partex ndash CyScope httpwwwsysmex-parteccomproductsmicroscopyhtml httpwwwsysmex-parteccomproductsprdouct-detailviewcyscopeR-malaria-3238html Technical Instruments httpwwwtechinstcomproductsphp TESCAN Brno sro - Tescan Q-PHASE multimodal holographic quantitative phase imaging system (QPi) optional fluorescence httpwwwtescancomenproductsq-phaseq-phase httpq-phasetescancom httpq-phasetescancomindexphptechnologyspecifications Ted Pella Inc ndash specialty light microscopy and electron microscopy supplies httpswwwtedpellacom Texas Instruments ndash DLP 4100 development kit (digital light processingrsquo DMD digital micromirror device) httpwwwticomtooldlpd4x00kit

ThorLabs ndash iCyte imaging cytometer multiphoton confocal EnVista digital slide scanning microscopes httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7473 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7494 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=5696 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=6570 TIRF Labs lightguide TIRF prism TIRF TIRF-Electrochemistry httpwwwtirf-labscom httpwwwtirf-labscomtechnologieshtml TissueVision - Serial Two Photon Tomography (image volume ablate imaged volume with multiphoton laser repeat) httpwwwtissuevisioncomtechnology Tokai Hit - stage top incubator httpwwwtokaihitcomenglishproduct_guidanceoptionhtml TopoNomos Ltd ndash Toponome Imaging Cycler ndash immunofluorescence (100plex) httpwwwtoposnomoscomtechnologyhtml Ultivue Inc ndash DNA-PAINT ndash reagents data processing service httpwwwultivuecom httpwwwultivuecomproducts UMech Technologies ndash Cytovar HCS up to 16 excitation wavelengths httpcloudumechcomproducts httpcloudumechcomproductsmodelC16 Visitech ndash vt-iSIM instant super-resolution microscopy up to 1000 frames per second confocal scanners and light engines httpwwwvisitechcoukvt-isimhtml httpwwwvisitechcoukproductshtml Visitron Systems GmbH - high speed imaging systems httpwwwvisitronde Visualsonics (Fujifilm) - photoacoustic imaging httpwwwvisualsonicscomproductstechnology-overview Wicked Lasers httpwwwwickedlaserscom httpwwwwickedlaserscomarctic WITec Wissenschaftliche Instrumente und Technologie GmbH - imaging systems for FLIM Raman AFM and SNOM analysis httpwitecdeproducts httpwwwwitec-instrumentscom WM Keck Center for Adaptive Optical Microscopy (CfAOM) at UC Santa Cruz httpscfaomsoeucscedu httpcfaoucolickorgpgallery Yokogawa Corp ndash spinning disk confocal scanner live cell imager high content screener confocal quantitative cytometer httpwwwyokogawacomsolutionsproducts-platformslife-science httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-scanner-unit-csu httpwwwyokogawacomsolutionsproducts-platformslife-scienceall-in-one-live-cell-imaging-solution httpwwwyokogawacomsolutionsproducts-platformslife-sciencehigh-throughput-cytological-discovery-system httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-quantitative-image-cytometer Zellkraftwerk (ChipCytometry) ndash immunofluorescence (80plex) httpwwwzellkraftwerkcomProducts2phtml httpwwwzellkraftwerkcomZKWOnephtmlSoftware

httpwwwchipcytometrycomtechnologyphtml Fluorescence Spectra Data and Graphing Sites PubSpectra ndash Excel file data download httpsworksbepresscomgmcnamara9 BD Biosciences ndash spectrum viewer Brilliant fluorophores httpwwwbdbiosciencescomussspectrumviewer httpwwwbdbiosciencescomusapplicationssspectrumguidepage BioLegend ndash spectra analyzer Brilliant Violet fluorophores httpwwwbiolegendcomspectraanalyzer httpwwwbiolegendcombrilliantviolet Chroma Technology httpswwwchromacomspectra-viewer eBioscience (Affymetrix ThermoFisher) ndash fluorPlan ndash a multi-laser spectra viewer httpwwwebiosciencecomresourcesfluorplan-spectra-viewerhtm Spectra Viewer (requires Java) Evrogen ndash Spectrum Viewer httpevrogencomspectra-viewerflashviewerhtml Fluorophoresorg ndash Fluorescent Substances httpwwwfluorophorestugrazatsubstance I Love GFP httpssitesgooglecomsiteilovegfpHomefps Lambert and Thorn UCSF Fluorescent protein properties httpnicucsfeduFPvisualization Leica Microsystem - ldquoFluoScoutrdquo httpwwwleica-microsystemscomfluoscout

Molecular Probes Invitrogen Thermo Fisher ndash Fluorescence SpectraViewer httpwwwthermofishercomusenhomelife-sciencecell-analysislabeling-chemistryfluorescence-spectraviewerhtml httpsitunesapplecomusappfluorescence-spectraviewerid421031826 (iTunes App) Nightsea - Compendium of spectra web sites httpwwwnightseacomsfa-sharingfluorescence-spectra-viewers Omega Optical ldquoCurvomatricrdquo httpswwwomegafilterscomcurvomatic

PhotoChemCAD 20 (Jonathan S Lindsey) dye spectra database and chemistry calculator NIRvana Sciences httpwwwphotochemcadcom httpnirvanasciencescompage_id=3088 UCSF (Lambert Thorn 2016) - Fluorescent protein properties httpnicucsfeduFPvisualization University of Arizona - Fluorescent Spectra Database httpwwwspectraarizonaedu Semrock - Searchlight httpssearchlightsemrockcom Spectroscopy Ninja ndash links to spectral and fluorescence data Spekwin32 spectroscopy software httpwwweffemm2deinfoinfo_specdatahtml

httpwwweffemm2deindexhtml Zeiss ndash interactive fluorescence dye and filter database overview dyes overview filter sets httpswwwmicro-shopzeisscoms=50479761ad21e5ampl=enampp=usampf=fampa=i httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=d httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=f Researcher Labs Alby Diaspro ndash IIT httpwwwlambsitindexphppage=People Alice Ting ndash MIT httpwwwtinglaborgresearch Allen Institute for Brain Science httpwwwalleninstituteorgwhat-we-dobrain-science Allen Institute for Cell Science httpwwwalleninstituteorgwhat-we-docell-science Amina Qutub - Rice University - How are human cells designed lab httpsqutublaborgqutub-lab Amy Herr UC Berkeley ndash Single cell Westerns httpherrlabberkeleyedu Amy Palmer ndash UC Boulder httpspalmerlabcoloradoedu Andrew York ndash Calico Life Sciences httpswwwcalicolabscomteam-memberandrew-york Anne Carpenter ndash Broad Institute CellProfiler httpspersonalbroadinstituteorganne Arjun Raj UPenn single molecule RNA FISH quantitative understanding cellular functions httprajlabseasupenneduindexhtml httpwwwpopscicomsciencearticle2013-09arjun-raj Atsuko Miyawaki - Laboratory for Cell Function Dynamics (CFDS) Fucci2 fluorescent proteins cell cycle indicator httpwwwbrainrikenjpenfacultydetails30 httpcfdsbrainrikenjp httpcfdsbrainrikenjpFuccihtml Aydogan Ozcan - UCLA - new imaging and sensing architectures httpinnovateeeuclaeduwelcomehtml httpwwwhhmiorgscientistsaydogan-ozcan Badri Roysam - UH - FARSIGHT Toolkit httpwwweeuhedufacultyroysam httpwwwfarsight-toolkitorgwikiMain_Page Brian J Ford ndash microscopist and popularizer httpsuklinkedincominprofbrianjford Carolyn Larabell ndashNational Center for X-ray Tomography (LBNL) UCSF httpncxtlblgovq=carolyn httpprofilesucsfeducarolynlarabell Clare Waterman ndash NHLBI NIH

httpswwwnhlbinihgovresearchintramuralresearcherspiwaterman-clare Dana Peer - Columbia University - Computational Systems Biology viSNE and more software httpwwwc2b2columbiaedudanapeerlabhtml httpwwwc2b2columbiaedudanapeerlabhtmlcythtml David Mayerich - UH - STIM Laboratory Scalable Tissue Imaging and Modeling httpwwweeuhedufacultymayerich httpstimeeuhedu David Piston WUSTL httpwwwcellbiologywustledufacultytenureddavid-w-piston-phd Diane Lidke and Keith Lidke - University of New Mexico httppathologyunmeduresearchfaculty-laboratoriesthe-lidke-laboratoryindexhtml httppanda3physunmedu~klidke Donna Arndt-Jovin and Thomas Jovin - Max Planck Institute for Biophysical Chemistry Laboratory of Cellular Dynamics httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsDonnaArdndt-JovinResearchAreasAndProjects httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsChairmanThomasJovinResearchAreasAndProjects Ed Boyden ndash MIT Media Lab ndash expansion microscopy (ExM) optogenetics httpsyntheticneurobiologyorg httpsyntheticneurobiologyorgprotocols httpsyntheticneurobiologyorgpublications httpwwwtedcomtalksed_boyden_baby_diapers_inspired_this_new_way_to_study_the_brain httpwwwextbiocombuycell Elizabeth Blackburn ndash Salk Institute - Telomeres httpswwwsalkeduscientistelizabeth-blackburn httpsenwikipediaorgwikiElizabeth_Blackburn httpswwwnobelprizeorgnobel_prizesmedicinelaureates2009blackburn-factshtml Elizabeth Hillman - Columbia university - SCAPE (Swept Confocally-Aligned Planar Excitation) high speed 3D microscopy DyCE (dynamic contrast enhancement to image and segment small animal organs live) Neuroimaging amp Neurovascular Coupling httporionbmecolumbiaedu~hillmanInstrumentationhtml httporionbmecolumbiaedu~hillmanSCAPEhtml httporionbmecolumbiaedu~hillmanMolecularhtml httporionbmecolumbiaedu~hillmanBrain_Imaginghtml Eric Betzig ndash UCSF (moving from HHMI Janelia Farm in 2016) httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014betzig-factshtml Eva Sevick-Muraca ndash UT Health Science Center at Houston molecular imaging clinical NIR fluoresceince imaging httpswwwutheduimmprofilehtmid=1005459 httpswwwutheduimmcentersmolecular-imaginghtm Evelin Schrock - Technische Universitaumlt Dresden spectral karyotyping cytogenetics httpswwwresearchgatenetprofileEvelin_Schrock Garry Nolan Stanford University ndash Mass cytometry MIBI-ToF high throughput imaging mass cytometry (42plex) httpwebstanfordedugroupnolanresourceshtml httpwebstanfordedugroupnolantechnologieshtml George McNamara ndash Cell Morphometry (41) Figure 1 right top two panels (55) The Chase (2016 temporal area maps lsquodynamic morphologyrsquo) (76) newsletter series on ldquoThe Chaserdquo (73) direct Vimeo movie of ldquoThe Chaserdquo Tiki_Goddess linkedin 10+plex blog httpsworksbepresscomgmcnamara41 httpsworksbepresscomgmcnamara55 httpsworksbepresscomgmcnamara76

httpsworksbepresscomgmcnamara73 httpsvimeocom175151196 httphomeearthlinknet~tiki_goddess httpswwwlinkedincomingeorgemcnamara httpswwwlinkedincompulsebd-biosciences-listed-tandems-horizon-brilliant-violets-mcnamara Gillian Griffiths - University of Cambridge - T-cell immunological synapse httpwwwcimrcamacukresearchprincipal-investigatorsprincipal-investigators-a-hgriffiths Hari Shroff NIBIB NIH httpswwwnibibnihgovlabs-at-nibibsection-high-resolution-optical-imaging-hroi HHMI Janelia Farm Research Campus (JFRC) - Advanced Imaging Center Open Science httpswwwjaneliaorgopen-scienceadvanced-imaging-center-aic httpswwwjaneliaorgopen-science Jeanne Lawrence University of Massachussetts Medical School httpwwwumassmededucellbiolabslawrencepersonnelprincipal-investigator Jennifer Lippincott-Schwartz ndash HHMI Janelia Farm httpswwwjaneliaorgpeoplejennifer-lippincott-schwartz Jin Zhang ndash UCSD httpprofilesucsdedujinzhang Joe DeRisi - UCSF - 3D printable lab stuff httpderisilabucsfeduindexphppage=3D John Russ Chris Russ Fovea Pro plugins for Adobe Photoshop httpwwwdrjohnrusscomindexhtml httpwwwdrjohnrusscombookshtml httpwwwreindeergraphicscomfoveaprotutorialhtml Julie Theriot httpcmgmstanfordedutheriot Karl Deisseroth ndash Stanford University ndash CLARITY optical tissue clearing Optogenetics httpclarityresourcecenterorg httpwebstanfordedugroupdlaboptogeneticsindexhtml Karsten Koumlnig (Koenig) - Saarland University and JenLab GmbH - biophotonics httpwwwbltuni-saarlanddeindex_ehtm httpwwwjenlabde httpwwwthelastescape-filmcom Karsten Rodenacker ndash image measurements httpkaro03bplacednetkaroMeMisc_WWWpdfMicrosoftWord-EQUAPATpdf Kevin Eliceiri ndash UW-Madison Open Source Photonics and Software Laboratory for Optical and Computational Instrumentation (LOCI) wwwlociwiscedu Klaus Kemp ndash Microlife Services ndash diatoms and other prepared microscope slides httpwwwdiatomscouk Kurt Thorn UCSF httpthornlabucsfedu httpsnicucsfedublog httpnicucsfeduFPvisualization httpgigapancomgigapans163370 Lihong Wang - WUSTL - Optical Imaging Laboratory photoacoustic tomography

httpoilabseaswustledu httpoilabseaswustleduresearch_0html Loren Looger - HHMI JFRC - iGluSnFr fluorescent protein biosensor httpswwwjaneliaorglablooger-lab Mary-Lou Pardue ndash MIT (first ever in situ hybridization with J Gall) httpsbiologymitedupeoplemary_lou_pardue httpsenwikipediaorgwikiMary-Lou_Pardue Nancy Allbritton - UNC - Chemical cytometry microraft arrays organ-on-a-chip httpswwwbmencsueduindexphpcomponentcomprofileruserprofilenlallbri httpwwwbmeuncedulabsallbritton Navin Varadarajan - UH - single-cell Lab httpwwwcheeuhedufacultyvaradarajan httpsinglecellcheeuheducontacthtml Nicholas Shaner - Scintillon Institute - mNeonGreen httpwwwscintillonorgshaner_lab Rebecca Richards-Kortum httpbioengineeringriceedufacultyrebecca_richards-kortumaspx Robert Campbell - Fluorescent proteins optogenetic proteins httpcampbellwebchemualbertaca httpcampbellwebchemualbertacaprojects-2 Robert Murphy ndash Cell measurements web services httpmurphylabwebcmueduservices Sabine Mai - University of Manitoba - Genomic Centre for Cancer Research and Diagnosis (GCCRD) - httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBPlatformsGCCRDhtml httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBScientistsMaiAwardshtml Sally Ward and Raimund Ober - Texas AampM University - httpwwwwardoberlabcom Simon Watkins - U Pittsburgh Center for Biologic Imaging httpwwwcbppittedufacultywatkinshtml httpwwwcbppittedufacultylabwatkinshtml httpwwwcbipittedu Stefan Hell ndash Deparment Hell NanoBiopohotonics httpwwwmpibpcmpgdehell httpsenwikipediaorgwikiStefan_Hell httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014hell-factshtml Sunney Xie Harvard httpsbernsteinharvardedu Susan Cox ndash 3B microscopy httpwwwcoxphysicscomindexhtml httpwwwcoxphysicscom3b Radim Chmeliacutek - Center for innovative microscopy Experimental biophotonics group httpswwwceiteceuceitec-butexperimental-biophotonicsrg3 httpwwwbiophotczhome Taekjip Ha ndash Johns Hopkins University ndash single molecules httphamedjhmiedu

Thomas Ried ndash NCI NIH SKYM-FISH and CGH Database httpsccrcancergovGenetics-Branchthomas-ried httpsccrcancergovGenetics-Branchthomas-riedqt-staff_profile_tabs=9qt-staff_profile_tabs ftpftpncbinlmnihgovsky-cghDATA httpswwwncbinlmnihgovdbvar Viviana Gradinaru ndash CalTech ndash CLARITYPACT Optogenetics httpwwwbbecaltecheducontentviviana-gradinaru httpglabcaltechedu Vladislav Verkhusha - near infrared fluorescent proteins httpwwweinsteinyuedulabsvlad-verkhushadefaultaspx httpwwweinsteinyueduresearchfacilitiesfluorescent WE Moerner ndash Stanford University httpwebstanfordedugroupmoerner Willard Wiggans ndash micro gallery httpwwwwillard-wigancomgallery Wolf Frommer ndash Molecular sensors httpbiosensordpbcarnegiescienceedu (fluorescent protein biosensors table) Xiaowei Zhuang = Harvard httpzhuangharvardedu Yuval Garini - Bar-Ilan University - Nano-Bio-Photonics laboratory httpgarinilabbiuacil Microscopy Magazines Imaging amp Microscopy httpwwwimaging-gitcommagazine Laser Focus World httpwwwlaserfocusworldcomindexhtml Microscopy amp Analysis httpwwwmicroscopy-analysiscom Microscopy Today httpwwwmicroscopy-todaycom Microscopy-UK httpwwwmicroscopy-ukorguk Photonics Spectra Biophotonics httpwwwphotonicscomPublicationsaspx The Microscope Journal httpmcriorgv72the-microscope-journal RMS Infocus Magazine httpwwwrmsorgukstudy-readinfocus-magazinehtml Nobel Prizes in Light Microscopy and Related Fields Chemistry 1925 colloids (light sheet) Zsigmondy (Siedentopf Zsigmondy 1902) httpswwwnobelprizeorgnobel_prizeschemistrylaureates1925

Chemistry 2000 conductive polymers Heeger MacDiarmid Shirakawa (Brilliant Violets Ultraviolets Blues) httpwwwnobelprizeorgnobel_prizeschemistrylaureates2000 Chemistry 2008 green fluorescent protein GFP Shimomura Chalfie Tsien httpwwwnobelprizeorgnobel_prizeschemistrylaureates2008 Chemistry 2014 super-resolved fluorescence microscopy Betzig Hell Moerner httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014 Physics 1953 Phase Contrast Zernike httpswwwnobelprizeorgnobel_prizesphysicslaureates1953 Physics 2009 invention of an imaging semiconductor circuit ndash the CCD sensor Kao Boyle Smith httpwwwnobelprizeorgnobel_prizesphysicslaureates2009 Physics 2014 efficient blue light emitting diodes Akasaki Amano Nakamura httpwwwnobelprizeorgnobel_prizesphysicslaureates2014 Physiology or Medicine 2006 Fire and Mello RNA interference ndash gene silencing by double stranded RNA httpwwwnobelprizeorgnobel_prizesmedicinelaureates2006 Physiology or Medicine 2006 Capecchi Evans Smithies specific gene modifications in mice by the use of embryonic stem cells httpwwwnobelprizeorgnobel_prizesmedicinelaureates2007 Physiology or Medicine 2009 Blackburn Greider Szostak how chromosomes are protected by telomeres and telomerase httpwwwnobelprizeorgnobel_prizesmedicinelaureates2009 Physiology or Medicine 2012 Gurdon Yamamanka matured cells can be reprogrammed to become pluripotent httpwwwnobelprizeorgnobel_prizesmedicinelaureates2012

Table 442 Fluorophores Photophysics Data

Fluorophore Abs or Ex max (nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Acridine orange 271 520 27000 020 5

Alexa Fluor 430 431 541 16000 055 9

Alexa Fluor 488 495 519 71000 094 67

Alexa Fluor 532 532 553 81000 080 65

Alexa Fluor 546 556 573 104000 096 100

Alexa Fluor 568 578 603 91300 075 69

Alexa Fluor 594 590 617 73000 064 47

Allophycocyanin (APC) 650 660 700000 068 476

Atto 390 390 479 24000 090 22

Atto 425 436 484 45000 065 29

Atto 430LS 433 547 32000 065 21

Atto 465 453 508 75000 075 56

Atto 490LS 496 661 40000 030 12

Atto 520 525 547 105000 095 100

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 9: McNamara 20161006 revised draft tables for CPHG Light ...

Porvair Sciences - clear bottom assay plates httpwwwporvair-sciencescomenservices-menulife-sciencesclear-bottom-assay-plates Ted Pella Inc - glass bottom dishes clear wall or black wall (manufactured by WillCo Wells) httpswwwtedpellacomsection_html706dishhtm Warner Instruments (Harvard Apparatus) - culture dishes perfusion systems httpswwwwarneronlinecomproduct_cat_infocfmid=1322 Willco Wells - glass bottom dishes wwwwillcowellscom World Precision Instruments - Fluorodish glass bottom dishes httpswwwwpiinccomproductslaboratory-suppliesfd35-100-fluorodish-cell-culture-dish-35mm-23mm-well-pkg-of-100 Microscopes Microscopy Accessories (accessorize) Reagents Resources 3scan ndash knife edge scanning microscope (images slices repeats through specimen) httpwww3scancomdata-2 89North (affiliated with Chroma Technology Corp) httpwww89northcom Abberior Instruments ndash STED RESOLFT precision localization super-resolution microscopes STEDYCON convert any fluorescence microscope to STED httpabberior-instrumentscom httpabberior-instrumentscomproductscompact-lineabberior-stedy-con Acquifer ndash HIVE imaging machine (computer hardware) for high content screening big data httpswwwacquiferde Adobe Systems Inc httpwwwAdobecom httpscreativeadobecomproductsdownloadphotoshop Affymetrix eBioscience (ThermoFisher) - microarrays httpwwwaffymetrixcomestorebrowselevel_one_category_template_onejspparent=35796ampcategory=35796 httpwwwaffymetrixcomestorecatalog131547AFFYGeneChip26231743B+System+3000Dx+v22623423B1_1 Agilent Technologies ndash SureScan microarray scanner (array CGH microRNA SNPs CNV) httpwwwgenomicsagilentcomenMicroarray-Scanner-Processing-HardwareSureScan-Microarray-Scannercid=AG-PT-144 Andor Technology (Oxford Instruments) ndash sCMOS cameras Dragonfly spinning disk confocal Revolution DSD2 differential spinning disk confocal photostimulation (fluorescence recovery after photobleaching optogenetics) Mosaic3 DMDDLP high speed light patterning (optogenetics structured illumination) MicroPoint pulsed UV laser for ablation DNA damage photobleachingactivation uncaging accessories httpwwwandorcomscientific-camerasneo-and-zyla-scmos-cameras httpwwwandorcommicroscopy-systemsdragonfly httpwwwandorcommicroscopy-systemsrevolution-dsd httpwwwandorcommicroscopy-systemsphotostimulation httpwwwandorcommicroscopy-systemsphotostimulationmosaic httpwwwandorcommicroscopy-systemsphotostimulationmicropoint httpwwwandorcommicroscopy-systemsmicroscopy-components Apogee Instruments Inc (Andor Technology) ndash CCD cameras and filter wheels (mostly marketed for astronomy) httpwwwccdcomandorhtml Applied Scientific Instrumentation Inc ndash light sheet imager (iSPIM diSPIM)

wwwasiimagingcom httpwwwasiimagingcomindexphpproductslight-sheet-microscopyselective-plane-illumination-microscopy-ispim-dispim Applied NanoFluorescence LLC ndash NS1 NanoSpectralyzer (Raman and UV-VISNIR) NS MiniTracer near infrared spectrometer NFM NanoFluorescence microscope multi-laser light source single wall carbon nanotubes (NIR II fluorophores) httpappliednanocomproductshtml httpappliednanocomproductsns1html httpappliednanocomproductsproduct-list77-ns-minitracerhtml httpappliednanocomproductsnfmhtml httpappliednanocomproductsls-nhtml httpwwwnanowerkcomnewsnewsid=24132php Applied Spectral Imaging Inc httpwwwspectral-imagingcom ArgoLight ndash fluorescence resolution test target slides httpargolightcom AttoCube - attoMICROSCOPY overview attoCFM - Multichannel cryogenic (low temperature) confocal fluorescence microscopes 08 NA objective lenses 400-1000 nm spectral range httpwwwattocubecom httpwwwattocubecomattomicroscopyintroductiontab-2 httpwwwattocubecomattodownloads AutoQuant (Media Cybernetics) spatial deconvolution httpwwwmediacycomautoquantx3 Becker amp Hickl GmbH httpwwwbecker-hicklcomproductshtm Berkeley Lights Inc ndash manueuver into nanowells incubate recover 4000 single cells per chip httpswwwberkeleylightscomtechnology Bioaxial ndash Codim imaging conical diffraction beam shaper for super-resolution (4 sub-images) httpwwwbioaxialcomcodim-imaging Bioptechs - Live-Cell Micro-Observation Products httpwwwbioptechscom Bionumbers - database of useful biological numbers httpbionumbershmsharvardeduKeyNumbersaspx Biostatus ndash DRAQ5 DRAQ7 ApopTRAK CyTRAK Orange CyGel HypoxiTRAK httpwwwbiostatuscomProducts Bio-Tek ndash Cytation 3 Cell Imaging Multi-Mode Reader Lionheart FX Automated Live Cell Imager httpwwwbiotekcomproductsimagingcytation3_cell_imaging_multi_mode_readerhtml httpwwwbiotekcomproductsimaginglionheartfx_automated_live_cell_imagerhtml Biovision Technologies ndash distributor for several imagers including VT-iSIM instant super-resolution microscope httpbiovision-technologiescom httpbiovision-technologiescomsystemshtml httpbiovision-technologiescomvtisimhtml Bitplane (Andor Oxford Instruments) ndash Imaris imaging software httpwwwbitplanecom BMV Optical - custom lens assemblies and optical filters wwwbmvopticalcom

Bruker (previously Prairie Technologies Vutara) ndash Opterra confocal Ultima Multiphoton Vutara 352 single molecule localization microscopes httpswwwbrukercomproductsfluorescence-microscopesopterra-confocal-microscopyoverviewhtml httpswwwbrukercomproductsfluorescence-microscopesultima-multiphoton-microscopyhtml httpswwwbrukercomproductsfluorescence-microscopesvutara-super-resolution-microscopyoverviewhtml Cairn Research ndash standard and custom accessories ex Light Sheet Illuminator MultiCam (4 cameras) custom design httpswwwcairn-researchcouk httpswwwcairn-researchcoukproductl-spi-single-plane-illuminator (dual L-SPI for 4 illumination directions) httpswwwcairn-researchcoukproductmulticam httpswwwcairn-researchcoukcustom-design Cameca ndash NanoSIMS 50L (7plex stable isotope imaging) httpwwwcamecacominstruments-for-researchnanosimsaspx CellMic (formerly Holomic) - blood analysis or fluorescence imaging cytometer on a cell phone httpwwwcellmiccomcontentadvanced-technologies httpwwwcellmiccomcontentfluorescent-imaging-cytometry-and-e-coli-detection-on-a-cell-phone CellOptic ndash FINCH (Fresnel INcoherence Correlation Holography) httpwwwcellopticcomindex2html CellProfiler ndash High content screening (HCS) image processing and analysis software httpcellprofilerorg ClearLight Diagnostics - CLARITY Optimized Light Sheet Microscopy (3D tissue optical clearing + light sheet imaging) httpwwwclearlightdxcomindexhtml Confocalnl ndash Rescan confocal microscopy to obtain 170 nm resolution with any pinhole diameter httpwwwconfocalnl CoolLED ndash LED light sources httpwwwcoolledcomproduct-detailpe-4000 Crest Optics SRL ndash X-Light confocal X-Light V2 + VCS (VideoConfocal super-resolution) httpwwwcrestoptcom httpwwwcrestoptcomhtmlx-light_v2_vcshtml Cytoskeleton Inc - live cell imaging reagents Spirochrome SiR bioimaging probes httpwwwcytoskeletoncomlive-cell-reagents httpwwwcytoskeletoncomlive-cell-reagentsspirochrome CytoViva ndash darkfield imaging hypspectral imaging httpwwwcytovivacomproducts3d-enhanced-darkfield-imaging httpwwwcytovivacomproductshyperspectral-imaging-2hyperspectral-imaging Data Translation Inc - digitizer cards httpwwwdatxcom Delmic BV - combined correlative scanning electron microscope with inverted fluorescence microscope httpwwwdelmiccomdelphi httpswwwdelphimicroscopecom httpwwwdelmiccomsecom-super-resolution Digital Light Innovations (DLi) - CELscope C-mount LED Microscope using Texas Instruments DLP illuminator with a simple stand httpswwwdlinnovationscomdli-deep-dives-celscope-c-mount-led-microscope Double Helix LLC ndash single molecule localization microscope (Piestun) httpdoublehelixopticscom Edinburgh Super-resolution Imaging Consortium (ESRIC)

httpwwwesricorg Energetiq ndash Deep ultraviolet (DUV high radiance 170-2100 nm) laser driven light source (LDLS) httpwwwenergetiqcom Epi Technology - CaliCube - Cube for fluorescence light path to inspect epi Illumination light source (lamp) fiber optic or liquid light guide httpwwwepitechnologycomepitechnology-1 Essen Biosciences ndash Incucyte Zoom (imager inside incubator) httpwwwessenbiosciencecomenproductsincucyte Estigen Tissue Science ndash manual and automated tissue arrayer (tissue microarray maker) httpwwwestigencom Euro-Bioimaging httpwwweurobioimagingeu Excelitas Technologies (formerly Lumen Dynamics) ndash X-Cite LEDs httpwwwexcelitascomPagesProductX-Cite-LED-Solutionsaspx Expansion Technologies Inc (extbio) ndash Expansion microscopy httpwwwextbiocombuycell FEI (formerly Till Photonics) (Thermo Fisher) ndash correlative LM-EM single molecule Cryo-EM httpswwwfeicomlife-sciencescellular-biology httpswwwfeicomlife-sciencescellular-biologycorrelative-microscopy httpswwwfeicomlife-sciencesstructural-biology Femtonics - Multi-phton microscopes software accessories caged glutamate reagents services httpfemtonicseuproducts First Light Imaging ndash C-Red NIR imaging (800-2500 nm NIR windows I II III 650-950 nm 1100-1350 nm 1600-1870 nm[Shi et al 2015]) high speed visible EMCCD (400-1000 nm) httpwwwfirst-lightfrcategoryrangesinfrared Fluidigm ndash Helios imaging CyTOF mass cytometer (42plex) Callisto (32 independent chambers dose with up to 16 independent factors for 1-1000 cell populations culture up to 3 week) Polaris functional genomics meets imaging (48 single cells up to 24 hours after single cell selection from a population) httpswwwfluidigmcomproductshelios httpswwwfluidigmcomproductscallisto httpswwwfluidigmcomproductspolaris GattaQuant - nanorulers for high resolution microscopes and super-resolution microscopes performance testing httpwwwgattaquantcomNanoruler GE Healthcare life Sciences Applied Precision ndash DeltaVision deconvolution OMX OMX SR httpwwwgelifesciencescomwebappwcsstoresservletproductByIdenGELifeSciences-us29065728 httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usproductsAlternativeProductStructure_2380729065721 httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usproductsAlternativeProductStructure_2380729115476 German BioImagingorg httpwwwgermanbioimagingorgwikiindexphpMain_Page httpwwwgermanbioimagingorgwikiindexphpWorkgroup6SoftwarePackages GIGAmacro ndash Magnify2 gigapixel imagery oof macroscopic and microscopic objects Terapixel macro image httpwwwgigamacrocomgigapixel-macro-imaging-system httpwwwgigamacrocomworlds-first-terapixel-macro-image

Glencoe Software ndash OMERO Plus enterprise data management for scientific images and any associated metadata (OME = Open Microscopy Environment) DataViewer PathViewer httpsglencoesoftwarecomomeroplushtml httpsglencoesoftwarecomdataviewerhtml httpsglencoesoftwarecompathviewerhtml Gooch amp Housego ndash spectral imager httpsgoochandhousegocomminiature-spectral-imaging-camera httpwwwghinstrumentscomproductsspectral-imaging-synthesishsi-440c-hyperspectral-imaging-system Hindsight Imaging ndash spectral imaging httphindsight-imagingcom Horiba Scientific - SWIFT ultra-fast Raman confocal imaging Raman spectroscopy httpwwwhoribacomscientificproductsraman-spectroscopyraman-imagingswift httpwwwhoribacomscientificproductsraman-spectroscopyraman-imaging httpwwwhoribacomscientificproductsraman-spectroscopy IATIA Ultima Capital ndash QPm (quantitative phase microscopy) httpwwwultimacapitalnetiatiaimagingPublicationsIatia20ImagingapplicationNotesqpmApplicationWithConfocalMicroscopespdf Ibidi - heating and incubation systems optical O2 measurement systems Nanolive 3D Cell Explorer pump system gas incubation system httpibidicomxtproductsenInstruments-AccessoriesHeating-Incubation-Systems httpibidicomxtproductsenInstruments-Accessoriesibidi-OPAL-Optical-O2-Measurement-System httpibidicomxtproductsenInstruments-AccessoriesNanolive-3D-Cell-Explorer httpibidicomxtproductsenInstruments-Accessoriesibidi-Pump-System httpibidicomxtproductsenInstruments-AccessoriesHeating-Incubation-Systemsibidi-Gas-Incubation-System iLAbSolutions (Agilent Technologies) - Instrument management and scheduling software (cores and labs) httpwwwilabsolutionscominstrument-access-control ImageJ - Fiji ImageJ NIH ImageJ ImageJ ndash Fiji (Fiji is just ImageJ) is the main download site httpfijisc httpsimagejnihgovij wwwimagejnet Inscopix ndash nVista in vivo mouse brain imaging miniature microscope httpswwwinscopixcomproducts Intelligent Imaging Innovations Inc (3i) ndash Slidebook imaging software Lattice light sheet (high speed gentle to cells high resolution imaging) Dual-view Inverted Selective Plane Illumination (diSPIM) VIVO 2-Photon (VIVO 2P) multiphoton microscopy Everest intravital imaging Marianas 3D real-time deconvolution timelapse spinning disk FRAP TIRF FLIM single molecule environmental control Phasor - optogenetic photostimulation using digital holography Yokogawa spinning disk confocal units wwwintelligent-imagingcom httpswwwintelligent-imagingcomslidebookphp httpswwwintelligent-imagingcomsystemsphplattice httpswwwintelligent-imagingcomsystemsphpdispim httpswwwintelligent-imagingcomsystemsphptwophoton httpswwwintelligent-imagingcomsystemsphpeverest httpswwwintelligent-imagingcomsystemsphpmarianas httpswwwintelligent-imagingcomoptogeneticsphp httpswwwintelligent-imagingcomsdcphp ISS Inc ndash fluorescence lifetime imaging microscopy fluorescence correlation spectroscopy (FCS) confocal imaging httpwwwisscommicroscopyindexhtml JenLab GmbH cyto-microscopy multiphoton tomography httpwwwjenlabdeproducts250html httpwwwjenlabde2PM-Cryo1330html

httpwwwjenlabdeMultiphoton-Tomography680html Jenoptik - microscope cameras httpswwwjenoptikcomproductscameras-and-imaging-modulesmicroscope-cameras JPK Instruments - integrated atomic force microscope (AFM) force sensing optical tweezers optical trapping single cell force spectroscopy (SCFS) httpwwwjpkcomindex2enhtml httpusajpkcomoptical-tweezers-optical-trapping29ushtml httpusajpkcomcellular-adhesion-cytomechanics30ushtml Keyence ndash VK-X confocal (upright) BZ-X700 widefield (inverted) httpwwwkeyencecomssproductsmicroscopevkx httpwwwkeyencecomssproductsmicroscopebz-x700indexjsp KK Technology - CapiScope HVCS Handheld Video Capillaroscopy System (CytoScan) httpwwwkktechnologycomhvcshtml LaVision BioTec ndash TriMscope Multiphoton TriM Scope II Adaptive Optics UltraMicroscope II light sheet httpwwwlavisionbiotecde httpwwwlavisionbiotecdetrim-scope-overviewhtml httpwwwlavisionbiotecdetrim-scope-ii-adaptive-opticshtml httpwwwlavisionbiotecdeultramicroscope-ii-introductionhtml Laxco ndash upright and inverted microscopes httpwwwlaxcoinccomMICROSCOPES Lego ndash Lego Idea Microscopes httpsideaslegocomprojects44370 httpwwwnico71frlego-working-microscope Li-Cor ndash near-infared fluorescent dyes and in vivo imaging agents in vivo and Western blot imaging systems httpswwwlicorcombioproductsreagents httpswwwlicorcombioproductsreagentsirdyebrightsite_imaging_agents httpswwwlicorcombioproductsimaging_systemsodyssey_familyhtml httpswwwlicorcombioproductsimaging_systemspearl httpswwwlicorcombioproductsimaging_systemscdigit Life Imaging Services - ldquothe Ludin chamberrsquo ldquothe cube amp the boxrdquo httpwwwlischthechamberhtml httpwwwlischtheboxhtml Lightform Inc ndash PARISS imaging spectrometer httplightforminccom LMU Bioimaging httpwwwbioimagingbmcmeduni-muenchendelinkswebsitesindexhtml httpwwwbioimagingbmcmeduni-muenchendelearneduwebsitesindexhtml Ludl Electronic Products Ltd ndash automated XY stages focus motors filter wheels httpwwwludlcom

LumaCyte ndash Laser force Cytology (laser trap meets microfluidics to suspend and manipulate single cells) httpwwwlumacytecomabouttechnology Lumencor ndash LEDs fluorescence light sources httplumencorcomproducts Luxcel ndash mitochondrial and cellular functions O2 sensor reagents httpluxcelcomproduct+list Luxendo GmbH ndash light sheet imager

wwwluxendoeu Lyncee tec - digital holography microscopy (DHM) high content screening by DHM httpwwwlynceeteccom httpwwwlynceeteccomhigh-content-screening Mad City Labs Inc - nanopositioning wwwmadcitylabscom Mauna Kea Technologies ndash CellVizio confocal laser endomicroscopy httpwwwmaunakeatechcomenhealthcare-professionalscellvizio-endomicroscopy-0 MBF Bioscience - stereology and neuron morphology quantitative imaging httpwwwmbfbiosciencecom McCrone Group wwwmccronecominstrument-sales Media Cybernetics Inc ndash Image Premier 3D AutoQuant X3 deconvolution httpwwwmediacycom Meiji Techno America wwwmeijitechnocom MesoLens Ltd httpwwwmesolenscomproducttechnical-specifications httpwwwmesolenscomimages httpswwwbiophotonicsstrathacukresearch_1htm Meyer Instruments ndash Pathscan Enabler GigaMacro digital pathology telepathology httpmeyerinstcom httpmeyerinstcompathscan-enabler-5 httpmeyerinstcomgigamacro-gigapixel-macro-imaging httpmeyerinstcomhomescanners httprealtimetelepathologycom Microarrays - Large-Scale Gene Expression and Microarray Links and Resources httpswwwebiacukarrayexpress Micro-Manager ndash Device Support ndash tabulates many microscope cameras and motorized accessories every new camera and accessory should have a uManager driver to enable simple use with Fiji ImageJ httpsmicro-managerorg httpsmicro-managerorgwikiDevice_Support httpsopen-imagingcom Microvolution ndash (near) instant gratification spatial deconvolution using NVidia GPU card(s) httpmicrovolutioncom Mightex Systems ndash optogenetics DMDDLP illuminator (digital micro-mirror device digital light processing) httpwwwmightexsystemscomindexphpcPath=245 Millipore-Sigma Merck KGaA (Amnis Corp CellASIC EMD Millipore) ndash ImageStreamX and FlowSight imaging flow cytometers ONIX2 Microperfusion System for microscopes httpswwwemdmilliporecom httpswwwemdmilliporecomUSenlife-science-researchcell-analysisamnis-imaging-flow-cytometersQ6ubqBm3UAAAFLCKIpygJnav httpwwwemdmilliporecomUSenlife-science-researchcell-culture-systemscellASIC-live-cell-analysisd1CbqBw58AAAE_0j13MnAnav Mitutoyo America Corp wwwmitutoyocom httpecatalogmitutoyocomMF-U-Series-176-High-power-Multi-function-Measuring-Microscopes-C1413aspx

Molecular Devices Corporation Universal Imaging Corporation (Danaher) ndash MetaMorph MetaFluor high content systems (HCS) httpswwwmoleculardevicescomsystemsmetamorph-research-imaging httpmdccusthelpcomappanswersdetaila_id19319 httpswwwmoleculardevicescomsystemshigh-content-imaging Molecular Machines amp Industries - laser microdissection and tweezer systems httpwwwmolecular-machinescomhome MUSE Microscopy Inc ndash Deep UV illumination for shallow depth of field imaging httpwwwmusemicrocom Micro Video Instruments Inc - DarkLite illuminator httpwwwmvi-inccom NanoEnTek ndash JuLI Stage (imager inside incubator or on lab bench) httpwwwjulistagecom National Instruments ndash LabView software httpwwwnicomen-ushtml Navitar - Hoffman Modulation Contrast (HMC alternative to differential interference contrast phase contrast) custom lens design UVDUVNUV imaging lenses httpsnavitarcommarketsmicroscopy httpsnavitarcomproductsimaging-opticscustom-microscope-objectivescustom-microscope-objectives httpsnavitarcomproductsimaging-opticsuv-imaging National Center for X-ray Tomography (NCXT) ndash soft X-ray tomography (CT of hydrated cells) XM-2 dedicated biological SXT microscope Prof Carolyn Larabell Director (see also SiriusXT) httpncxtlblgov httpncxtlblgovsxt httpncxtlblgovmanual httpncxtlblgovq=carolyn Neogenomics (Clarient) ndash MultiOmyx immunofluorescence or DNA FISH (ldquo60plexrdquo) httpneogenomicscomPharma-ServicesLab-ServicesMultiOmyxTechnologyMultiOmyx-IF-Assay-DNA-FISH-assay-NGS-from-ROI Nexcelom ndash Celigo imaging cytometer Cellometer cell counters httpwwwnexcelomcomCeligoindexphp httpwwwnexcelomcomProducts Nikon ndash Ti-LAPP modular illumination system (for Nikon Ti series microscopes) TIRF Optogenetics httpswwwnikoninstrumentscomProductsPhotostimulation-and-TIRFTi-LAPP Nirmidas Biotech httpwwwnirmidascomtechnologynir httpwwwnirmidascomproductsniriidye NVidia ndash Pascal 10+ Gbps GPU cards for instant gratification deconvolution (software from Microvolutioncom SVInl) httpwwwgeforcecomhardware10seriesgeforce-gtx-1080 httpwwwgeforcecomhardware10seriestitan-x-pascal httpwwwnvidiacomobjectquadro-graphics-with-pascalhtml Ocean Optics ndash spectrometers httpoceanopticscomproduct-categorymodular-spectrometers Oko-Lab stage top incubator httpwwwoko-labcomstage-top Open Microscopy Environment (OME) ndash OMERO (see also Glencoe Software) Bio-Formats LOCI

httpswwwopenmicroscopyorgsite httpswwwopenmicroscopyorgsiteproductsomero httpswwwopenmicroscopyorgsiteproductsbio-formats httpswwwopenmicroscopyorgsitesupportbio-formats52supported-formatshtml httpswwwopenmicroscopyorgsiteaboutdevelopment-teamskevin OpenSPIM ndash do-it-yourself selective plane illumination microscopy (light sheet imaging) httpopenspimorgWelcome_to_the_OpenSPIM_Wiki OpenSpinMicroscopy ndash do-it-yourself SPIMDSLMOPT microscopes httpssitesgooglecomsiteopenspinmicroscopy Ovizio ndash differential digital holography (similar to quantitative phase imaging) httpwwwoviziocomenHome httpwwwoviziocomenMicroscopesQMod Oxford Gene Technologies ndash microarrays ndash cytogenetics molecule genetics cancer research pre-implantation genetic diagnosis httpwwwogtcomclinical_genetics Oxford Nanoimaging ndash single molecule(s) localization fluorescence resonance energy transfer (FRET) (Kapanidis) wwwoxfordnicom Pathology Devices ndash LiveCell stage top incubator amp controller tissue microarrayers (TMA makers) httpwwwpathologydevicescomLiveCellhtm httpwwwpathologydevicescomTMArrayerhtm PeCon GmbH ndash microscope incubators httpwwwpeconbiz Pembroke Instruments ndash spectrometers mini-lasers httppembrokeinstrumentscomqmini-spectrometer httppembrokeinstrumentscommini-lasers PerkinElmer ndash in vivo imaging systems (bioluminescence NIR fluorescence) Vectra digital slide scanner httpwwwperkinelmercomcategoryin-vivo-imaging-instruments httpwwwperkinelmercomcategoryquantitative-pathology-imaging-instruments Phi Optics ndash CellVista SLIM Pro (quantitative phase microscopy) httpphiopticscom Photometrics (Roper Scientific) ndash DualView QuadView httpwwwphotometricscom httpwwwphotometricscomproductsmultichannel Photon Technology International httpwwwpti-njcomindexhtml

PicoQuant GmbH ndash fluorescence lifetime imaging microscopes (FLIM) STED 3D-EasySTED httpswwwpicoquantcomproductscategoryfluorescence-microscopes httpswwwpicoquantcomapplicationscategorylife-sciencested httpwwweasystedorg Physik Instrumente GmbH amp Co KG (PI) - Nanopositioning Applications for Microscopy Neuroscience and Metrology httpswwwphysikinstrumentecomen httpwwwpi-usausindexphp PreSens Prescision Sensing GmbH - VisiSens measure and visualize Oxygen pH or carbon dioxide distributions httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-biological-researchhtml httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-life-science-researchhtml Prior Scientific

httpwwwprior-uscom Profusa Inc - Lumee tissue-integrated biosensors scaffolds httpprofusacomtechnology Reindeer Graphics Inc ndash OptiPix Fovea Pro 9plugins for Adobe Photoshop 6 and CS series) httpwwwreindeergraphicscom Renishaw - StreamLine fast chemical imaging Raman spectroscopy httpwwwrenishawcomenstreamline-generate-chemical-images-rapidly--9449 httpwwwrenishawcomenraman-spectroscopy--6150 Sanford Burnham Prebys ndash High Content Screening httpwwwsbpdiscoveryorgtechnologysrPagesLaJolla_HighContentScreeningaspx ScopeM - Scientific Center for Optical and Electron Microscopy - ETH Zurich httpwwwscopemethzch SiriusXT - soft X-ray tomography (SXT) microscope (CT scan hydrated cell) httpsiriusxtcom SpectraGenetics - Fluorogen Activating Peptides (FAPs) new genetically encoded ldquobinaryrdquo reporters httpspectrageneticscomproductsvectors-for-expressing-fluorogen-activating-proteinsfap-technology-overview Spirochrome - Silicon Rhodamine (SiR) and other fluorescent reagents probes for bioimaging httpspirochromecom Stanford Photonics Inc httpwwwstanfordphotonicscom httpwwwstanfordphotonicscomLife20SciencesLifeScihtm

Stream Technologies Inc ndash ColorFlow lens (multi-wavelength emission onto a camera) httpwwwstreamtechinccomproducts Sutter Instrument Company httpwwwsuttercom httpwwwsuttercomMICROSCOPESindexhtml httpwwwsuttercomIMAGINGindexhtml SVI Huygens ndash Professional (general image analysis) deconvolution NVidia GPU deconvolution httpssvinlHuygensProfessional httpssvinlHuygensDeconvolution httpssvinlHuygensGPU Sysmex Partex ndash CyScope httpwwwsysmex-parteccomproductsmicroscopyhtml httpwwwsysmex-parteccomproductsprdouct-detailviewcyscopeR-malaria-3238html Technical Instruments httpwwwtechinstcomproductsphp TESCAN Brno sro - Tescan Q-PHASE multimodal holographic quantitative phase imaging system (QPi) optional fluorescence httpwwwtescancomenproductsq-phaseq-phase httpq-phasetescancom httpq-phasetescancomindexphptechnologyspecifications Ted Pella Inc ndash specialty light microscopy and electron microscopy supplies httpswwwtedpellacom Texas Instruments ndash DLP 4100 development kit (digital light processingrsquo DMD digital micromirror device) httpwwwticomtooldlpd4x00kit

ThorLabs ndash iCyte imaging cytometer multiphoton confocal EnVista digital slide scanning microscopes httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7473 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7494 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=5696 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=6570 TIRF Labs lightguide TIRF prism TIRF TIRF-Electrochemistry httpwwwtirf-labscom httpwwwtirf-labscomtechnologieshtml TissueVision - Serial Two Photon Tomography (image volume ablate imaged volume with multiphoton laser repeat) httpwwwtissuevisioncomtechnology Tokai Hit - stage top incubator httpwwwtokaihitcomenglishproduct_guidanceoptionhtml TopoNomos Ltd ndash Toponome Imaging Cycler ndash immunofluorescence (100plex) httpwwwtoposnomoscomtechnologyhtml Ultivue Inc ndash DNA-PAINT ndash reagents data processing service httpwwwultivuecom httpwwwultivuecomproducts UMech Technologies ndash Cytovar HCS up to 16 excitation wavelengths httpcloudumechcomproducts httpcloudumechcomproductsmodelC16 Visitech ndash vt-iSIM instant super-resolution microscopy up to 1000 frames per second confocal scanners and light engines httpwwwvisitechcoukvt-isimhtml httpwwwvisitechcoukproductshtml Visitron Systems GmbH - high speed imaging systems httpwwwvisitronde Visualsonics (Fujifilm) - photoacoustic imaging httpwwwvisualsonicscomproductstechnology-overview Wicked Lasers httpwwwwickedlaserscom httpwwwwickedlaserscomarctic WITec Wissenschaftliche Instrumente und Technologie GmbH - imaging systems for FLIM Raman AFM and SNOM analysis httpwitecdeproducts httpwwwwitec-instrumentscom WM Keck Center for Adaptive Optical Microscopy (CfAOM) at UC Santa Cruz httpscfaomsoeucscedu httpcfaoucolickorgpgallery Yokogawa Corp ndash spinning disk confocal scanner live cell imager high content screener confocal quantitative cytometer httpwwwyokogawacomsolutionsproducts-platformslife-science httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-scanner-unit-csu httpwwwyokogawacomsolutionsproducts-platformslife-scienceall-in-one-live-cell-imaging-solution httpwwwyokogawacomsolutionsproducts-platformslife-sciencehigh-throughput-cytological-discovery-system httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-quantitative-image-cytometer Zellkraftwerk (ChipCytometry) ndash immunofluorescence (80plex) httpwwwzellkraftwerkcomProducts2phtml httpwwwzellkraftwerkcomZKWOnephtmlSoftware

httpwwwchipcytometrycomtechnologyphtml Fluorescence Spectra Data and Graphing Sites PubSpectra ndash Excel file data download httpsworksbepresscomgmcnamara9 BD Biosciences ndash spectrum viewer Brilliant fluorophores httpwwwbdbiosciencescomussspectrumviewer httpwwwbdbiosciencescomusapplicationssspectrumguidepage BioLegend ndash spectra analyzer Brilliant Violet fluorophores httpwwwbiolegendcomspectraanalyzer httpwwwbiolegendcombrilliantviolet Chroma Technology httpswwwchromacomspectra-viewer eBioscience (Affymetrix ThermoFisher) ndash fluorPlan ndash a multi-laser spectra viewer httpwwwebiosciencecomresourcesfluorplan-spectra-viewerhtm Spectra Viewer (requires Java) Evrogen ndash Spectrum Viewer httpevrogencomspectra-viewerflashviewerhtml Fluorophoresorg ndash Fluorescent Substances httpwwwfluorophorestugrazatsubstance I Love GFP httpssitesgooglecomsiteilovegfpHomefps Lambert and Thorn UCSF Fluorescent protein properties httpnicucsfeduFPvisualization Leica Microsystem - ldquoFluoScoutrdquo httpwwwleica-microsystemscomfluoscout

Molecular Probes Invitrogen Thermo Fisher ndash Fluorescence SpectraViewer httpwwwthermofishercomusenhomelife-sciencecell-analysislabeling-chemistryfluorescence-spectraviewerhtml httpsitunesapplecomusappfluorescence-spectraviewerid421031826 (iTunes App) Nightsea - Compendium of spectra web sites httpwwwnightseacomsfa-sharingfluorescence-spectra-viewers Omega Optical ldquoCurvomatricrdquo httpswwwomegafilterscomcurvomatic

PhotoChemCAD 20 (Jonathan S Lindsey) dye spectra database and chemistry calculator NIRvana Sciences httpwwwphotochemcadcom httpnirvanasciencescompage_id=3088 UCSF (Lambert Thorn 2016) - Fluorescent protein properties httpnicucsfeduFPvisualization University of Arizona - Fluorescent Spectra Database httpwwwspectraarizonaedu Semrock - Searchlight httpssearchlightsemrockcom Spectroscopy Ninja ndash links to spectral and fluorescence data Spekwin32 spectroscopy software httpwwweffemm2deinfoinfo_specdatahtml

httpwwweffemm2deindexhtml Zeiss ndash interactive fluorescence dye and filter database overview dyes overview filter sets httpswwwmicro-shopzeisscoms=50479761ad21e5ampl=enampp=usampf=fampa=i httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=d httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=f Researcher Labs Alby Diaspro ndash IIT httpwwwlambsitindexphppage=People Alice Ting ndash MIT httpwwwtinglaborgresearch Allen Institute for Brain Science httpwwwalleninstituteorgwhat-we-dobrain-science Allen Institute for Cell Science httpwwwalleninstituteorgwhat-we-docell-science Amina Qutub - Rice University - How are human cells designed lab httpsqutublaborgqutub-lab Amy Herr UC Berkeley ndash Single cell Westerns httpherrlabberkeleyedu Amy Palmer ndash UC Boulder httpspalmerlabcoloradoedu Andrew York ndash Calico Life Sciences httpswwwcalicolabscomteam-memberandrew-york Anne Carpenter ndash Broad Institute CellProfiler httpspersonalbroadinstituteorganne Arjun Raj UPenn single molecule RNA FISH quantitative understanding cellular functions httprajlabseasupenneduindexhtml httpwwwpopscicomsciencearticle2013-09arjun-raj Atsuko Miyawaki - Laboratory for Cell Function Dynamics (CFDS) Fucci2 fluorescent proteins cell cycle indicator httpwwwbrainrikenjpenfacultydetails30 httpcfdsbrainrikenjp httpcfdsbrainrikenjpFuccihtml Aydogan Ozcan - UCLA - new imaging and sensing architectures httpinnovateeeuclaeduwelcomehtml httpwwwhhmiorgscientistsaydogan-ozcan Badri Roysam - UH - FARSIGHT Toolkit httpwwweeuhedufacultyroysam httpwwwfarsight-toolkitorgwikiMain_Page Brian J Ford ndash microscopist and popularizer httpsuklinkedincominprofbrianjford Carolyn Larabell ndashNational Center for X-ray Tomography (LBNL) UCSF httpncxtlblgovq=carolyn httpprofilesucsfeducarolynlarabell Clare Waterman ndash NHLBI NIH

httpswwwnhlbinihgovresearchintramuralresearcherspiwaterman-clare Dana Peer - Columbia University - Computational Systems Biology viSNE and more software httpwwwc2b2columbiaedudanapeerlabhtml httpwwwc2b2columbiaedudanapeerlabhtmlcythtml David Mayerich - UH - STIM Laboratory Scalable Tissue Imaging and Modeling httpwwweeuhedufacultymayerich httpstimeeuhedu David Piston WUSTL httpwwwcellbiologywustledufacultytenureddavid-w-piston-phd Diane Lidke and Keith Lidke - University of New Mexico httppathologyunmeduresearchfaculty-laboratoriesthe-lidke-laboratoryindexhtml httppanda3physunmedu~klidke Donna Arndt-Jovin and Thomas Jovin - Max Planck Institute for Biophysical Chemistry Laboratory of Cellular Dynamics httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsDonnaArdndt-JovinResearchAreasAndProjects httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsChairmanThomasJovinResearchAreasAndProjects Ed Boyden ndash MIT Media Lab ndash expansion microscopy (ExM) optogenetics httpsyntheticneurobiologyorg httpsyntheticneurobiologyorgprotocols httpsyntheticneurobiologyorgpublications httpwwwtedcomtalksed_boyden_baby_diapers_inspired_this_new_way_to_study_the_brain httpwwwextbiocombuycell Elizabeth Blackburn ndash Salk Institute - Telomeres httpswwwsalkeduscientistelizabeth-blackburn httpsenwikipediaorgwikiElizabeth_Blackburn httpswwwnobelprizeorgnobel_prizesmedicinelaureates2009blackburn-factshtml Elizabeth Hillman - Columbia university - SCAPE (Swept Confocally-Aligned Planar Excitation) high speed 3D microscopy DyCE (dynamic contrast enhancement to image and segment small animal organs live) Neuroimaging amp Neurovascular Coupling httporionbmecolumbiaedu~hillmanInstrumentationhtml httporionbmecolumbiaedu~hillmanSCAPEhtml httporionbmecolumbiaedu~hillmanMolecularhtml httporionbmecolumbiaedu~hillmanBrain_Imaginghtml Eric Betzig ndash UCSF (moving from HHMI Janelia Farm in 2016) httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014betzig-factshtml Eva Sevick-Muraca ndash UT Health Science Center at Houston molecular imaging clinical NIR fluoresceince imaging httpswwwutheduimmprofilehtmid=1005459 httpswwwutheduimmcentersmolecular-imaginghtm Evelin Schrock - Technische Universitaumlt Dresden spectral karyotyping cytogenetics httpswwwresearchgatenetprofileEvelin_Schrock Garry Nolan Stanford University ndash Mass cytometry MIBI-ToF high throughput imaging mass cytometry (42plex) httpwebstanfordedugroupnolanresourceshtml httpwebstanfordedugroupnolantechnologieshtml George McNamara ndash Cell Morphometry (41) Figure 1 right top two panels (55) The Chase (2016 temporal area maps lsquodynamic morphologyrsquo) (76) newsletter series on ldquoThe Chaserdquo (73) direct Vimeo movie of ldquoThe Chaserdquo Tiki_Goddess linkedin 10+plex blog httpsworksbepresscomgmcnamara41 httpsworksbepresscomgmcnamara55 httpsworksbepresscomgmcnamara76

httpsworksbepresscomgmcnamara73 httpsvimeocom175151196 httphomeearthlinknet~tiki_goddess httpswwwlinkedincomingeorgemcnamara httpswwwlinkedincompulsebd-biosciences-listed-tandems-horizon-brilliant-violets-mcnamara Gillian Griffiths - University of Cambridge - T-cell immunological synapse httpwwwcimrcamacukresearchprincipal-investigatorsprincipal-investigators-a-hgriffiths Hari Shroff NIBIB NIH httpswwwnibibnihgovlabs-at-nibibsection-high-resolution-optical-imaging-hroi HHMI Janelia Farm Research Campus (JFRC) - Advanced Imaging Center Open Science httpswwwjaneliaorgopen-scienceadvanced-imaging-center-aic httpswwwjaneliaorgopen-science Jeanne Lawrence University of Massachussetts Medical School httpwwwumassmededucellbiolabslawrencepersonnelprincipal-investigator Jennifer Lippincott-Schwartz ndash HHMI Janelia Farm httpswwwjaneliaorgpeoplejennifer-lippincott-schwartz Jin Zhang ndash UCSD httpprofilesucsdedujinzhang Joe DeRisi - UCSF - 3D printable lab stuff httpderisilabucsfeduindexphppage=3D John Russ Chris Russ Fovea Pro plugins for Adobe Photoshop httpwwwdrjohnrusscomindexhtml httpwwwdrjohnrusscombookshtml httpwwwreindeergraphicscomfoveaprotutorialhtml Julie Theriot httpcmgmstanfordedutheriot Karl Deisseroth ndash Stanford University ndash CLARITY optical tissue clearing Optogenetics httpclarityresourcecenterorg httpwebstanfordedugroupdlaboptogeneticsindexhtml Karsten Koumlnig (Koenig) - Saarland University and JenLab GmbH - biophotonics httpwwwbltuni-saarlanddeindex_ehtm httpwwwjenlabde httpwwwthelastescape-filmcom Karsten Rodenacker ndash image measurements httpkaro03bplacednetkaroMeMisc_WWWpdfMicrosoftWord-EQUAPATpdf Kevin Eliceiri ndash UW-Madison Open Source Photonics and Software Laboratory for Optical and Computational Instrumentation (LOCI) wwwlociwiscedu Klaus Kemp ndash Microlife Services ndash diatoms and other prepared microscope slides httpwwwdiatomscouk Kurt Thorn UCSF httpthornlabucsfedu httpsnicucsfedublog httpnicucsfeduFPvisualization httpgigapancomgigapans163370 Lihong Wang - WUSTL - Optical Imaging Laboratory photoacoustic tomography

httpoilabseaswustledu httpoilabseaswustleduresearch_0html Loren Looger - HHMI JFRC - iGluSnFr fluorescent protein biosensor httpswwwjaneliaorglablooger-lab Mary-Lou Pardue ndash MIT (first ever in situ hybridization with J Gall) httpsbiologymitedupeoplemary_lou_pardue httpsenwikipediaorgwikiMary-Lou_Pardue Nancy Allbritton - UNC - Chemical cytometry microraft arrays organ-on-a-chip httpswwwbmencsueduindexphpcomponentcomprofileruserprofilenlallbri httpwwwbmeuncedulabsallbritton Navin Varadarajan - UH - single-cell Lab httpwwwcheeuhedufacultyvaradarajan httpsinglecellcheeuheducontacthtml Nicholas Shaner - Scintillon Institute - mNeonGreen httpwwwscintillonorgshaner_lab Rebecca Richards-Kortum httpbioengineeringriceedufacultyrebecca_richards-kortumaspx Robert Campbell - Fluorescent proteins optogenetic proteins httpcampbellwebchemualbertaca httpcampbellwebchemualbertacaprojects-2 Robert Murphy ndash Cell measurements web services httpmurphylabwebcmueduservices Sabine Mai - University of Manitoba - Genomic Centre for Cancer Research and Diagnosis (GCCRD) - httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBPlatformsGCCRDhtml httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBScientistsMaiAwardshtml Sally Ward and Raimund Ober - Texas AampM University - httpwwwwardoberlabcom Simon Watkins - U Pittsburgh Center for Biologic Imaging httpwwwcbppittedufacultywatkinshtml httpwwwcbppittedufacultylabwatkinshtml httpwwwcbipittedu Stefan Hell ndash Deparment Hell NanoBiopohotonics httpwwwmpibpcmpgdehell httpsenwikipediaorgwikiStefan_Hell httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014hell-factshtml Sunney Xie Harvard httpsbernsteinharvardedu Susan Cox ndash 3B microscopy httpwwwcoxphysicscomindexhtml httpwwwcoxphysicscom3b Radim Chmeliacutek - Center for innovative microscopy Experimental biophotonics group httpswwwceiteceuceitec-butexperimental-biophotonicsrg3 httpwwwbiophotczhome Taekjip Ha ndash Johns Hopkins University ndash single molecules httphamedjhmiedu

Thomas Ried ndash NCI NIH SKYM-FISH and CGH Database httpsccrcancergovGenetics-Branchthomas-ried httpsccrcancergovGenetics-Branchthomas-riedqt-staff_profile_tabs=9qt-staff_profile_tabs ftpftpncbinlmnihgovsky-cghDATA httpswwwncbinlmnihgovdbvar Viviana Gradinaru ndash CalTech ndash CLARITYPACT Optogenetics httpwwwbbecaltecheducontentviviana-gradinaru httpglabcaltechedu Vladislav Verkhusha - near infrared fluorescent proteins httpwwweinsteinyuedulabsvlad-verkhushadefaultaspx httpwwweinsteinyueduresearchfacilitiesfluorescent WE Moerner ndash Stanford University httpwebstanfordedugroupmoerner Willard Wiggans ndash micro gallery httpwwwwillard-wigancomgallery Wolf Frommer ndash Molecular sensors httpbiosensordpbcarnegiescienceedu (fluorescent protein biosensors table) Xiaowei Zhuang = Harvard httpzhuangharvardedu Yuval Garini - Bar-Ilan University - Nano-Bio-Photonics laboratory httpgarinilabbiuacil Microscopy Magazines Imaging amp Microscopy httpwwwimaging-gitcommagazine Laser Focus World httpwwwlaserfocusworldcomindexhtml Microscopy amp Analysis httpwwwmicroscopy-analysiscom Microscopy Today httpwwwmicroscopy-todaycom Microscopy-UK httpwwwmicroscopy-ukorguk Photonics Spectra Biophotonics httpwwwphotonicscomPublicationsaspx The Microscope Journal httpmcriorgv72the-microscope-journal RMS Infocus Magazine httpwwwrmsorgukstudy-readinfocus-magazinehtml Nobel Prizes in Light Microscopy and Related Fields Chemistry 1925 colloids (light sheet) Zsigmondy (Siedentopf Zsigmondy 1902) httpswwwnobelprizeorgnobel_prizeschemistrylaureates1925

Chemistry 2000 conductive polymers Heeger MacDiarmid Shirakawa (Brilliant Violets Ultraviolets Blues) httpwwwnobelprizeorgnobel_prizeschemistrylaureates2000 Chemistry 2008 green fluorescent protein GFP Shimomura Chalfie Tsien httpwwwnobelprizeorgnobel_prizeschemistrylaureates2008 Chemistry 2014 super-resolved fluorescence microscopy Betzig Hell Moerner httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014 Physics 1953 Phase Contrast Zernike httpswwwnobelprizeorgnobel_prizesphysicslaureates1953 Physics 2009 invention of an imaging semiconductor circuit ndash the CCD sensor Kao Boyle Smith httpwwwnobelprizeorgnobel_prizesphysicslaureates2009 Physics 2014 efficient blue light emitting diodes Akasaki Amano Nakamura httpwwwnobelprizeorgnobel_prizesphysicslaureates2014 Physiology or Medicine 2006 Fire and Mello RNA interference ndash gene silencing by double stranded RNA httpwwwnobelprizeorgnobel_prizesmedicinelaureates2006 Physiology or Medicine 2006 Capecchi Evans Smithies specific gene modifications in mice by the use of embryonic stem cells httpwwwnobelprizeorgnobel_prizesmedicinelaureates2007 Physiology or Medicine 2009 Blackburn Greider Szostak how chromosomes are protected by telomeres and telomerase httpwwwnobelprizeorgnobel_prizesmedicinelaureates2009 Physiology or Medicine 2012 Gurdon Yamamanka matured cells can be reprogrammed to become pluripotent httpwwwnobelprizeorgnobel_prizesmedicinelaureates2012

Table 442 Fluorophores Photophysics Data

Fluorophore Abs or Ex max (nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Acridine orange 271 520 27000 020 5

Alexa Fluor 430 431 541 16000 055 9

Alexa Fluor 488 495 519 71000 094 67

Alexa Fluor 532 532 553 81000 080 65

Alexa Fluor 546 556 573 104000 096 100

Alexa Fluor 568 578 603 91300 075 69

Alexa Fluor 594 590 617 73000 064 47

Allophycocyanin (APC) 650 660 700000 068 476

Atto 390 390 479 24000 090 22

Atto 425 436 484 45000 065 29

Atto 430LS 433 547 32000 065 21

Atto 465 453 508 75000 075 56

Atto 490LS 496 661 40000 030 12

Atto 520 525 547 105000 095 100

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 10: McNamara 20161006 revised draft tables for CPHG Light ...

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httpwwwesricorg Energetiq ndash Deep ultraviolet (DUV high radiance 170-2100 nm) laser driven light source (LDLS) httpwwwenergetiqcom Epi Technology - CaliCube - Cube for fluorescence light path to inspect epi Illumination light source (lamp) fiber optic or liquid light guide httpwwwepitechnologycomepitechnology-1 Essen Biosciences ndash Incucyte Zoom (imager inside incubator) httpwwwessenbiosciencecomenproductsincucyte Estigen Tissue Science ndash manual and automated tissue arrayer (tissue microarray maker) httpwwwestigencom Euro-Bioimaging httpwwweurobioimagingeu Excelitas Technologies (formerly Lumen Dynamics) ndash X-Cite LEDs httpwwwexcelitascomPagesProductX-Cite-LED-Solutionsaspx Expansion Technologies Inc (extbio) ndash Expansion microscopy httpwwwextbiocombuycell FEI (formerly Till Photonics) (Thermo Fisher) ndash correlative LM-EM single molecule Cryo-EM httpswwwfeicomlife-sciencescellular-biology httpswwwfeicomlife-sciencescellular-biologycorrelative-microscopy httpswwwfeicomlife-sciencesstructural-biology Femtonics - Multi-phton microscopes software accessories caged glutamate reagents services httpfemtonicseuproducts First Light Imaging ndash C-Red NIR imaging (800-2500 nm NIR windows I II III 650-950 nm 1100-1350 nm 1600-1870 nm[Shi et al 2015]) high speed visible EMCCD (400-1000 nm) httpwwwfirst-lightfrcategoryrangesinfrared Fluidigm ndash Helios imaging CyTOF mass cytometer (42plex) Callisto (32 independent chambers dose with up to 16 independent factors for 1-1000 cell populations culture up to 3 week) Polaris functional genomics meets imaging (48 single cells up to 24 hours after single cell selection from a population) httpswwwfluidigmcomproductshelios httpswwwfluidigmcomproductscallisto httpswwwfluidigmcomproductspolaris GattaQuant - nanorulers for high resolution microscopes and super-resolution microscopes performance testing httpwwwgattaquantcomNanoruler GE Healthcare life Sciences Applied Precision ndash DeltaVision deconvolution OMX OMX SR httpwwwgelifesciencescomwebappwcsstoresservletproductByIdenGELifeSciences-us29065728 httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usproductsAlternativeProductStructure_2380729065721 httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usproductsAlternativeProductStructure_2380729115476 German BioImagingorg httpwwwgermanbioimagingorgwikiindexphpMain_Page httpwwwgermanbioimagingorgwikiindexphpWorkgroup6SoftwarePackages GIGAmacro ndash Magnify2 gigapixel imagery oof macroscopic and microscopic objects Terapixel macro image httpwwwgigamacrocomgigapixel-macro-imaging-system httpwwwgigamacrocomworlds-first-terapixel-macro-image

Glencoe Software ndash OMERO Plus enterprise data management for scientific images and any associated metadata (OME = Open Microscopy Environment) DataViewer PathViewer httpsglencoesoftwarecomomeroplushtml httpsglencoesoftwarecomdataviewerhtml httpsglencoesoftwarecompathviewerhtml Gooch amp Housego ndash spectral imager httpsgoochandhousegocomminiature-spectral-imaging-camera httpwwwghinstrumentscomproductsspectral-imaging-synthesishsi-440c-hyperspectral-imaging-system Hindsight Imaging ndash spectral imaging httphindsight-imagingcom Horiba Scientific - SWIFT ultra-fast Raman confocal imaging Raman spectroscopy httpwwwhoribacomscientificproductsraman-spectroscopyraman-imagingswift httpwwwhoribacomscientificproductsraman-spectroscopyraman-imaging httpwwwhoribacomscientificproductsraman-spectroscopy IATIA Ultima Capital ndash QPm (quantitative phase microscopy) httpwwwultimacapitalnetiatiaimagingPublicationsIatia20ImagingapplicationNotesqpmApplicationWithConfocalMicroscopespdf Ibidi - heating and incubation systems optical O2 measurement systems Nanolive 3D Cell Explorer pump system gas incubation system httpibidicomxtproductsenInstruments-AccessoriesHeating-Incubation-Systems httpibidicomxtproductsenInstruments-Accessoriesibidi-OPAL-Optical-O2-Measurement-System httpibidicomxtproductsenInstruments-AccessoriesNanolive-3D-Cell-Explorer httpibidicomxtproductsenInstruments-Accessoriesibidi-Pump-System httpibidicomxtproductsenInstruments-AccessoriesHeating-Incubation-Systemsibidi-Gas-Incubation-System iLAbSolutions (Agilent Technologies) - Instrument management and scheduling software (cores and labs) httpwwwilabsolutionscominstrument-access-control ImageJ - Fiji ImageJ NIH ImageJ ImageJ ndash Fiji (Fiji is just ImageJ) is the main download site httpfijisc httpsimagejnihgovij wwwimagejnet Inscopix ndash nVista in vivo mouse brain imaging miniature microscope httpswwwinscopixcomproducts Intelligent Imaging Innovations Inc (3i) ndash Slidebook imaging software Lattice light sheet (high speed gentle to cells high resolution imaging) Dual-view Inverted Selective Plane Illumination (diSPIM) VIVO 2-Photon (VIVO 2P) multiphoton microscopy Everest intravital imaging Marianas 3D real-time deconvolution timelapse spinning disk FRAP TIRF FLIM single molecule environmental control Phasor - optogenetic photostimulation using digital holography Yokogawa spinning disk confocal units wwwintelligent-imagingcom httpswwwintelligent-imagingcomslidebookphp httpswwwintelligent-imagingcomsystemsphplattice httpswwwintelligent-imagingcomsystemsphpdispim httpswwwintelligent-imagingcomsystemsphptwophoton httpswwwintelligent-imagingcomsystemsphpeverest httpswwwintelligent-imagingcomsystemsphpmarianas httpswwwintelligent-imagingcomoptogeneticsphp httpswwwintelligent-imagingcomsdcphp ISS Inc ndash fluorescence lifetime imaging microscopy fluorescence correlation spectroscopy (FCS) confocal imaging httpwwwisscommicroscopyindexhtml JenLab GmbH cyto-microscopy multiphoton tomography httpwwwjenlabdeproducts250html httpwwwjenlabde2PM-Cryo1330html

httpwwwjenlabdeMultiphoton-Tomography680html Jenoptik - microscope cameras httpswwwjenoptikcomproductscameras-and-imaging-modulesmicroscope-cameras JPK Instruments - integrated atomic force microscope (AFM) force sensing optical tweezers optical trapping single cell force spectroscopy (SCFS) httpwwwjpkcomindex2enhtml httpusajpkcomoptical-tweezers-optical-trapping29ushtml httpusajpkcomcellular-adhesion-cytomechanics30ushtml Keyence ndash VK-X confocal (upright) BZ-X700 widefield (inverted) httpwwwkeyencecomssproductsmicroscopevkx httpwwwkeyencecomssproductsmicroscopebz-x700indexjsp KK Technology - CapiScope HVCS Handheld Video Capillaroscopy System (CytoScan) httpwwwkktechnologycomhvcshtml LaVision BioTec ndash TriMscope Multiphoton TriM Scope II Adaptive Optics UltraMicroscope II light sheet httpwwwlavisionbiotecde httpwwwlavisionbiotecdetrim-scope-overviewhtml httpwwwlavisionbiotecdetrim-scope-ii-adaptive-opticshtml httpwwwlavisionbiotecdeultramicroscope-ii-introductionhtml Laxco ndash upright and inverted microscopes httpwwwlaxcoinccomMICROSCOPES Lego ndash Lego Idea Microscopes httpsideaslegocomprojects44370 httpwwwnico71frlego-working-microscope Li-Cor ndash near-infared fluorescent dyes and in vivo imaging agents in vivo and Western blot imaging systems httpswwwlicorcombioproductsreagents httpswwwlicorcombioproductsreagentsirdyebrightsite_imaging_agents httpswwwlicorcombioproductsimaging_systemsodyssey_familyhtml httpswwwlicorcombioproductsimaging_systemspearl httpswwwlicorcombioproductsimaging_systemscdigit Life Imaging Services - ldquothe Ludin chamberrsquo ldquothe cube amp the boxrdquo httpwwwlischthechamberhtml httpwwwlischtheboxhtml Lightform Inc ndash PARISS imaging spectrometer httplightforminccom LMU Bioimaging httpwwwbioimagingbmcmeduni-muenchendelinkswebsitesindexhtml httpwwwbioimagingbmcmeduni-muenchendelearneduwebsitesindexhtml Ludl Electronic Products Ltd ndash automated XY stages focus motors filter wheels httpwwwludlcom

LumaCyte ndash Laser force Cytology (laser trap meets microfluidics to suspend and manipulate single cells) httpwwwlumacytecomabouttechnology Lumencor ndash LEDs fluorescence light sources httplumencorcomproducts Luxcel ndash mitochondrial and cellular functions O2 sensor reagents httpluxcelcomproduct+list Luxendo GmbH ndash light sheet imager

wwwluxendoeu Lyncee tec - digital holography microscopy (DHM) high content screening by DHM httpwwwlynceeteccom httpwwwlynceeteccomhigh-content-screening Mad City Labs Inc - nanopositioning wwwmadcitylabscom Mauna Kea Technologies ndash CellVizio confocal laser endomicroscopy httpwwwmaunakeatechcomenhealthcare-professionalscellvizio-endomicroscopy-0 MBF Bioscience - stereology and neuron morphology quantitative imaging httpwwwmbfbiosciencecom McCrone Group wwwmccronecominstrument-sales Media Cybernetics Inc ndash Image Premier 3D AutoQuant X3 deconvolution httpwwwmediacycom Meiji Techno America wwwmeijitechnocom MesoLens Ltd httpwwwmesolenscomproducttechnical-specifications httpwwwmesolenscomimages httpswwwbiophotonicsstrathacukresearch_1htm Meyer Instruments ndash Pathscan Enabler GigaMacro digital pathology telepathology httpmeyerinstcom httpmeyerinstcompathscan-enabler-5 httpmeyerinstcomgigamacro-gigapixel-macro-imaging httpmeyerinstcomhomescanners httprealtimetelepathologycom Microarrays - Large-Scale Gene Expression and Microarray Links and Resources httpswwwebiacukarrayexpress Micro-Manager ndash Device Support ndash tabulates many microscope cameras and motorized accessories every new camera and accessory should have a uManager driver to enable simple use with Fiji ImageJ httpsmicro-managerorg httpsmicro-managerorgwikiDevice_Support httpsopen-imagingcom Microvolution ndash (near) instant gratification spatial deconvolution using NVidia GPU card(s) httpmicrovolutioncom Mightex Systems ndash optogenetics DMDDLP illuminator (digital micro-mirror device digital light processing) httpwwwmightexsystemscomindexphpcPath=245 Millipore-Sigma Merck KGaA (Amnis Corp CellASIC EMD Millipore) ndash ImageStreamX and FlowSight imaging flow cytometers ONIX2 Microperfusion System for microscopes httpswwwemdmilliporecom httpswwwemdmilliporecomUSenlife-science-researchcell-analysisamnis-imaging-flow-cytometersQ6ubqBm3UAAAFLCKIpygJnav httpwwwemdmilliporecomUSenlife-science-researchcell-culture-systemscellASIC-live-cell-analysisd1CbqBw58AAAE_0j13MnAnav Mitutoyo America Corp wwwmitutoyocom httpecatalogmitutoyocomMF-U-Series-176-High-power-Multi-function-Measuring-Microscopes-C1413aspx

Molecular Devices Corporation Universal Imaging Corporation (Danaher) ndash MetaMorph MetaFluor high content systems (HCS) httpswwwmoleculardevicescomsystemsmetamorph-research-imaging httpmdccusthelpcomappanswersdetaila_id19319 httpswwwmoleculardevicescomsystemshigh-content-imaging Molecular Machines amp Industries - laser microdissection and tweezer systems httpwwwmolecular-machinescomhome MUSE Microscopy Inc ndash Deep UV illumination for shallow depth of field imaging httpwwwmusemicrocom Micro Video Instruments Inc - DarkLite illuminator httpwwwmvi-inccom NanoEnTek ndash JuLI Stage (imager inside incubator or on lab bench) httpwwwjulistagecom National Instruments ndash LabView software httpwwwnicomen-ushtml Navitar - Hoffman Modulation Contrast (HMC alternative to differential interference contrast phase contrast) custom lens design UVDUVNUV imaging lenses httpsnavitarcommarketsmicroscopy httpsnavitarcomproductsimaging-opticscustom-microscope-objectivescustom-microscope-objectives httpsnavitarcomproductsimaging-opticsuv-imaging National Center for X-ray Tomography (NCXT) ndash soft X-ray tomography (CT of hydrated cells) XM-2 dedicated biological SXT microscope Prof Carolyn Larabell Director (see also SiriusXT) httpncxtlblgov httpncxtlblgovsxt httpncxtlblgovmanual httpncxtlblgovq=carolyn Neogenomics (Clarient) ndash MultiOmyx immunofluorescence or DNA FISH (ldquo60plexrdquo) httpneogenomicscomPharma-ServicesLab-ServicesMultiOmyxTechnologyMultiOmyx-IF-Assay-DNA-FISH-assay-NGS-from-ROI Nexcelom ndash Celigo imaging cytometer Cellometer cell counters httpwwwnexcelomcomCeligoindexphp httpwwwnexcelomcomProducts Nikon ndash Ti-LAPP modular illumination system (for Nikon Ti series microscopes) TIRF Optogenetics httpswwwnikoninstrumentscomProductsPhotostimulation-and-TIRFTi-LAPP Nirmidas Biotech httpwwwnirmidascomtechnologynir httpwwwnirmidascomproductsniriidye NVidia ndash Pascal 10+ Gbps GPU cards for instant gratification deconvolution (software from Microvolutioncom SVInl) httpwwwgeforcecomhardware10seriesgeforce-gtx-1080 httpwwwgeforcecomhardware10seriestitan-x-pascal httpwwwnvidiacomobjectquadro-graphics-with-pascalhtml Ocean Optics ndash spectrometers httpoceanopticscomproduct-categorymodular-spectrometers Oko-Lab stage top incubator httpwwwoko-labcomstage-top Open Microscopy Environment (OME) ndash OMERO (see also Glencoe Software) Bio-Formats LOCI

httpswwwopenmicroscopyorgsite httpswwwopenmicroscopyorgsiteproductsomero httpswwwopenmicroscopyorgsiteproductsbio-formats httpswwwopenmicroscopyorgsitesupportbio-formats52supported-formatshtml httpswwwopenmicroscopyorgsiteaboutdevelopment-teamskevin OpenSPIM ndash do-it-yourself selective plane illumination microscopy (light sheet imaging) httpopenspimorgWelcome_to_the_OpenSPIM_Wiki OpenSpinMicroscopy ndash do-it-yourself SPIMDSLMOPT microscopes httpssitesgooglecomsiteopenspinmicroscopy Ovizio ndash differential digital holography (similar to quantitative phase imaging) httpwwwoviziocomenHome httpwwwoviziocomenMicroscopesQMod Oxford Gene Technologies ndash microarrays ndash cytogenetics molecule genetics cancer research pre-implantation genetic diagnosis httpwwwogtcomclinical_genetics Oxford Nanoimaging ndash single molecule(s) localization fluorescence resonance energy transfer (FRET) (Kapanidis) wwwoxfordnicom Pathology Devices ndash LiveCell stage top incubator amp controller tissue microarrayers (TMA makers) httpwwwpathologydevicescomLiveCellhtm httpwwwpathologydevicescomTMArrayerhtm PeCon GmbH ndash microscope incubators httpwwwpeconbiz Pembroke Instruments ndash spectrometers mini-lasers httppembrokeinstrumentscomqmini-spectrometer httppembrokeinstrumentscommini-lasers PerkinElmer ndash in vivo imaging systems (bioluminescence NIR fluorescence) Vectra digital slide scanner httpwwwperkinelmercomcategoryin-vivo-imaging-instruments httpwwwperkinelmercomcategoryquantitative-pathology-imaging-instruments Phi Optics ndash CellVista SLIM Pro (quantitative phase microscopy) httpphiopticscom Photometrics (Roper Scientific) ndash DualView QuadView httpwwwphotometricscom httpwwwphotometricscomproductsmultichannel Photon Technology International httpwwwpti-njcomindexhtml

PicoQuant GmbH ndash fluorescence lifetime imaging microscopes (FLIM) STED 3D-EasySTED httpswwwpicoquantcomproductscategoryfluorescence-microscopes httpswwwpicoquantcomapplicationscategorylife-sciencested httpwwweasystedorg Physik Instrumente GmbH amp Co KG (PI) - Nanopositioning Applications for Microscopy Neuroscience and Metrology httpswwwphysikinstrumentecomen httpwwwpi-usausindexphp PreSens Prescision Sensing GmbH - VisiSens measure and visualize Oxygen pH or carbon dioxide distributions httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-biological-researchhtml httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-life-science-researchhtml Prior Scientific

httpwwwprior-uscom Profusa Inc - Lumee tissue-integrated biosensors scaffolds httpprofusacomtechnology Reindeer Graphics Inc ndash OptiPix Fovea Pro 9plugins for Adobe Photoshop 6 and CS series) httpwwwreindeergraphicscom Renishaw - StreamLine fast chemical imaging Raman spectroscopy httpwwwrenishawcomenstreamline-generate-chemical-images-rapidly--9449 httpwwwrenishawcomenraman-spectroscopy--6150 Sanford Burnham Prebys ndash High Content Screening httpwwwsbpdiscoveryorgtechnologysrPagesLaJolla_HighContentScreeningaspx ScopeM - Scientific Center for Optical and Electron Microscopy - ETH Zurich httpwwwscopemethzch SiriusXT - soft X-ray tomography (SXT) microscope (CT scan hydrated cell) httpsiriusxtcom SpectraGenetics - Fluorogen Activating Peptides (FAPs) new genetically encoded ldquobinaryrdquo reporters httpspectrageneticscomproductsvectors-for-expressing-fluorogen-activating-proteinsfap-technology-overview Spirochrome - Silicon Rhodamine (SiR) and other fluorescent reagents probes for bioimaging httpspirochromecom Stanford Photonics Inc httpwwwstanfordphotonicscom httpwwwstanfordphotonicscomLife20SciencesLifeScihtm

Stream Technologies Inc ndash ColorFlow lens (multi-wavelength emission onto a camera) httpwwwstreamtechinccomproducts Sutter Instrument Company httpwwwsuttercom httpwwwsuttercomMICROSCOPESindexhtml httpwwwsuttercomIMAGINGindexhtml SVI Huygens ndash Professional (general image analysis) deconvolution NVidia GPU deconvolution httpssvinlHuygensProfessional httpssvinlHuygensDeconvolution httpssvinlHuygensGPU Sysmex Partex ndash CyScope httpwwwsysmex-parteccomproductsmicroscopyhtml httpwwwsysmex-parteccomproductsprdouct-detailviewcyscopeR-malaria-3238html Technical Instruments httpwwwtechinstcomproductsphp TESCAN Brno sro - Tescan Q-PHASE multimodal holographic quantitative phase imaging system (QPi) optional fluorescence httpwwwtescancomenproductsq-phaseq-phase httpq-phasetescancom httpq-phasetescancomindexphptechnologyspecifications Ted Pella Inc ndash specialty light microscopy and electron microscopy supplies httpswwwtedpellacom Texas Instruments ndash DLP 4100 development kit (digital light processingrsquo DMD digital micromirror device) httpwwwticomtooldlpd4x00kit

ThorLabs ndash iCyte imaging cytometer multiphoton confocal EnVista digital slide scanning microscopes httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7473 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7494 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=5696 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=6570 TIRF Labs lightguide TIRF prism TIRF TIRF-Electrochemistry httpwwwtirf-labscom httpwwwtirf-labscomtechnologieshtml TissueVision - Serial Two Photon Tomography (image volume ablate imaged volume with multiphoton laser repeat) httpwwwtissuevisioncomtechnology Tokai Hit - stage top incubator httpwwwtokaihitcomenglishproduct_guidanceoptionhtml TopoNomos Ltd ndash Toponome Imaging Cycler ndash immunofluorescence (100plex) httpwwwtoposnomoscomtechnologyhtml Ultivue Inc ndash DNA-PAINT ndash reagents data processing service httpwwwultivuecom httpwwwultivuecomproducts UMech Technologies ndash Cytovar HCS up to 16 excitation wavelengths httpcloudumechcomproducts httpcloudumechcomproductsmodelC16 Visitech ndash vt-iSIM instant super-resolution microscopy up to 1000 frames per second confocal scanners and light engines httpwwwvisitechcoukvt-isimhtml httpwwwvisitechcoukproductshtml Visitron Systems GmbH - high speed imaging systems httpwwwvisitronde Visualsonics (Fujifilm) - photoacoustic imaging httpwwwvisualsonicscomproductstechnology-overview Wicked Lasers httpwwwwickedlaserscom httpwwwwickedlaserscomarctic WITec Wissenschaftliche Instrumente und Technologie GmbH - imaging systems for FLIM Raman AFM and SNOM analysis httpwitecdeproducts httpwwwwitec-instrumentscom WM Keck Center for Adaptive Optical Microscopy (CfAOM) at UC Santa Cruz httpscfaomsoeucscedu httpcfaoucolickorgpgallery Yokogawa Corp ndash spinning disk confocal scanner live cell imager high content screener confocal quantitative cytometer httpwwwyokogawacomsolutionsproducts-platformslife-science httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-scanner-unit-csu httpwwwyokogawacomsolutionsproducts-platformslife-scienceall-in-one-live-cell-imaging-solution httpwwwyokogawacomsolutionsproducts-platformslife-sciencehigh-throughput-cytological-discovery-system httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-quantitative-image-cytometer Zellkraftwerk (ChipCytometry) ndash immunofluorescence (80plex) httpwwwzellkraftwerkcomProducts2phtml httpwwwzellkraftwerkcomZKWOnephtmlSoftware

httpwwwchipcytometrycomtechnologyphtml Fluorescence Spectra Data and Graphing Sites PubSpectra ndash Excel file data download httpsworksbepresscomgmcnamara9 BD Biosciences ndash spectrum viewer Brilliant fluorophores httpwwwbdbiosciencescomussspectrumviewer httpwwwbdbiosciencescomusapplicationssspectrumguidepage BioLegend ndash spectra analyzer Brilliant Violet fluorophores httpwwwbiolegendcomspectraanalyzer httpwwwbiolegendcombrilliantviolet Chroma Technology httpswwwchromacomspectra-viewer eBioscience (Affymetrix ThermoFisher) ndash fluorPlan ndash a multi-laser spectra viewer httpwwwebiosciencecomresourcesfluorplan-spectra-viewerhtm Spectra Viewer (requires Java) Evrogen ndash Spectrum Viewer httpevrogencomspectra-viewerflashviewerhtml Fluorophoresorg ndash Fluorescent Substances httpwwwfluorophorestugrazatsubstance I Love GFP httpssitesgooglecomsiteilovegfpHomefps Lambert and Thorn UCSF Fluorescent protein properties httpnicucsfeduFPvisualization Leica Microsystem - ldquoFluoScoutrdquo httpwwwleica-microsystemscomfluoscout

Molecular Probes Invitrogen Thermo Fisher ndash Fluorescence SpectraViewer httpwwwthermofishercomusenhomelife-sciencecell-analysislabeling-chemistryfluorescence-spectraviewerhtml httpsitunesapplecomusappfluorescence-spectraviewerid421031826 (iTunes App) Nightsea - Compendium of spectra web sites httpwwwnightseacomsfa-sharingfluorescence-spectra-viewers Omega Optical ldquoCurvomatricrdquo httpswwwomegafilterscomcurvomatic

PhotoChemCAD 20 (Jonathan S Lindsey) dye spectra database and chemistry calculator NIRvana Sciences httpwwwphotochemcadcom httpnirvanasciencescompage_id=3088 UCSF (Lambert Thorn 2016) - Fluorescent protein properties httpnicucsfeduFPvisualization University of Arizona - Fluorescent Spectra Database httpwwwspectraarizonaedu Semrock - Searchlight httpssearchlightsemrockcom Spectroscopy Ninja ndash links to spectral and fluorescence data Spekwin32 spectroscopy software httpwwweffemm2deinfoinfo_specdatahtml

httpwwweffemm2deindexhtml Zeiss ndash interactive fluorescence dye and filter database overview dyes overview filter sets httpswwwmicro-shopzeisscoms=50479761ad21e5ampl=enampp=usampf=fampa=i httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=d httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=f Researcher Labs Alby Diaspro ndash IIT httpwwwlambsitindexphppage=People Alice Ting ndash MIT httpwwwtinglaborgresearch Allen Institute for Brain Science httpwwwalleninstituteorgwhat-we-dobrain-science Allen Institute for Cell Science httpwwwalleninstituteorgwhat-we-docell-science Amina Qutub - Rice University - How are human cells designed lab httpsqutublaborgqutub-lab Amy Herr UC Berkeley ndash Single cell Westerns httpherrlabberkeleyedu Amy Palmer ndash UC Boulder httpspalmerlabcoloradoedu Andrew York ndash Calico Life Sciences httpswwwcalicolabscomteam-memberandrew-york Anne Carpenter ndash Broad Institute CellProfiler httpspersonalbroadinstituteorganne Arjun Raj UPenn single molecule RNA FISH quantitative understanding cellular functions httprajlabseasupenneduindexhtml httpwwwpopscicomsciencearticle2013-09arjun-raj Atsuko Miyawaki - Laboratory for Cell Function Dynamics (CFDS) Fucci2 fluorescent proteins cell cycle indicator httpwwwbrainrikenjpenfacultydetails30 httpcfdsbrainrikenjp httpcfdsbrainrikenjpFuccihtml Aydogan Ozcan - UCLA - new imaging and sensing architectures httpinnovateeeuclaeduwelcomehtml httpwwwhhmiorgscientistsaydogan-ozcan Badri Roysam - UH - FARSIGHT Toolkit httpwwweeuhedufacultyroysam httpwwwfarsight-toolkitorgwikiMain_Page Brian J Ford ndash microscopist and popularizer httpsuklinkedincominprofbrianjford Carolyn Larabell ndashNational Center for X-ray Tomography (LBNL) UCSF httpncxtlblgovq=carolyn httpprofilesucsfeducarolynlarabell Clare Waterman ndash NHLBI NIH

httpswwwnhlbinihgovresearchintramuralresearcherspiwaterman-clare Dana Peer - Columbia University - Computational Systems Biology viSNE and more software httpwwwc2b2columbiaedudanapeerlabhtml httpwwwc2b2columbiaedudanapeerlabhtmlcythtml David Mayerich - UH - STIM Laboratory Scalable Tissue Imaging and Modeling httpwwweeuhedufacultymayerich httpstimeeuhedu David Piston WUSTL httpwwwcellbiologywustledufacultytenureddavid-w-piston-phd Diane Lidke and Keith Lidke - University of New Mexico httppathologyunmeduresearchfaculty-laboratoriesthe-lidke-laboratoryindexhtml httppanda3physunmedu~klidke Donna Arndt-Jovin and Thomas Jovin - Max Planck Institute for Biophysical Chemistry Laboratory of Cellular Dynamics httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsDonnaArdndt-JovinResearchAreasAndProjects httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsChairmanThomasJovinResearchAreasAndProjects Ed Boyden ndash MIT Media Lab ndash expansion microscopy (ExM) optogenetics httpsyntheticneurobiologyorg httpsyntheticneurobiologyorgprotocols httpsyntheticneurobiologyorgpublications httpwwwtedcomtalksed_boyden_baby_diapers_inspired_this_new_way_to_study_the_brain httpwwwextbiocombuycell Elizabeth Blackburn ndash Salk Institute - Telomeres httpswwwsalkeduscientistelizabeth-blackburn httpsenwikipediaorgwikiElizabeth_Blackburn httpswwwnobelprizeorgnobel_prizesmedicinelaureates2009blackburn-factshtml Elizabeth Hillman - Columbia university - SCAPE (Swept Confocally-Aligned Planar Excitation) high speed 3D microscopy DyCE (dynamic contrast enhancement to image and segment small animal organs live) Neuroimaging amp Neurovascular Coupling httporionbmecolumbiaedu~hillmanInstrumentationhtml httporionbmecolumbiaedu~hillmanSCAPEhtml httporionbmecolumbiaedu~hillmanMolecularhtml httporionbmecolumbiaedu~hillmanBrain_Imaginghtml Eric Betzig ndash UCSF (moving from HHMI Janelia Farm in 2016) httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014betzig-factshtml Eva Sevick-Muraca ndash UT Health Science Center at Houston molecular imaging clinical NIR fluoresceince imaging httpswwwutheduimmprofilehtmid=1005459 httpswwwutheduimmcentersmolecular-imaginghtm Evelin Schrock - Technische Universitaumlt Dresden spectral karyotyping cytogenetics httpswwwresearchgatenetprofileEvelin_Schrock Garry Nolan Stanford University ndash Mass cytometry MIBI-ToF high throughput imaging mass cytometry (42plex) httpwebstanfordedugroupnolanresourceshtml httpwebstanfordedugroupnolantechnologieshtml George McNamara ndash Cell Morphometry (41) Figure 1 right top two panels (55) The Chase (2016 temporal area maps lsquodynamic morphologyrsquo) (76) newsletter series on ldquoThe Chaserdquo (73) direct Vimeo movie of ldquoThe Chaserdquo Tiki_Goddess linkedin 10+plex blog httpsworksbepresscomgmcnamara41 httpsworksbepresscomgmcnamara55 httpsworksbepresscomgmcnamara76

httpsworksbepresscomgmcnamara73 httpsvimeocom175151196 httphomeearthlinknet~tiki_goddess httpswwwlinkedincomingeorgemcnamara httpswwwlinkedincompulsebd-biosciences-listed-tandems-horizon-brilliant-violets-mcnamara Gillian Griffiths - University of Cambridge - T-cell immunological synapse httpwwwcimrcamacukresearchprincipal-investigatorsprincipal-investigators-a-hgriffiths Hari Shroff NIBIB NIH httpswwwnibibnihgovlabs-at-nibibsection-high-resolution-optical-imaging-hroi HHMI Janelia Farm Research Campus (JFRC) - Advanced Imaging Center Open Science httpswwwjaneliaorgopen-scienceadvanced-imaging-center-aic httpswwwjaneliaorgopen-science Jeanne Lawrence University of Massachussetts Medical School httpwwwumassmededucellbiolabslawrencepersonnelprincipal-investigator Jennifer Lippincott-Schwartz ndash HHMI Janelia Farm httpswwwjaneliaorgpeoplejennifer-lippincott-schwartz Jin Zhang ndash UCSD httpprofilesucsdedujinzhang Joe DeRisi - UCSF - 3D printable lab stuff httpderisilabucsfeduindexphppage=3D John Russ Chris Russ Fovea Pro plugins for Adobe Photoshop httpwwwdrjohnrusscomindexhtml httpwwwdrjohnrusscombookshtml httpwwwreindeergraphicscomfoveaprotutorialhtml Julie Theriot httpcmgmstanfordedutheriot Karl Deisseroth ndash Stanford University ndash CLARITY optical tissue clearing Optogenetics httpclarityresourcecenterorg httpwebstanfordedugroupdlaboptogeneticsindexhtml Karsten Koumlnig (Koenig) - Saarland University and JenLab GmbH - biophotonics httpwwwbltuni-saarlanddeindex_ehtm httpwwwjenlabde httpwwwthelastescape-filmcom Karsten Rodenacker ndash image measurements httpkaro03bplacednetkaroMeMisc_WWWpdfMicrosoftWord-EQUAPATpdf Kevin Eliceiri ndash UW-Madison Open Source Photonics and Software Laboratory for Optical and Computational Instrumentation (LOCI) wwwlociwiscedu Klaus Kemp ndash Microlife Services ndash diatoms and other prepared microscope slides httpwwwdiatomscouk Kurt Thorn UCSF httpthornlabucsfedu httpsnicucsfedublog httpnicucsfeduFPvisualization httpgigapancomgigapans163370 Lihong Wang - WUSTL - Optical Imaging Laboratory photoacoustic tomography

httpoilabseaswustledu httpoilabseaswustleduresearch_0html Loren Looger - HHMI JFRC - iGluSnFr fluorescent protein biosensor httpswwwjaneliaorglablooger-lab Mary-Lou Pardue ndash MIT (first ever in situ hybridization with J Gall) httpsbiologymitedupeoplemary_lou_pardue httpsenwikipediaorgwikiMary-Lou_Pardue Nancy Allbritton - UNC - Chemical cytometry microraft arrays organ-on-a-chip httpswwwbmencsueduindexphpcomponentcomprofileruserprofilenlallbri httpwwwbmeuncedulabsallbritton Navin Varadarajan - UH - single-cell Lab httpwwwcheeuhedufacultyvaradarajan httpsinglecellcheeuheducontacthtml Nicholas Shaner - Scintillon Institute - mNeonGreen httpwwwscintillonorgshaner_lab Rebecca Richards-Kortum httpbioengineeringriceedufacultyrebecca_richards-kortumaspx Robert Campbell - Fluorescent proteins optogenetic proteins httpcampbellwebchemualbertaca httpcampbellwebchemualbertacaprojects-2 Robert Murphy ndash Cell measurements web services httpmurphylabwebcmueduservices Sabine Mai - University of Manitoba - Genomic Centre for Cancer Research and Diagnosis (GCCRD) - httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBPlatformsGCCRDhtml httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBScientistsMaiAwardshtml Sally Ward and Raimund Ober - Texas AampM University - httpwwwwardoberlabcom Simon Watkins - U Pittsburgh Center for Biologic Imaging httpwwwcbppittedufacultywatkinshtml httpwwwcbppittedufacultylabwatkinshtml httpwwwcbipittedu Stefan Hell ndash Deparment Hell NanoBiopohotonics httpwwwmpibpcmpgdehell httpsenwikipediaorgwikiStefan_Hell httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014hell-factshtml Sunney Xie Harvard httpsbernsteinharvardedu Susan Cox ndash 3B microscopy httpwwwcoxphysicscomindexhtml httpwwwcoxphysicscom3b Radim Chmeliacutek - Center for innovative microscopy Experimental biophotonics group httpswwwceiteceuceitec-butexperimental-biophotonicsrg3 httpwwwbiophotczhome Taekjip Ha ndash Johns Hopkins University ndash single molecules httphamedjhmiedu

Thomas Ried ndash NCI NIH SKYM-FISH and CGH Database httpsccrcancergovGenetics-Branchthomas-ried httpsccrcancergovGenetics-Branchthomas-riedqt-staff_profile_tabs=9qt-staff_profile_tabs ftpftpncbinlmnihgovsky-cghDATA httpswwwncbinlmnihgovdbvar Viviana Gradinaru ndash CalTech ndash CLARITYPACT Optogenetics httpwwwbbecaltecheducontentviviana-gradinaru httpglabcaltechedu Vladislav Verkhusha - near infrared fluorescent proteins httpwwweinsteinyuedulabsvlad-verkhushadefaultaspx httpwwweinsteinyueduresearchfacilitiesfluorescent WE Moerner ndash Stanford University httpwebstanfordedugroupmoerner Willard Wiggans ndash micro gallery httpwwwwillard-wigancomgallery Wolf Frommer ndash Molecular sensors httpbiosensordpbcarnegiescienceedu (fluorescent protein biosensors table) Xiaowei Zhuang = Harvard httpzhuangharvardedu Yuval Garini - Bar-Ilan University - Nano-Bio-Photonics laboratory httpgarinilabbiuacil Microscopy Magazines Imaging amp Microscopy httpwwwimaging-gitcommagazine Laser Focus World httpwwwlaserfocusworldcomindexhtml Microscopy amp Analysis httpwwwmicroscopy-analysiscom Microscopy Today httpwwwmicroscopy-todaycom Microscopy-UK httpwwwmicroscopy-ukorguk Photonics Spectra Biophotonics httpwwwphotonicscomPublicationsaspx The Microscope Journal httpmcriorgv72the-microscope-journal RMS Infocus Magazine httpwwwrmsorgukstudy-readinfocus-magazinehtml Nobel Prizes in Light Microscopy and Related Fields Chemistry 1925 colloids (light sheet) Zsigmondy (Siedentopf Zsigmondy 1902) httpswwwnobelprizeorgnobel_prizeschemistrylaureates1925

Chemistry 2000 conductive polymers Heeger MacDiarmid Shirakawa (Brilliant Violets Ultraviolets Blues) httpwwwnobelprizeorgnobel_prizeschemistrylaureates2000 Chemistry 2008 green fluorescent protein GFP Shimomura Chalfie Tsien httpwwwnobelprizeorgnobel_prizeschemistrylaureates2008 Chemistry 2014 super-resolved fluorescence microscopy Betzig Hell Moerner httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014 Physics 1953 Phase Contrast Zernike httpswwwnobelprizeorgnobel_prizesphysicslaureates1953 Physics 2009 invention of an imaging semiconductor circuit ndash the CCD sensor Kao Boyle Smith httpwwwnobelprizeorgnobel_prizesphysicslaureates2009 Physics 2014 efficient blue light emitting diodes Akasaki Amano Nakamura httpwwwnobelprizeorgnobel_prizesphysicslaureates2014 Physiology or Medicine 2006 Fire and Mello RNA interference ndash gene silencing by double stranded RNA httpwwwnobelprizeorgnobel_prizesmedicinelaureates2006 Physiology or Medicine 2006 Capecchi Evans Smithies specific gene modifications in mice by the use of embryonic stem cells httpwwwnobelprizeorgnobel_prizesmedicinelaureates2007 Physiology or Medicine 2009 Blackburn Greider Szostak how chromosomes are protected by telomeres and telomerase httpwwwnobelprizeorgnobel_prizesmedicinelaureates2009 Physiology or Medicine 2012 Gurdon Yamamanka matured cells can be reprogrammed to become pluripotent httpwwwnobelprizeorgnobel_prizesmedicinelaureates2012

Table 442 Fluorophores Photophysics Data

Fluorophore Abs or Ex max (nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Acridine orange 271 520 27000 020 5

Alexa Fluor 430 431 541 16000 055 9

Alexa Fluor 488 495 519 71000 094 67

Alexa Fluor 532 532 553 81000 080 65

Alexa Fluor 546 556 573 104000 096 100

Alexa Fluor 568 578 603 91300 075 69

Alexa Fluor 594 590 617 73000 064 47

Allophycocyanin (APC) 650 660 700000 068 476

Atto 390 390 479 24000 090 22

Atto 425 436 484 45000 065 29

Atto 430LS 433 547 32000 065 21

Atto 465 453 508 75000 075 56

Atto 490LS 496 661 40000 030 12

Atto 520 525 547 105000 095 100

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 11: McNamara 20161006 revised draft tables for CPHG Light ...

Bruker (previously Prairie Technologies Vutara) ndash Opterra confocal Ultima Multiphoton Vutara 352 single molecule localization microscopes httpswwwbrukercomproductsfluorescence-microscopesopterra-confocal-microscopyoverviewhtml httpswwwbrukercomproductsfluorescence-microscopesultima-multiphoton-microscopyhtml httpswwwbrukercomproductsfluorescence-microscopesvutara-super-resolution-microscopyoverviewhtml Cairn Research ndash standard and custom accessories ex Light Sheet Illuminator MultiCam (4 cameras) custom design httpswwwcairn-researchcouk httpswwwcairn-researchcoukproductl-spi-single-plane-illuminator (dual L-SPI for 4 illumination directions) httpswwwcairn-researchcoukproductmulticam httpswwwcairn-researchcoukcustom-design Cameca ndash NanoSIMS 50L (7plex stable isotope imaging) httpwwwcamecacominstruments-for-researchnanosimsaspx CellMic (formerly Holomic) - blood analysis or fluorescence imaging cytometer on a cell phone httpwwwcellmiccomcontentadvanced-technologies httpwwwcellmiccomcontentfluorescent-imaging-cytometry-and-e-coli-detection-on-a-cell-phone CellOptic ndash FINCH (Fresnel INcoherence Correlation Holography) httpwwwcellopticcomindex2html CellProfiler ndash High content screening (HCS) image processing and analysis software httpcellprofilerorg ClearLight Diagnostics - CLARITY Optimized Light Sheet Microscopy (3D tissue optical clearing + light sheet imaging) httpwwwclearlightdxcomindexhtml Confocalnl ndash Rescan confocal microscopy to obtain 170 nm resolution with any pinhole diameter httpwwwconfocalnl CoolLED ndash LED light sources httpwwwcoolledcomproduct-detailpe-4000 Crest Optics SRL ndash X-Light confocal X-Light V2 + VCS (VideoConfocal super-resolution) httpwwwcrestoptcom httpwwwcrestoptcomhtmlx-light_v2_vcshtml Cytoskeleton Inc - live cell imaging reagents Spirochrome SiR bioimaging probes httpwwwcytoskeletoncomlive-cell-reagents httpwwwcytoskeletoncomlive-cell-reagentsspirochrome CytoViva ndash darkfield imaging hypspectral imaging httpwwwcytovivacomproducts3d-enhanced-darkfield-imaging httpwwwcytovivacomproductshyperspectral-imaging-2hyperspectral-imaging Data Translation Inc - digitizer cards httpwwwdatxcom Delmic BV - combined correlative scanning electron microscope with inverted fluorescence microscope httpwwwdelmiccomdelphi httpswwwdelphimicroscopecom httpwwwdelmiccomsecom-super-resolution Digital Light Innovations (DLi) - CELscope C-mount LED Microscope using Texas Instruments DLP illuminator with a simple stand httpswwwdlinnovationscomdli-deep-dives-celscope-c-mount-led-microscope Double Helix LLC ndash single molecule localization microscope (Piestun) httpdoublehelixopticscom Edinburgh Super-resolution Imaging Consortium (ESRIC)

httpwwwesricorg Energetiq ndash Deep ultraviolet (DUV high radiance 170-2100 nm) laser driven light source (LDLS) httpwwwenergetiqcom Epi Technology - CaliCube - Cube for fluorescence light path to inspect epi Illumination light source (lamp) fiber optic or liquid light guide httpwwwepitechnologycomepitechnology-1 Essen Biosciences ndash Incucyte Zoom (imager inside incubator) httpwwwessenbiosciencecomenproductsincucyte Estigen Tissue Science ndash manual and automated tissue arrayer (tissue microarray maker) httpwwwestigencom Euro-Bioimaging httpwwweurobioimagingeu Excelitas Technologies (formerly Lumen Dynamics) ndash X-Cite LEDs httpwwwexcelitascomPagesProductX-Cite-LED-Solutionsaspx Expansion Technologies Inc (extbio) ndash Expansion microscopy httpwwwextbiocombuycell FEI (formerly Till Photonics) (Thermo Fisher) ndash correlative LM-EM single molecule Cryo-EM httpswwwfeicomlife-sciencescellular-biology httpswwwfeicomlife-sciencescellular-biologycorrelative-microscopy httpswwwfeicomlife-sciencesstructural-biology Femtonics - Multi-phton microscopes software accessories caged glutamate reagents services httpfemtonicseuproducts First Light Imaging ndash C-Red NIR imaging (800-2500 nm NIR windows I II III 650-950 nm 1100-1350 nm 1600-1870 nm[Shi et al 2015]) high speed visible EMCCD (400-1000 nm) httpwwwfirst-lightfrcategoryrangesinfrared Fluidigm ndash Helios imaging CyTOF mass cytometer (42plex) Callisto (32 independent chambers dose with up to 16 independent factors for 1-1000 cell populations culture up to 3 week) Polaris functional genomics meets imaging (48 single cells up to 24 hours after single cell selection from a population) httpswwwfluidigmcomproductshelios httpswwwfluidigmcomproductscallisto httpswwwfluidigmcomproductspolaris GattaQuant - nanorulers for high resolution microscopes and super-resolution microscopes performance testing httpwwwgattaquantcomNanoruler GE Healthcare life Sciences Applied Precision ndash DeltaVision deconvolution OMX OMX SR httpwwwgelifesciencescomwebappwcsstoresservletproductByIdenGELifeSciences-us29065728 httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usproductsAlternativeProductStructure_2380729065721 httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usproductsAlternativeProductStructure_2380729115476 German BioImagingorg httpwwwgermanbioimagingorgwikiindexphpMain_Page httpwwwgermanbioimagingorgwikiindexphpWorkgroup6SoftwarePackages GIGAmacro ndash Magnify2 gigapixel imagery oof macroscopic and microscopic objects Terapixel macro image httpwwwgigamacrocomgigapixel-macro-imaging-system httpwwwgigamacrocomworlds-first-terapixel-macro-image

Glencoe Software ndash OMERO Plus enterprise data management for scientific images and any associated metadata (OME = Open Microscopy Environment) DataViewer PathViewer httpsglencoesoftwarecomomeroplushtml httpsglencoesoftwarecomdataviewerhtml httpsglencoesoftwarecompathviewerhtml Gooch amp Housego ndash spectral imager httpsgoochandhousegocomminiature-spectral-imaging-camera httpwwwghinstrumentscomproductsspectral-imaging-synthesishsi-440c-hyperspectral-imaging-system Hindsight Imaging ndash spectral imaging httphindsight-imagingcom Horiba Scientific - SWIFT ultra-fast Raman confocal imaging Raman spectroscopy httpwwwhoribacomscientificproductsraman-spectroscopyraman-imagingswift httpwwwhoribacomscientificproductsraman-spectroscopyraman-imaging httpwwwhoribacomscientificproductsraman-spectroscopy IATIA Ultima Capital ndash QPm (quantitative phase microscopy) httpwwwultimacapitalnetiatiaimagingPublicationsIatia20ImagingapplicationNotesqpmApplicationWithConfocalMicroscopespdf Ibidi - heating and incubation systems optical O2 measurement systems Nanolive 3D Cell Explorer pump system gas incubation system httpibidicomxtproductsenInstruments-AccessoriesHeating-Incubation-Systems httpibidicomxtproductsenInstruments-Accessoriesibidi-OPAL-Optical-O2-Measurement-System httpibidicomxtproductsenInstruments-AccessoriesNanolive-3D-Cell-Explorer httpibidicomxtproductsenInstruments-Accessoriesibidi-Pump-System httpibidicomxtproductsenInstruments-AccessoriesHeating-Incubation-Systemsibidi-Gas-Incubation-System iLAbSolutions (Agilent Technologies) - Instrument management and scheduling software (cores and labs) httpwwwilabsolutionscominstrument-access-control ImageJ - Fiji ImageJ NIH ImageJ ImageJ ndash Fiji (Fiji is just ImageJ) is the main download site httpfijisc httpsimagejnihgovij wwwimagejnet Inscopix ndash nVista in vivo mouse brain imaging miniature microscope httpswwwinscopixcomproducts Intelligent Imaging Innovations Inc (3i) ndash Slidebook imaging software Lattice light sheet (high speed gentle to cells high resolution imaging) Dual-view Inverted Selective Plane Illumination (diSPIM) VIVO 2-Photon (VIVO 2P) multiphoton microscopy Everest intravital imaging Marianas 3D real-time deconvolution timelapse spinning disk FRAP TIRF FLIM single molecule environmental control Phasor - optogenetic photostimulation using digital holography Yokogawa spinning disk confocal units wwwintelligent-imagingcom httpswwwintelligent-imagingcomslidebookphp httpswwwintelligent-imagingcomsystemsphplattice httpswwwintelligent-imagingcomsystemsphpdispim httpswwwintelligent-imagingcomsystemsphptwophoton httpswwwintelligent-imagingcomsystemsphpeverest httpswwwintelligent-imagingcomsystemsphpmarianas httpswwwintelligent-imagingcomoptogeneticsphp httpswwwintelligent-imagingcomsdcphp ISS Inc ndash fluorescence lifetime imaging microscopy fluorescence correlation spectroscopy (FCS) confocal imaging httpwwwisscommicroscopyindexhtml JenLab GmbH cyto-microscopy multiphoton tomography httpwwwjenlabdeproducts250html httpwwwjenlabde2PM-Cryo1330html

httpwwwjenlabdeMultiphoton-Tomography680html Jenoptik - microscope cameras httpswwwjenoptikcomproductscameras-and-imaging-modulesmicroscope-cameras JPK Instruments - integrated atomic force microscope (AFM) force sensing optical tweezers optical trapping single cell force spectroscopy (SCFS) httpwwwjpkcomindex2enhtml httpusajpkcomoptical-tweezers-optical-trapping29ushtml httpusajpkcomcellular-adhesion-cytomechanics30ushtml Keyence ndash VK-X confocal (upright) BZ-X700 widefield (inverted) httpwwwkeyencecomssproductsmicroscopevkx httpwwwkeyencecomssproductsmicroscopebz-x700indexjsp KK Technology - CapiScope HVCS Handheld Video Capillaroscopy System (CytoScan) httpwwwkktechnologycomhvcshtml LaVision BioTec ndash TriMscope Multiphoton TriM Scope II Adaptive Optics UltraMicroscope II light sheet httpwwwlavisionbiotecde httpwwwlavisionbiotecdetrim-scope-overviewhtml httpwwwlavisionbiotecdetrim-scope-ii-adaptive-opticshtml httpwwwlavisionbiotecdeultramicroscope-ii-introductionhtml Laxco ndash upright and inverted microscopes httpwwwlaxcoinccomMICROSCOPES Lego ndash Lego Idea Microscopes httpsideaslegocomprojects44370 httpwwwnico71frlego-working-microscope Li-Cor ndash near-infared fluorescent dyes and in vivo imaging agents in vivo and Western blot imaging systems httpswwwlicorcombioproductsreagents httpswwwlicorcombioproductsreagentsirdyebrightsite_imaging_agents httpswwwlicorcombioproductsimaging_systemsodyssey_familyhtml httpswwwlicorcombioproductsimaging_systemspearl httpswwwlicorcombioproductsimaging_systemscdigit Life Imaging Services - ldquothe Ludin chamberrsquo ldquothe cube amp the boxrdquo httpwwwlischthechamberhtml httpwwwlischtheboxhtml Lightform Inc ndash PARISS imaging spectrometer httplightforminccom LMU Bioimaging httpwwwbioimagingbmcmeduni-muenchendelinkswebsitesindexhtml httpwwwbioimagingbmcmeduni-muenchendelearneduwebsitesindexhtml Ludl Electronic Products Ltd ndash automated XY stages focus motors filter wheels httpwwwludlcom

LumaCyte ndash Laser force Cytology (laser trap meets microfluidics to suspend and manipulate single cells) httpwwwlumacytecomabouttechnology Lumencor ndash LEDs fluorescence light sources httplumencorcomproducts Luxcel ndash mitochondrial and cellular functions O2 sensor reagents httpluxcelcomproduct+list Luxendo GmbH ndash light sheet imager

wwwluxendoeu Lyncee tec - digital holography microscopy (DHM) high content screening by DHM httpwwwlynceeteccom httpwwwlynceeteccomhigh-content-screening Mad City Labs Inc - nanopositioning wwwmadcitylabscom Mauna Kea Technologies ndash CellVizio confocal laser endomicroscopy httpwwwmaunakeatechcomenhealthcare-professionalscellvizio-endomicroscopy-0 MBF Bioscience - stereology and neuron morphology quantitative imaging httpwwwmbfbiosciencecom McCrone Group wwwmccronecominstrument-sales Media Cybernetics Inc ndash Image Premier 3D AutoQuant X3 deconvolution httpwwwmediacycom Meiji Techno America wwwmeijitechnocom MesoLens Ltd httpwwwmesolenscomproducttechnical-specifications httpwwwmesolenscomimages httpswwwbiophotonicsstrathacukresearch_1htm Meyer Instruments ndash Pathscan Enabler GigaMacro digital pathology telepathology httpmeyerinstcom httpmeyerinstcompathscan-enabler-5 httpmeyerinstcomgigamacro-gigapixel-macro-imaging httpmeyerinstcomhomescanners httprealtimetelepathologycom Microarrays - Large-Scale Gene Expression and Microarray Links and Resources httpswwwebiacukarrayexpress Micro-Manager ndash Device Support ndash tabulates many microscope cameras and motorized accessories every new camera and accessory should have a uManager driver to enable simple use with Fiji ImageJ httpsmicro-managerorg httpsmicro-managerorgwikiDevice_Support httpsopen-imagingcom Microvolution ndash (near) instant gratification spatial deconvolution using NVidia GPU card(s) httpmicrovolutioncom Mightex Systems ndash optogenetics DMDDLP illuminator (digital micro-mirror device digital light processing) httpwwwmightexsystemscomindexphpcPath=245 Millipore-Sigma Merck KGaA (Amnis Corp CellASIC EMD Millipore) ndash ImageStreamX and FlowSight imaging flow cytometers ONIX2 Microperfusion System for microscopes httpswwwemdmilliporecom httpswwwemdmilliporecomUSenlife-science-researchcell-analysisamnis-imaging-flow-cytometersQ6ubqBm3UAAAFLCKIpygJnav httpwwwemdmilliporecomUSenlife-science-researchcell-culture-systemscellASIC-live-cell-analysisd1CbqBw58AAAE_0j13MnAnav Mitutoyo America Corp wwwmitutoyocom httpecatalogmitutoyocomMF-U-Series-176-High-power-Multi-function-Measuring-Microscopes-C1413aspx

Molecular Devices Corporation Universal Imaging Corporation (Danaher) ndash MetaMorph MetaFluor high content systems (HCS) httpswwwmoleculardevicescomsystemsmetamorph-research-imaging httpmdccusthelpcomappanswersdetaila_id19319 httpswwwmoleculardevicescomsystemshigh-content-imaging Molecular Machines amp Industries - laser microdissection and tweezer systems httpwwwmolecular-machinescomhome MUSE Microscopy Inc ndash Deep UV illumination for shallow depth of field imaging httpwwwmusemicrocom Micro Video Instruments Inc - DarkLite illuminator httpwwwmvi-inccom NanoEnTek ndash JuLI Stage (imager inside incubator or on lab bench) httpwwwjulistagecom National Instruments ndash LabView software httpwwwnicomen-ushtml Navitar - Hoffman Modulation Contrast (HMC alternative to differential interference contrast phase contrast) custom lens design UVDUVNUV imaging lenses httpsnavitarcommarketsmicroscopy httpsnavitarcomproductsimaging-opticscustom-microscope-objectivescustom-microscope-objectives httpsnavitarcomproductsimaging-opticsuv-imaging National Center for X-ray Tomography (NCXT) ndash soft X-ray tomography (CT of hydrated cells) XM-2 dedicated biological SXT microscope Prof Carolyn Larabell Director (see also SiriusXT) httpncxtlblgov httpncxtlblgovsxt httpncxtlblgovmanual httpncxtlblgovq=carolyn Neogenomics (Clarient) ndash MultiOmyx immunofluorescence or DNA FISH (ldquo60plexrdquo) httpneogenomicscomPharma-ServicesLab-ServicesMultiOmyxTechnologyMultiOmyx-IF-Assay-DNA-FISH-assay-NGS-from-ROI Nexcelom ndash Celigo imaging cytometer Cellometer cell counters httpwwwnexcelomcomCeligoindexphp httpwwwnexcelomcomProducts Nikon ndash Ti-LAPP modular illumination system (for Nikon Ti series microscopes) TIRF Optogenetics httpswwwnikoninstrumentscomProductsPhotostimulation-and-TIRFTi-LAPP Nirmidas Biotech httpwwwnirmidascomtechnologynir httpwwwnirmidascomproductsniriidye NVidia ndash Pascal 10+ Gbps GPU cards for instant gratification deconvolution (software from Microvolutioncom SVInl) httpwwwgeforcecomhardware10seriesgeforce-gtx-1080 httpwwwgeforcecomhardware10seriestitan-x-pascal httpwwwnvidiacomobjectquadro-graphics-with-pascalhtml Ocean Optics ndash spectrometers httpoceanopticscomproduct-categorymodular-spectrometers Oko-Lab stage top incubator httpwwwoko-labcomstage-top Open Microscopy Environment (OME) ndash OMERO (see also Glencoe Software) Bio-Formats LOCI

httpswwwopenmicroscopyorgsite httpswwwopenmicroscopyorgsiteproductsomero httpswwwopenmicroscopyorgsiteproductsbio-formats httpswwwopenmicroscopyorgsitesupportbio-formats52supported-formatshtml httpswwwopenmicroscopyorgsiteaboutdevelopment-teamskevin OpenSPIM ndash do-it-yourself selective plane illumination microscopy (light sheet imaging) httpopenspimorgWelcome_to_the_OpenSPIM_Wiki OpenSpinMicroscopy ndash do-it-yourself SPIMDSLMOPT microscopes httpssitesgooglecomsiteopenspinmicroscopy Ovizio ndash differential digital holography (similar to quantitative phase imaging) httpwwwoviziocomenHome httpwwwoviziocomenMicroscopesQMod Oxford Gene Technologies ndash microarrays ndash cytogenetics molecule genetics cancer research pre-implantation genetic diagnosis httpwwwogtcomclinical_genetics Oxford Nanoimaging ndash single molecule(s) localization fluorescence resonance energy transfer (FRET) (Kapanidis) wwwoxfordnicom Pathology Devices ndash LiveCell stage top incubator amp controller tissue microarrayers (TMA makers) httpwwwpathologydevicescomLiveCellhtm httpwwwpathologydevicescomTMArrayerhtm PeCon GmbH ndash microscope incubators httpwwwpeconbiz Pembroke Instruments ndash spectrometers mini-lasers httppembrokeinstrumentscomqmini-spectrometer httppembrokeinstrumentscommini-lasers PerkinElmer ndash in vivo imaging systems (bioluminescence NIR fluorescence) Vectra digital slide scanner httpwwwperkinelmercomcategoryin-vivo-imaging-instruments httpwwwperkinelmercomcategoryquantitative-pathology-imaging-instruments Phi Optics ndash CellVista SLIM Pro (quantitative phase microscopy) httpphiopticscom Photometrics (Roper Scientific) ndash DualView QuadView httpwwwphotometricscom httpwwwphotometricscomproductsmultichannel Photon Technology International httpwwwpti-njcomindexhtml

PicoQuant GmbH ndash fluorescence lifetime imaging microscopes (FLIM) STED 3D-EasySTED httpswwwpicoquantcomproductscategoryfluorescence-microscopes httpswwwpicoquantcomapplicationscategorylife-sciencested httpwwweasystedorg Physik Instrumente GmbH amp Co KG (PI) - Nanopositioning Applications for Microscopy Neuroscience and Metrology httpswwwphysikinstrumentecomen httpwwwpi-usausindexphp PreSens Prescision Sensing GmbH - VisiSens measure and visualize Oxygen pH or carbon dioxide distributions httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-biological-researchhtml httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-life-science-researchhtml Prior Scientific

httpwwwprior-uscom Profusa Inc - Lumee tissue-integrated biosensors scaffolds httpprofusacomtechnology Reindeer Graphics Inc ndash OptiPix Fovea Pro 9plugins for Adobe Photoshop 6 and CS series) httpwwwreindeergraphicscom Renishaw - StreamLine fast chemical imaging Raman spectroscopy httpwwwrenishawcomenstreamline-generate-chemical-images-rapidly--9449 httpwwwrenishawcomenraman-spectroscopy--6150 Sanford Burnham Prebys ndash High Content Screening httpwwwsbpdiscoveryorgtechnologysrPagesLaJolla_HighContentScreeningaspx ScopeM - Scientific Center for Optical and Electron Microscopy - ETH Zurich httpwwwscopemethzch SiriusXT - soft X-ray tomography (SXT) microscope (CT scan hydrated cell) httpsiriusxtcom SpectraGenetics - Fluorogen Activating Peptides (FAPs) new genetically encoded ldquobinaryrdquo reporters httpspectrageneticscomproductsvectors-for-expressing-fluorogen-activating-proteinsfap-technology-overview Spirochrome - Silicon Rhodamine (SiR) and other fluorescent reagents probes for bioimaging httpspirochromecom Stanford Photonics Inc httpwwwstanfordphotonicscom httpwwwstanfordphotonicscomLife20SciencesLifeScihtm

Stream Technologies Inc ndash ColorFlow lens (multi-wavelength emission onto a camera) httpwwwstreamtechinccomproducts Sutter Instrument Company httpwwwsuttercom httpwwwsuttercomMICROSCOPESindexhtml httpwwwsuttercomIMAGINGindexhtml SVI Huygens ndash Professional (general image analysis) deconvolution NVidia GPU deconvolution httpssvinlHuygensProfessional httpssvinlHuygensDeconvolution httpssvinlHuygensGPU Sysmex Partex ndash CyScope httpwwwsysmex-parteccomproductsmicroscopyhtml httpwwwsysmex-parteccomproductsprdouct-detailviewcyscopeR-malaria-3238html Technical Instruments httpwwwtechinstcomproductsphp TESCAN Brno sro - Tescan Q-PHASE multimodal holographic quantitative phase imaging system (QPi) optional fluorescence httpwwwtescancomenproductsq-phaseq-phase httpq-phasetescancom httpq-phasetescancomindexphptechnologyspecifications Ted Pella Inc ndash specialty light microscopy and electron microscopy supplies httpswwwtedpellacom Texas Instruments ndash DLP 4100 development kit (digital light processingrsquo DMD digital micromirror device) httpwwwticomtooldlpd4x00kit

ThorLabs ndash iCyte imaging cytometer multiphoton confocal EnVista digital slide scanning microscopes httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7473 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7494 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=5696 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=6570 TIRF Labs lightguide TIRF prism TIRF TIRF-Electrochemistry httpwwwtirf-labscom httpwwwtirf-labscomtechnologieshtml TissueVision - Serial Two Photon Tomography (image volume ablate imaged volume with multiphoton laser repeat) httpwwwtissuevisioncomtechnology Tokai Hit - stage top incubator httpwwwtokaihitcomenglishproduct_guidanceoptionhtml TopoNomos Ltd ndash Toponome Imaging Cycler ndash immunofluorescence (100plex) httpwwwtoposnomoscomtechnologyhtml Ultivue Inc ndash DNA-PAINT ndash reagents data processing service httpwwwultivuecom httpwwwultivuecomproducts UMech Technologies ndash Cytovar HCS up to 16 excitation wavelengths httpcloudumechcomproducts httpcloudumechcomproductsmodelC16 Visitech ndash vt-iSIM instant super-resolution microscopy up to 1000 frames per second confocal scanners and light engines httpwwwvisitechcoukvt-isimhtml httpwwwvisitechcoukproductshtml Visitron Systems GmbH - high speed imaging systems httpwwwvisitronde Visualsonics (Fujifilm) - photoacoustic imaging httpwwwvisualsonicscomproductstechnology-overview Wicked Lasers httpwwwwickedlaserscom httpwwwwickedlaserscomarctic WITec Wissenschaftliche Instrumente und Technologie GmbH - imaging systems for FLIM Raman AFM and SNOM analysis httpwitecdeproducts httpwwwwitec-instrumentscom WM Keck Center for Adaptive Optical Microscopy (CfAOM) at UC Santa Cruz httpscfaomsoeucscedu httpcfaoucolickorgpgallery Yokogawa Corp ndash spinning disk confocal scanner live cell imager high content screener confocal quantitative cytometer httpwwwyokogawacomsolutionsproducts-platformslife-science httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-scanner-unit-csu httpwwwyokogawacomsolutionsproducts-platformslife-scienceall-in-one-live-cell-imaging-solution httpwwwyokogawacomsolutionsproducts-platformslife-sciencehigh-throughput-cytological-discovery-system httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-quantitative-image-cytometer Zellkraftwerk (ChipCytometry) ndash immunofluorescence (80plex) httpwwwzellkraftwerkcomProducts2phtml httpwwwzellkraftwerkcomZKWOnephtmlSoftware

httpwwwchipcytometrycomtechnologyphtml Fluorescence Spectra Data and Graphing Sites PubSpectra ndash Excel file data download httpsworksbepresscomgmcnamara9 BD Biosciences ndash spectrum viewer Brilliant fluorophores httpwwwbdbiosciencescomussspectrumviewer httpwwwbdbiosciencescomusapplicationssspectrumguidepage BioLegend ndash spectra analyzer Brilliant Violet fluorophores httpwwwbiolegendcomspectraanalyzer httpwwwbiolegendcombrilliantviolet Chroma Technology httpswwwchromacomspectra-viewer eBioscience (Affymetrix ThermoFisher) ndash fluorPlan ndash a multi-laser spectra viewer httpwwwebiosciencecomresourcesfluorplan-spectra-viewerhtm Spectra Viewer (requires Java) Evrogen ndash Spectrum Viewer httpevrogencomspectra-viewerflashviewerhtml Fluorophoresorg ndash Fluorescent Substances httpwwwfluorophorestugrazatsubstance I Love GFP httpssitesgooglecomsiteilovegfpHomefps Lambert and Thorn UCSF Fluorescent protein properties httpnicucsfeduFPvisualization Leica Microsystem - ldquoFluoScoutrdquo httpwwwleica-microsystemscomfluoscout

Molecular Probes Invitrogen Thermo Fisher ndash Fluorescence SpectraViewer httpwwwthermofishercomusenhomelife-sciencecell-analysislabeling-chemistryfluorescence-spectraviewerhtml httpsitunesapplecomusappfluorescence-spectraviewerid421031826 (iTunes App) Nightsea - Compendium of spectra web sites httpwwwnightseacomsfa-sharingfluorescence-spectra-viewers Omega Optical ldquoCurvomatricrdquo httpswwwomegafilterscomcurvomatic

PhotoChemCAD 20 (Jonathan S Lindsey) dye spectra database and chemistry calculator NIRvana Sciences httpwwwphotochemcadcom httpnirvanasciencescompage_id=3088 UCSF (Lambert Thorn 2016) - Fluorescent protein properties httpnicucsfeduFPvisualization University of Arizona - Fluorescent Spectra Database httpwwwspectraarizonaedu Semrock - Searchlight httpssearchlightsemrockcom Spectroscopy Ninja ndash links to spectral and fluorescence data Spekwin32 spectroscopy software httpwwweffemm2deinfoinfo_specdatahtml

httpwwweffemm2deindexhtml Zeiss ndash interactive fluorescence dye and filter database overview dyes overview filter sets httpswwwmicro-shopzeisscoms=50479761ad21e5ampl=enampp=usampf=fampa=i httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=d httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=f Researcher Labs Alby Diaspro ndash IIT httpwwwlambsitindexphppage=People Alice Ting ndash MIT httpwwwtinglaborgresearch Allen Institute for Brain Science httpwwwalleninstituteorgwhat-we-dobrain-science Allen Institute for Cell Science httpwwwalleninstituteorgwhat-we-docell-science Amina Qutub - Rice University - How are human cells designed lab httpsqutublaborgqutub-lab Amy Herr UC Berkeley ndash Single cell Westerns httpherrlabberkeleyedu Amy Palmer ndash UC Boulder httpspalmerlabcoloradoedu Andrew York ndash Calico Life Sciences httpswwwcalicolabscomteam-memberandrew-york Anne Carpenter ndash Broad Institute CellProfiler httpspersonalbroadinstituteorganne Arjun Raj UPenn single molecule RNA FISH quantitative understanding cellular functions httprajlabseasupenneduindexhtml httpwwwpopscicomsciencearticle2013-09arjun-raj Atsuko Miyawaki - Laboratory for Cell Function Dynamics (CFDS) Fucci2 fluorescent proteins cell cycle indicator httpwwwbrainrikenjpenfacultydetails30 httpcfdsbrainrikenjp httpcfdsbrainrikenjpFuccihtml Aydogan Ozcan - UCLA - new imaging and sensing architectures httpinnovateeeuclaeduwelcomehtml httpwwwhhmiorgscientistsaydogan-ozcan Badri Roysam - UH - FARSIGHT Toolkit httpwwweeuhedufacultyroysam httpwwwfarsight-toolkitorgwikiMain_Page Brian J Ford ndash microscopist and popularizer httpsuklinkedincominprofbrianjford Carolyn Larabell ndashNational Center for X-ray Tomography (LBNL) UCSF httpncxtlblgovq=carolyn httpprofilesucsfeducarolynlarabell Clare Waterman ndash NHLBI NIH

httpswwwnhlbinihgovresearchintramuralresearcherspiwaterman-clare Dana Peer - Columbia University - Computational Systems Biology viSNE and more software httpwwwc2b2columbiaedudanapeerlabhtml httpwwwc2b2columbiaedudanapeerlabhtmlcythtml David Mayerich - UH - STIM Laboratory Scalable Tissue Imaging and Modeling httpwwweeuhedufacultymayerich httpstimeeuhedu David Piston WUSTL httpwwwcellbiologywustledufacultytenureddavid-w-piston-phd Diane Lidke and Keith Lidke - University of New Mexico httppathologyunmeduresearchfaculty-laboratoriesthe-lidke-laboratoryindexhtml httppanda3physunmedu~klidke Donna Arndt-Jovin and Thomas Jovin - Max Planck Institute for Biophysical Chemistry Laboratory of Cellular Dynamics httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsDonnaArdndt-JovinResearchAreasAndProjects httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsChairmanThomasJovinResearchAreasAndProjects Ed Boyden ndash MIT Media Lab ndash expansion microscopy (ExM) optogenetics httpsyntheticneurobiologyorg httpsyntheticneurobiologyorgprotocols httpsyntheticneurobiologyorgpublications httpwwwtedcomtalksed_boyden_baby_diapers_inspired_this_new_way_to_study_the_brain httpwwwextbiocombuycell Elizabeth Blackburn ndash Salk Institute - Telomeres httpswwwsalkeduscientistelizabeth-blackburn httpsenwikipediaorgwikiElizabeth_Blackburn httpswwwnobelprizeorgnobel_prizesmedicinelaureates2009blackburn-factshtml Elizabeth Hillman - Columbia university - SCAPE (Swept Confocally-Aligned Planar Excitation) high speed 3D microscopy DyCE (dynamic contrast enhancement to image and segment small animal organs live) Neuroimaging amp Neurovascular Coupling httporionbmecolumbiaedu~hillmanInstrumentationhtml httporionbmecolumbiaedu~hillmanSCAPEhtml httporionbmecolumbiaedu~hillmanMolecularhtml httporionbmecolumbiaedu~hillmanBrain_Imaginghtml Eric Betzig ndash UCSF (moving from HHMI Janelia Farm in 2016) httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014betzig-factshtml Eva Sevick-Muraca ndash UT Health Science Center at Houston molecular imaging clinical NIR fluoresceince imaging httpswwwutheduimmprofilehtmid=1005459 httpswwwutheduimmcentersmolecular-imaginghtm Evelin Schrock - Technische Universitaumlt Dresden spectral karyotyping cytogenetics httpswwwresearchgatenetprofileEvelin_Schrock Garry Nolan Stanford University ndash Mass cytometry MIBI-ToF high throughput imaging mass cytometry (42plex) httpwebstanfordedugroupnolanresourceshtml httpwebstanfordedugroupnolantechnologieshtml George McNamara ndash Cell Morphometry (41) Figure 1 right top two panels (55) The Chase (2016 temporal area maps lsquodynamic morphologyrsquo) (76) newsletter series on ldquoThe Chaserdquo (73) direct Vimeo movie of ldquoThe Chaserdquo Tiki_Goddess linkedin 10+plex blog httpsworksbepresscomgmcnamara41 httpsworksbepresscomgmcnamara55 httpsworksbepresscomgmcnamara76

httpsworksbepresscomgmcnamara73 httpsvimeocom175151196 httphomeearthlinknet~tiki_goddess httpswwwlinkedincomingeorgemcnamara httpswwwlinkedincompulsebd-biosciences-listed-tandems-horizon-brilliant-violets-mcnamara Gillian Griffiths - University of Cambridge - T-cell immunological synapse httpwwwcimrcamacukresearchprincipal-investigatorsprincipal-investigators-a-hgriffiths Hari Shroff NIBIB NIH httpswwwnibibnihgovlabs-at-nibibsection-high-resolution-optical-imaging-hroi HHMI Janelia Farm Research Campus (JFRC) - Advanced Imaging Center Open Science httpswwwjaneliaorgopen-scienceadvanced-imaging-center-aic httpswwwjaneliaorgopen-science Jeanne Lawrence University of Massachussetts Medical School httpwwwumassmededucellbiolabslawrencepersonnelprincipal-investigator Jennifer Lippincott-Schwartz ndash HHMI Janelia Farm httpswwwjaneliaorgpeoplejennifer-lippincott-schwartz Jin Zhang ndash UCSD httpprofilesucsdedujinzhang Joe DeRisi - UCSF - 3D printable lab stuff httpderisilabucsfeduindexphppage=3D John Russ Chris Russ Fovea Pro plugins for Adobe Photoshop httpwwwdrjohnrusscomindexhtml httpwwwdrjohnrusscombookshtml httpwwwreindeergraphicscomfoveaprotutorialhtml Julie Theriot httpcmgmstanfordedutheriot Karl Deisseroth ndash Stanford University ndash CLARITY optical tissue clearing Optogenetics httpclarityresourcecenterorg httpwebstanfordedugroupdlaboptogeneticsindexhtml Karsten Koumlnig (Koenig) - Saarland University and JenLab GmbH - biophotonics httpwwwbltuni-saarlanddeindex_ehtm httpwwwjenlabde httpwwwthelastescape-filmcom Karsten Rodenacker ndash image measurements httpkaro03bplacednetkaroMeMisc_WWWpdfMicrosoftWord-EQUAPATpdf Kevin Eliceiri ndash UW-Madison Open Source Photonics and Software Laboratory for Optical and Computational Instrumentation (LOCI) wwwlociwiscedu Klaus Kemp ndash Microlife Services ndash diatoms and other prepared microscope slides httpwwwdiatomscouk Kurt Thorn UCSF httpthornlabucsfedu httpsnicucsfedublog httpnicucsfeduFPvisualization httpgigapancomgigapans163370 Lihong Wang - WUSTL - Optical Imaging Laboratory photoacoustic tomography

httpoilabseaswustledu httpoilabseaswustleduresearch_0html Loren Looger - HHMI JFRC - iGluSnFr fluorescent protein biosensor httpswwwjaneliaorglablooger-lab Mary-Lou Pardue ndash MIT (first ever in situ hybridization with J Gall) httpsbiologymitedupeoplemary_lou_pardue httpsenwikipediaorgwikiMary-Lou_Pardue Nancy Allbritton - UNC - Chemical cytometry microraft arrays organ-on-a-chip httpswwwbmencsueduindexphpcomponentcomprofileruserprofilenlallbri httpwwwbmeuncedulabsallbritton Navin Varadarajan - UH - single-cell Lab httpwwwcheeuhedufacultyvaradarajan httpsinglecellcheeuheducontacthtml Nicholas Shaner - Scintillon Institute - mNeonGreen httpwwwscintillonorgshaner_lab Rebecca Richards-Kortum httpbioengineeringriceedufacultyrebecca_richards-kortumaspx Robert Campbell - Fluorescent proteins optogenetic proteins httpcampbellwebchemualbertaca httpcampbellwebchemualbertacaprojects-2 Robert Murphy ndash Cell measurements web services httpmurphylabwebcmueduservices Sabine Mai - University of Manitoba - Genomic Centre for Cancer Research and Diagnosis (GCCRD) - httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBPlatformsGCCRDhtml httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBScientistsMaiAwardshtml Sally Ward and Raimund Ober - Texas AampM University - httpwwwwardoberlabcom Simon Watkins - U Pittsburgh Center for Biologic Imaging httpwwwcbppittedufacultywatkinshtml httpwwwcbppittedufacultylabwatkinshtml httpwwwcbipittedu Stefan Hell ndash Deparment Hell NanoBiopohotonics httpwwwmpibpcmpgdehell httpsenwikipediaorgwikiStefan_Hell httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014hell-factshtml Sunney Xie Harvard httpsbernsteinharvardedu Susan Cox ndash 3B microscopy httpwwwcoxphysicscomindexhtml httpwwwcoxphysicscom3b Radim Chmeliacutek - Center for innovative microscopy Experimental biophotonics group httpswwwceiteceuceitec-butexperimental-biophotonicsrg3 httpwwwbiophotczhome Taekjip Ha ndash Johns Hopkins University ndash single molecules httphamedjhmiedu

Thomas Ried ndash NCI NIH SKYM-FISH and CGH Database httpsccrcancergovGenetics-Branchthomas-ried httpsccrcancergovGenetics-Branchthomas-riedqt-staff_profile_tabs=9qt-staff_profile_tabs ftpftpncbinlmnihgovsky-cghDATA httpswwwncbinlmnihgovdbvar Viviana Gradinaru ndash CalTech ndash CLARITYPACT Optogenetics httpwwwbbecaltecheducontentviviana-gradinaru httpglabcaltechedu Vladislav Verkhusha - near infrared fluorescent proteins httpwwweinsteinyuedulabsvlad-verkhushadefaultaspx httpwwweinsteinyueduresearchfacilitiesfluorescent WE Moerner ndash Stanford University httpwebstanfordedugroupmoerner Willard Wiggans ndash micro gallery httpwwwwillard-wigancomgallery Wolf Frommer ndash Molecular sensors httpbiosensordpbcarnegiescienceedu (fluorescent protein biosensors table) Xiaowei Zhuang = Harvard httpzhuangharvardedu Yuval Garini - Bar-Ilan University - Nano-Bio-Photonics laboratory httpgarinilabbiuacil Microscopy Magazines Imaging amp Microscopy httpwwwimaging-gitcommagazine Laser Focus World httpwwwlaserfocusworldcomindexhtml Microscopy amp Analysis httpwwwmicroscopy-analysiscom Microscopy Today httpwwwmicroscopy-todaycom Microscopy-UK httpwwwmicroscopy-ukorguk Photonics Spectra Biophotonics httpwwwphotonicscomPublicationsaspx The Microscope Journal httpmcriorgv72the-microscope-journal RMS Infocus Magazine httpwwwrmsorgukstudy-readinfocus-magazinehtml Nobel Prizes in Light Microscopy and Related Fields Chemistry 1925 colloids (light sheet) Zsigmondy (Siedentopf Zsigmondy 1902) httpswwwnobelprizeorgnobel_prizeschemistrylaureates1925

Chemistry 2000 conductive polymers Heeger MacDiarmid Shirakawa (Brilliant Violets Ultraviolets Blues) httpwwwnobelprizeorgnobel_prizeschemistrylaureates2000 Chemistry 2008 green fluorescent protein GFP Shimomura Chalfie Tsien httpwwwnobelprizeorgnobel_prizeschemistrylaureates2008 Chemistry 2014 super-resolved fluorescence microscopy Betzig Hell Moerner httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014 Physics 1953 Phase Contrast Zernike httpswwwnobelprizeorgnobel_prizesphysicslaureates1953 Physics 2009 invention of an imaging semiconductor circuit ndash the CCD sensor Kao Boyle Smith httpwwwnobelprizeorgnobel_prizesphysicslaureates2009 Physics 2014 efficient blue light emitting diodes Akasaki Amano Nakamura httpwwwnobelprizeorgnobel_prizesphysicslaureates2014 Physiology or Medicine 2006 Fire and Mello RNA interference ndash gene silencing by double stranded RNA httpwwwnobelprizeorgnobel_prizesmedicinelaureates2006 Physiology or Medicine 2006 Capecchi Evans Smithies specific gene modifications in mice by the use of embryonic stem cells httpwwwnobelprizeorgnobel_prizesmedicinelaureates2007 Physiology or Medicine 2009 Blackburn Greider Szostak how chromosomes are protected by telomeres and telomerase httpwwwnobelprizeorgnobel_prizesmedicinelaureates2009 Physiology or Medicine 2012 Gurdon Yamamanka matured cells can be reprogrammed to become pluripotent httpwwwnobelprizeorgnobel_prizesmedicinelaureates2012

Table 442 Fluorophores Photophysics Data

Fluorophore Abs or Ex max (nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Acridine orange 271 520 27000 020 5

Alexa Fluor 430 431 541 16000 055 9

Alexa Fluor 488 495 519 71000 094 67

Alexa Fluor 532 532 553 81000 080 65

Alexa Fluor 546 556 573 104000 096 100

Alexa Fluor 568 578 603 91300 075 69

Alexa Fluor 594 590 617 73000 064 47

Allophycocyanin (APC) 650 660 700000 068 476

Atto 390 390 479 24000 090 22

Atto 425 436 484 45000 065 29

Atto 430LS 433 547 32000 065 21

Atto 465 453 508 75000 075 56

Atto 490LS 496 661 40000 030 12

Atto 520 525 547 105000 095 100

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 12: McNamara 20161006 revised draft tables for CPHG Light ...

httpwwwesricorg Energetiq ndash Deep ultraviolet (DUV high radiance 170-2100 nm) laser driven light source (LDLS) httpwwwenergetiqcom Epi Technology - CaliCube - Cube for fluorescence light path to inspect epi Illumination light source (lamp) fiber optic or liquid light guide httpwwwepitechnologycomepitechnology-1 Essen Biosciences ndash Incucyte Zoom (imager inside incubator) httpwwwessenbiosciencecomenproductsincucyte Estigen Tissue Science ndash manual and automated tissue arrayer (tissue microarray maker) httpwwwestigencom Euro-Bioimaging httpwwweurobioimagingeu Excelitas Technologies (formerly Lumen Dynamics) ndash X-Cite LEDs httpwwwexcelitascomPagesProductX-Cite-LED-Solutionsaspx Expansion Technologies Inc (extbio) ndash Expansion microscopy httpwwwextbiocombuycell FEI (formerly Till Photonics) (Thermo Fisher) ndash correlative LM-EM single molecule Cryo-EM httpswwwfeicomlife-sciencescellular-biology httpswwwfeicomlife-sciencescellular-biologycorrelative-microscopy httpswwwfeicomlife-sciencesstructural-biology Femtonics - Multi-phton microscopes software accessories caged glutamate reagents services httpfemtonicseuproducts First Light Imaging ndash C-Red NIR imaging (800-2500 nm NIR windows I II III 650-950 nm 1100-1350 nm 1600-1870 nm[Shi et al 2015]) high speed visible EMCCD (400-1000 nm) httpwwwfirst-lightfrcategoryrangesinfrared Fluidigm ndash Helios imaging CyTOF mass cytometer (42plex) Callisto (32 independent chambers dose with up to 16 independent factors for 1-1000 cell populations culture up to 3 week) Polaris functional genomics meets imaging (48 single cells up to 24 hours after single cell selection from a population) httpswwwfluidigmcomproductshelios httpswwwfluidigmcomproductscallisto httpswwwfluidigmcomproductspolaris GattaQuant - nanorulers for high resolution microscopes and super-resolution microscopes performance testing httpwwwgattaquantcomNanoruler GE Healthcare life Sciences Applied Precision ndash DeltaVision deconvolution OMX OMX SR httpwwwgelifesciencescomwebappwcsstoresservletproductByIdenGELifeSciences-us29065728 httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usproductsAlternativeProductStructure_2380729065721 httpwwwgelifesciencescomwebappwcsstoresservletcatalogenGELifeSciences-usproductsAlternativeProductStructure_2380729115476 German BioImagingorg httpwwwgermanbioimagingorgwikiindexphpMain_Page httpwwwgermanbioimagingorgwikiindexphpWorkgroup6SoftwarePackages GIGAmacro ndash Magnify2 gigapixel imagery oof macroscopic and microscopic objects Terapixel macro image httpwwwgigamacrocomgigapixel-macro-imaging-system httpwwwgigamacrocomworlds-first-terapixel-macro-image

Glencoe Software ndash OMERO Plus enterprise data management for scientific images and any associated metadata (OME = Open Microscopy Environment) DataViewer PathViewer httpsglencoesoftwarecomomeroplushtml httpsglencoesoftwarecomdataviewerhtml httpsglencoesoftwarecompathviewerhtml Gooch amp Housego ndash spectral imager httpsgoochandhousegocomminiature-spectral-imaging-camera httpwwwghinstrumentscomproductsspectral-imaging-synthesishsi-440c-hyperspectral-imaging-system Hindsight Imaging ndash spectral imaging httphindsight-imagingcom Horiba Scientific - SWIFT ultra-fast Raman confocal imaging Raman spectroscopy httpwwwhoribacomscientificproductsraman-spectroscopyraman-imagingswift httpwwwhoribacomscientificproductsraman-spectroscopyraman-imaging httpwwwhoribacomscientificproductsraman-spectroscopy IATIA Ultima Capital ndash QPm (quantitative phase microscopy) httpwwwultimacapitalnetiatiaimagingPublicationsIatia20ImagingapplicationNotesqpmApplicationWithConfocalMicroscopespdf Ibidi - heating and incubation systems optical O2 measurement systems Nanolive 3D Cell Explorer pump system gas incubation system httpibidicomxtproductsenInstruments-AccessoriesHeating-Incubation-Systems httpibidicomxtproductsenInstruments-Accessoriesibidi-OPAL-Optical-O2-Measurement-System httpibidicomxtproductsenInstruments-AccessoriesNanolive-3D-Cell-Explorer httpibidicomxtproductsenInstruments-Accessoriesibidi-Pump-System httpibidicomxtproductsenInstruments-AccessoriesHeating-Incubation-Systemsibidi-Gas-Incubation-System iLAbSolutions (Agilent Technologies) - Instrument management and scheduling software (cores and labs) httpwwwilabsolutionscominstrument-access-control ImageJ - Fiji ImageJ NIH ImageJ ImageJ ndash Fiji (Fiji is just ImageJ) is the main download site httpfijisc httpsimagejnihgovij wwwimagejnet Inscopix ndash nVista in vivo mouse brain imaging miniature microscope httpswwwinscopixcomproducts Intelligent Imaging Innovations Inc (3i) ndash Slidebook imaging software Lattice light sheet (high speed gentle to cells high resolution imaging) Dual-view Inverted Selective Plane Illumination (diSPIM) VIVO 2-Photon (VIVO 2P) multiphoton microscopy Everest intravital imaging Marianas 3D real-time deconvolution timelapse spinning disk FRAP TIRF FLIM single molecule environmental control Phasor - optogenetic photostimulation using digital holography Yokogawa spinning disk confocal units wwwintelligent-imagingcom httpswwwintelligent-imagingcomslidebookphp httpswwwintelligent-imagingcomsystemsphplattice httpswwwintelligent-imagingcomsystemsphpdispim httpswwwintelligent-imagingcomsystemsphptwophoton httpswwwintelligent-imagingcomsystemsphpeverest httpswwwintelligent-imagingcomsystemsphpmarianas httpswwwintelligent-imagingcomoptogeneticsphp httpswwwintelligent-imagingcomsdcphp ISS Inc ndash fluorescence lifetime imaging microscopy fluorescence correlation spectroscopy (FCS) confocal imaging httpwwwisscommicroscopyindexhtml JenLab GmbH cyto-microscopy multiphoton tomography httpwwwjenlabdeproducts250html httpwwwjenlabde2PM-Cryo1330html

httpwwwjenlabdeMultiphoton-Tomography680html Jenoptik - microscope cameras httpswwwjenoptikcomproductscameras-and-imaging-modulesmicroscope-cameras JPK Instruments - integrated atomic force microscope (AFM) force sensing optical tweezers optical trapping single cell force spectroscopy (SCFS) httpwwwjpkcomindex2enhtml httpusajpkcomoptical-tweezers-optical-trapping29ushtml httpusajpkcomcellular-adhesion-cytomechanics30ushtml Keyence ndash VK-X confocal (upright) BZ-X700 widefield (inverted) httpwwwkeyencecomssproductsmicroscopevkx httpwwwkeyencecomssproductsmicroscopebz-x700indexjsp KK Technology - CapiScope HVCS Handheld Video Capillaroscopy System (CytoScan) httpwwwkktechnologycomhvcshtml LaVision BioTec ndash TriMscope Multiphoton TriM Scope II Adaptive Optics UltraMicroscope II light sheet httpwwwlavisionbiotecde httpwwwlavisionbiotecdetrim-scope-overviewhtml httpwwwlavisionbiotecdetrim-scope-ii-adaptive-opticshtml httpwwwlavisionbiotecdeultramicroscope-ii-introductionhtml Laxco ndash upright and inverted microscopes httpwwwlaxcoinccomMICROSCOPES Lego ndash Lego Idea Microscopes httpsideaslegocomprojects44370 httpwwwnico71frlego-working-microscope Li-Cor ndash near-infared fluorescent dyes and in vivo imaging agents in vivo and Western blot imaging systems httpswwwlicorcombioproductsreagents httpswwwlicorcombioproductsreagentsirdyebrightsite_imaging_agents httpswwwlicorcombioproductsimaging_systemsodyssey_familyhtml httpswwwlicorcombioproductsimaging_systemspearl httpswwwlicorcombioproductsimaging_systemscdigit Life Imaging Services - ldquothe Ludin chamberrsquo ldquothe cube amp the boxrdquo httpwwwlischthechamberhtml httpwwwlischtheboxhtml Lightform Inc ndash PARISS imaging spectrometer httplightforminccom LMU Bioimaging httpwwwbioimagingbmcmeduni-muenchendelinkswebsitesindexhtml httpwwwbioimagingbmcmeduni-muenchendelearneduwebsitesindexhtml Ludl Electronic Products Ltd ndash automated XY stages focus motors filter wheels httpwwwludlcom

LumaCyte ndash Laser force Cytology (laser trap meets microfluidics to suspend and manipulate single cells) httpwwwlumacytecomabouttechnology Lumencor ndash LEDs fluorescence light sources httplumencorcomproducts Luxcel ndash mitochondrial and cellular functions O2 sensor reagents httpluxcelcomproduct+list Luxendo GmbH ndash light sheet imager

wwwluxendoeu Lyncee tec - digital holography microscopy (DHM) high content screening by DHM httpwwwlynceeteccom httpwwwlynceeteccomhigh-content-screening Mad City Labs Inc - nanopositioning wwwmadcitylabscom Mauna Kea Technologies ndash CellVizio confocal laser endomicroscopy httpwwwmaunakeatechcomenhealthcare-professionalscellvizio-endomicroscopy-0 MBF Bioscience - stereology and neuron morphology quantitative imaging httpwwwmbfbiosciencecom McCrone Group wwwmccronecominstrument-sales Media Cybernetics Inc ndash Image Premier 3D AutoQuant X3 deconvolution httpwwwmediacycom Meiji Techno America wwwmeijitechnocom MesoLens Ltd httpwwwmesolenscomproducttechnical-specifications httpwwwmesolenscomimages httpswwwbiophotonicsstrathacukresearch_1htm Meyer Instruments ndash Pathscan Enabler GigaMacro digital pathology telepathology httpmeyerinstcom httpmeyerinstcompathscan-enabler-5 httpmeyerinstcomgigamacro-gigapixel-macro-imaging httpmeyerinstcomhomescanners httprealtimetelepathologycom Microarrays - Large-Scale Gene Expression and Microarray Links and Resources httpswwwebiacukarrayexpress Micro-Manager ndash Device Support ndash tabulates many microscope cameras and motorized accessories every new camera and accessory should have a uManager driver to enable simple use with Fiji ImageJ httpsmicro-managerorg httpsmicro-managerorgwikiDevice_Support httpsopen-imagingcom Microvolution ndash (near) instant gratification spatial deconvolution using NVidia GPU card(s) httpmicrovolutioncom Mightex Systems ndash optogenetics DMDDLP illuminator (digital micro-mirror device digital light processing) httpwwwmightexsystemscomindexphpcPath=245 Millipore-Sigma Merck KGaA (Amnis Corp CellASIC EMD Millipore) ndash ImageStreamX and FlowSight imaging flow cytometers ONIX2 Microperfusion System for microscopes httpswwwemdmilliporecom httpswwwemdmilliporecomUSenlife-science-researchcell-analysisamnis-imaging-flow-cytometersQ6ubqBm3UAAAFLCKIpygJnav httpwwwemdmilliporecomUSenlife-science-researchcell-culture-systemscellASIC-live-cell-analysisd1CbqBw58AAAE_0j13MnAnav Mitutoyo America Corp wwwmitutoyocom httpecatalogmitutoyocomMF-U-Series-176-High-power-Multi-function-Measuring-Microscopes-C1413aspx

Molecular Devices Corporation Universal Imaging Corporation (Danaher) ndash MetaMorph MetaFluor high content systems (HCS) httpswwwmoleculardevicescomsystemsmetamorph-research-imaging httpmdccusthelpcomappanswersdetaila_id19319 httpswwwmoleculardevicescomsystemshigh-content-imaging Molecular Machines amp Industries - laser microdissection and tweezer systems httpwwwmolecular-machinescomhome MUSE Microscopy Inc ndash Deep UV illumination for shallow depth of field imaging httpwwwmusemicrocom Micro Video Instruments Inc - DarkLite illuminator httpwwwmvi-inccom NanoEnTek ndash JuLI Stage (imager inside incubator or on lab bench) httpwwwjulistagecom National Instruments ndash LabView software httpwwwnicomen-ushtml Navitar - Hoffman Modulation Contrast (HMC alternative to differential interference contrast phase contrast) custom lens design UVDUVNUV imaging lenses httpsnavitarcommarketsmicroscopy httpsnavitarcomproductsimaging-opticscustom-microscope-objectivescustom-microscope-objectives httpsnavitarcomproductsimaging-opticsuv-imaging National Center for X-ray Tomography (NCXT) ndash soft X-ray tomography (CT of hydrated cells) XM-2 dedicated biological SXT microscope Prof Carolyn Larabell Director (see also SiriusXT) httpncxtlblgov httpncxtlblgovsxt httpncxtlblgovmanual httpncxtlblgovq=carolyn Neogenomics (Clarient) ndash MultiOmyx immunofluorescence or DNA FISH (ldquo60plexrdquo) httpneogenomicscomPharma-ServicesLab-ServicesMultiOmyxTechnologyMultiOmyx-IF-Assay-DNA-FISH-assay-NGS-from-ROI Nexcelom ndash Celigo imaging cytometer Cellometer cell counters httpwwwnexcelomcomCeligoindexphp httpwwwnexcelomcomProducts Nikon ndash Ti-LAPP modular illumination system (for Nikon Ti series microscopes) TIRF Optogenetics httpswwwnikoninstrumentscomProductsPhotostimulation-and-TIRFTi-LAPP Nirmidas Biotech httpwwwnirmidascomtechnologynir httpwwwnirmidascomproductsniriidye NVidia ndash Pascal 10+ Gbps GPU cards for instant gratification deconvolution (software from Microvolutioncom SVInl) httpwwwgeforcecomhardware10seriesgeforce-gtx-1080 httpwwwgeforcecomhardware10seriestitan-x-pascal httpwwwnvidiacomobjectquadro-graphics-with-pascalhtml Ocean Optics ndash spectrometers httpoceanopticscomproduct-categorymodular-spectrometers Oko-Lab stage top incubator httpwwwoko-labcomstage-top Open Microscopy Environment (OME) ndash OMERO (see also Glencoe Software) Bio-Formats LOCI

httpswwwopenmicroscopyorgsite httpswwwopenmicroscopyorgsiteproductsomero httpswwwopenmicroscopyorgsiteproductsbio-formats httpswwwopenmicroscopyorgsitesupportbio-formats52supported-formatshtml httpswwwopenmicroscopyorgsiteaboutdevelopment-teamskevin OpenSPIM ndash do-it-yourself selective plane illumination microscopy (light sheet imaging) httpopenspimorgWelcome_to_the_OpenSPIM_Wiki OpenSpinMicroscopy ndash do-it-yourself SPIMDSLMOPT microscopes httpssitesgooglecomsiteopenspinmicroscopy Ovizio ndash differential digital holography (similar to quantitative phase imaging) httpwwwoviziocomenHome httpwwwoviziocomenMicroscopesQMod Oxford Gene Technologies ndash microarrays ndash cytogenetics molecule genetics cancer research pre-implantation genetic diagnosis httpwwwogtcomclinical_genetics Oxford Nanoimaging ndash single molecule(s) localization fluorescence resonance energy transfer (FRET) (Kapanidis) wwwoxfordnicom Pathology Devices ndash LiveCell stage top incubator amp controller tissue microarrayers (TMA makers) httpwwwpathologydevicescomLiveCellhtm httpwwwpathologydevicescomTMArrayerhtm PeCon GmbH ndash microscope incubators httpwwwpeconbiz Pembroke Instruments ndash spectrometers mini-lasers httppembrokeinstrumentscomqmini-spectrometer httppembrokeinstrumentscommini-lasers PerkinElmer ndash in vivo imaging systems (bioluminescence NIR fluorescence) Vectra digital slide scanner httpwwwperkinelmercomcategoryin-vivo-imaging-instruments httpwwwperkinelmercomcategoryquantitative-pathology-imaging-instruments Phi Optics ndash CellVista SLIM Pro (quantitative phase microscopy) httpphiopticscom Photometrics (Roper Scientific) ndash DualView QuadView httpwwwphotometricscom httpwwwphotometricscomproductsmultichannel Photon Technology International httpwwwpti-njcomindexhtml

PicoQuant GmbH ndash fluorescence lifetime imaging microscopes (FLIM) STED 3D-EasySTED httpswwwpicoquantcomproductscategoryfluorescence-microscopes httpswwwpicoquantcomapplicationscategorylife-sciencested httpwwweasystedorg Physik Instrumente GmbH amp Co KG (PI) - Nanopositioning Applications for Microscopy Neuroscience and Metrology httpswwwphysikinstrumentecomen httpwwwpi-usausindexphp PreSens Prescision Sensing GmbH - VisiSens measure and visualize Oxygen pH or carbon dioxide distributions httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-biological-researchhtml httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-life-science-researchhtml Prior Scientific

httpwwwprior-uscom Profusa Inc - Lumee tissue-integrated biosensors scaffolds httpprofusacomtechnology Reindeer Graphics Inc ndash OptiPix Fovea Pro 9plugins for Adobe Photoshop 6 and CS series) httpwwwreindeergraphicscom Renishaw - StreamLine fast chemical imaging Raman spectroscopy httpwwwrenishawcomenstreamline-generate-chemical-images-rapidly--9449 httpwwwrenishawcomenraman-spectroscopy--6150 Sanford Burnham Prebys ndash High Content Screening httpwwwsbpdiscoveryorgtechnologysrPagesLaJolla_HighContentScreeningaspx ScopeM - Scientific Center for Optical and Electron Microscopy - ETH Zurich httpwwwscopemethzch SiriusXT - soft X-ray tomography (SXT) microscope (CT scan hydrated cell) httpsiriusxtcom SpectraGenetics - Fluorogen Activating Peptides (FAPs) new genetically encoded ldquobinaryrdquo reporters httpspectrageneticscomproductsvectors-for-expressing-fluorogen-activating-proteinsfap-technology-overview Spirochrome - Silicon Rhodamine (SiR) and other fluorescent reagents probes for bioimaging httpspirochromecom Stanford Photonics Inc httpwwwstanfordphotonicscom httpwwwstanfordphotonicscomLife20SciencesLifeScihtm

Stream Technologies Inc ndash ColorFlow lens (multi-wavelength emission onto a camera) httpwwwstreamtechinccomproducts Sutter Instrument Company httpwwwsuttercom httpwwwsuttercomMICROSCOPESindexhtml httpwwwsuttercomIMAGINGindexhtml SVI Huygens ndash Professional (general image analysis) deconvolution NVidia GPU deconvolution httpssvinlHuygensProfessional httpssvinlHuygensDeconvolution httpssvinlHuygensGPU Sysmex Partex ndash CyScope httpwwwsysmex-parteccomproductsmicroscopyhtml httpwwwsysmex-parteccomproductsprdouct-detailviewcyscopeR-malaria-3238html Technical Instruments httpwwwtechinstcomproductsphp TESCAN Brno sro - Tescan Q-PHASE multimodal holographic quantitative phase imaging system (QPi) optional fluorescence httpwwwtescancomenproductsq-phaseq-phase httpq-phasetescancom httpq-phasetescancomindexphptechnologyspecifications Ted Pella Inc ndash specialty light microscopy and electron microscopy supplies httpswwwtedpellacom Texas Instruments ndash DLP 4100 development kit (digital light processingrsquo DMD digital micromirror device) httpwwwticomtooldlpd4x00kit

ThorLabs ndash iCyte imaging cytometer multiphoton confocal EnVista digital slide scanning microscopes httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7473 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7494 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=5696 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=6570 TIRF Labs lightguide TIRF prism TIRF TIRF-Electrochemistry httpwwwtirf-labscom httpwwwtirf-labscomtechnologieshtml TissueVision - Serial Two Photon Tomography (image volume ablate imaged volume with multiphoton laser repeat) httpwwwtissuevisioncomtechnology Tokai Hit - stage top incubator httpwwwtokaihitcomenglishproduct_guidanceoptionhtml TopoNomos Ltd ndash Toponome Imaging Cycler ndash immunofluorescence (100plex) httpwwwtoposnomoscomtechnologyhtml Ultivue Inc ndash DNA-PAINT ndash reagents data processing service httpwwwultivuecom httpwwwultivuecomproducts UMech Technologies ndash Cytovar HCS up to 16 excitation wavelengths httpcloudumechcomproducts httpcloudumechcomproductsmodelC16 Visitech ndash vt-iSIM instant super-resolution microscopy up to 1000 frames per second confocal scanners and light engines httpwwwvisitechcoukvt-isimhtml httpwwwvisitechcoukproductshtml Visitron Systems GmbH - high speed imaging systems httpwwwvisitronde Visualsonics (Fujifilm) - photoacoustic imaging httpwwwvisualsonicscomproductstechnology-overview Wicked Lasers httpwwwwickedlaserscom httpwwwwickedlaserscomarctic WITec Wissenschaftliche Instrumente und Technologie GmbH - imaging systems for FLIM Raman AFM and SNOM analysis httpwitecdeproducts httpwwwwitec-instrumentscom WM Keck Center for Adaptive Optical Microscopy (CfAOM) at UC Santa Cruz httpscfaomsoeucscedu httpcfaoucolickorgpgallery Yokogawa Corp ndash spinning disk confocal scanner live cell imager high content screener confocal quantitative cytometer httpwwwyokogawacomsolutionsproducts-platformslife-science httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-scanner-unit-csu httpwwwyokogawacomsolutionsproducts-platformslife-scienceall-in-one-live-cell-imaging-solution httpwwwyokogawacomsolutionsproducts-platformslife-sciencehigh-throughput-cytological-discovery-system httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-quantitative-image-cytometer Zellkraftwerk (ChipCytometry) ndash immunofluorescence (80plex) httpwwwzellkraftwerkcomProducts2phtml httpwwwzellkraftwerkcomZKWOnephtmlSoftware

httpwwwchipcytometrycomtechnologyphtml Fluorescence Spectra Data and Graphing Sites PubSpectra ndash Excel file data download httpsworksbepresscomgmcnamara9 BD Biosciences ndash spectrum viewer Brilliant fluorophores httpwwwbdbiosciencescomussspectrumviewer httpwwwbdbiosciencescomusapplicationssspectrumguidepage BioLegend ndash spectra analyzer Brilliant Violet fluorophores httpwwwbiolegendcomspectraanalyzer httpwwwbiolegendcombrilliantviolet Chroma Technology httpswwwchromacomspectra-viewer eBioscience (Affymetrix ThermoFisher) ndash fluorPlan ndash a multi-laser spectra viewer httpwwwebiosciencecomresourcesfluorplan-spectra-viewerhtm Spectra Viewer (requires Java) Evrogen ndash Spectrum Viewer httpevrogencomspectra-viewerflashviewerhtml Fluorophoresorg ndash Fluorescent Substances httpwwwfluorophorestugrazatsubstance I Love GFP httpssitesgooglecomsiteilovegfpHomefps Lambert and Thorn UCSF Fluorescent protein properties httpnicucsfeduFPvisualization Leica Microsystem - ldquoFluoScoutrdquo httpwwwleica-microsystemscomfluoscout

Molecular Probes Invitrogen Thermo Fisher ndash Fluorescence SpectraViewer httpwwwthermofishercomusenhomelife-sciencecell-analysislabeling-chemistryfluorescence-spectraviewerhtml httpsitunesapplecomusappfluorescence-spectraviewerid421031826 (iTunes App) Nightsea - Compendium of spectra web sites httpwwwnightseacomsfa-sharingfluorescence-spectra-viewers Omega Optical ldquoCurvomatricrdquo httpswwwomegafilterscomcurvomatic

PhotoChemCAD 20 (Jonathan S Lindsey) dye spectra database and chemistry calculator NIRvana Sciences httpwwwphotochemcadcom httpnirvanasciencescompage_id=3088 UCSF (Lambert Thorn 2016) - Fluorescent protein properties httpnicucsfeduFPvisualization University of Arizona - Fluorescent Spectra Database httpwwwspectraarizonaedu Semrock - Searchlight httpssearchlightsemrockcom Spectroscopy Ninja ndash links to spectral and fluorescence data Spekwin32 spectroscopy software httpwwweffemm2deinfoinfo_specdatahtml

httpwwweffemm2deindexhtml Zeiss ndash interactive fluorescence dye and filter database overview dyes overview filter sets httpswwwmicro-shopzeisscoms=50479761ad21e5ampl=enampp=usampf=fampa=i httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=d httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=f Researcher Labs Alby Diaspro ndash IIT httpwwwlambsitindexphppage=People Alice Ting ndash MIT httpwwwtinglaborgresearch Allen Institute for Brain Science httpwwwalleninstituteorgwhat-we-dobrain-science Allen Institute for Cell Science httpwwwalleninstituteorgwhat-we-docell-science Amina Qutub - Rice University - How are human cells designed lab httpsqutublaborgqutub-lab Amy Herr UC Berkeley ndash Single cell Westerns httpherrlabberkeleyedu Amy Palmer ndash UC Boulder httpspalmerlabcoloradoedu Andrew York ndash Calico Life Sciences httpswwwcalicolabscomteam-memberandrew-york Anne Carpenter ndash Broad Institute CellProfiler httpspersonalbroadinstituteorganne Arjun Raj UPenn single molecule RNA FISH quantitative understanding cellular functions httprajlabseasupenneduindexhtml httpwwwpopscicomsciencearticle2013-09arjun-raj Atsuko Miyawaki - Laboratory for Cell Function Dynamics (CFDS) Fucci2 fluorescent proteins cell cycle indicator httpwwwbrainrikenjpenfacultydetails30 httpcfdsbrainrikenjp httpcfdsbrainrikenjpFuccihtml Aydogan Ozcan - UCLA - new imaging and sensing architectures httpinnovateeeuclaeduwelcomehtml httpwwwhhmiorgscientistsaydogan-ozcan Badri Roysam - UH - FARSIGHT Toolkit httpwwweeuhedufacultyroysam httpwwwfarsight-toolkitorgwikiMain_Page Brian J Ford ndash microscopist and popularizer httpsuklinkedincominprofbrianjford Carolyn Larabell ndashNational Center for X-ray Tomography (LBNL) UCSF httpncxtlblgovq=carolyn httpprofilesucsfeducarolynlarabell Clare Waterman ndash NHLBI NIH

httpswwwnhlbinihgovresearchintramuralresearcherspiwaterman-clare Dana Peer - Columbia University - Computational Systems Biology viSNE and more software httpwwwc2b2columbiaedudanapeerlabhtml httpwwwc2b2columbiaedudanapeerlabhtmlcythtml David Mayerich - UH - STIM Laboratory Scalable Tissue Imaging and Modeling httpwwweeuhedufacultymayerich httpstimeeuhedu David Piston WUSTL httpwwwcellbiologywustledufacultytenureddavid-w-piston-phd Diane Lidke and Keith Lidke - University of New Mexico httppathologyunmeduresearchfaculty-laboratoriesthe-lidke-laboratoryindexhtml httppanda3physunmedu~klidke Donna Arndt-Jovin and Thomas Jovin - Max Planck Institute for Biophysical Chemistry Laboratory of Cellular Dynamics httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsDonnaArdndt-JovinResearchAreasAndProjects httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsChairmanThomasJovinResearchAreasAndProjects Ed Boyden ndash MIT Media Lab ndash expansion microscopy (ExM) optogenetics httpsyntheticneurobiologyorg httpsyntheticneurobiologyorgprotocols httpsyntheticneurobiologyorgpublications httpwwwtedcomtalksed_boyden_baby_diapers_inspired_this_new_way_to_study_the_brain httpwwwextbiocombuycell Elizabeth Blackburn ndash Salk Institute - Telomeres httpswwwsalkeduscientistelizabeth-blackburn httpsenwikipediaorgwikiElizabeth_Blackburn httpswwwnobelprizeorgnobel_prizesmedicinelaureates2009blackburn-factshtml Elizabeth Hillman - Columbia university - SCAPE (Swept Confocally-Aligned Planar Excitation) high speed 3D microscopy DyCE (dynamic contrast enhancement to image and segment small animal organs live) Neuroimaging amp Neurovascular Coupling httporionbmecolumbiaedu~hillmanInstrumentationhtml httporionbmecolumbiaedu~hillmanSCAPEhtml httporionbmecolumbiaedu~hillmanMolecularhtml httporionbmecolumbiaedu~hillmanBrain_Imaginghtml Eric Betzig ndash UCSF (moving from HHMI Janelia Farm in 2016) httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014betzig-factshtml Eva Sevick-Muraca ndash UT Health Science Center at Houston molecular imaging clinical NIR fluoresceince imaging httpswwwutheduimmprofilehtmid=1005459 httpswwwutheduimmcentersmolecular-imaginghtm Evelin Schrock - Technische Universitaumlt Dresden spectral karyotyping cytogenetics httpswwwresearchgatenetprofileEvelin_Schrock Garry Nolan Stanford University ndash Mass cytometry MIBI-ToF high throughput imaging mass cytometry (42plex) httpwebstanfordedugroupnolanresourceshtml httpwebstanfordedugroupnolantechnologieshtml George McNamara ndash Cell Morphometry (41) Figure 1 right top two panels (55) The Chase (2016 temporal area maps lsquodynamic morphologyrsquo) (76) newsletter series on ldquoThe Chaserdquo (73) direct Vimeo movie of ldquoThe Chaserdquo Tiki_Goddess linkedin 10+plex blog httpsworksbepresscomgmcnamara41 httpsworksbepresscomgmcnamara55 httpsworksbepresscomgmcnamara76

httpsworksbepresscomgmcnamara73 httpsvimeocom175151196 httphomeearthlinknet~tiki_goddess httpswwwlinkedincomingeorgemcnamara httpswwwlinkedincompulsebd-biosciences-listed-tandems-horizon-brilliant-violets-mcnamara Gillian Griffiths - University of Cambridge - T-cell immunological synapse httpwwwcimrcamacukresearchprincipal-investigatorsprincipal-investigators-a-hgriffiths Hari Shroff NIBIB NIH httpswwwnibibnihgovlabs-at-nibibsection-high-resolution-optical-imaging-hroi HHMI Janelia Farm Research Campus (JFRC) - Advanced Imaging Center Open Science httpswwwjaneliaorgopen-scienceadvanced-imaging-center-aic httpswwwjaneliaorgopen-science Jeanne Lawrence University of Massachussetts Medical School httpwwwumassmededucellbiolabslawrencepersonnelprincipal-investigator Jennifer Lippincott-Schwartz ndash HHMI Janelia Farm httpswwwjaneliaorgpeoplejennifer-lippincott-schwartz Jin Zhang ndash UCSD httpprofilesucsdedujinzhang Joe DeRisi - UCSF - 3D printable lab stuff httpderisilabucsfeduindexphppage=3D John Russ Chris Russ Fovea Pro plugins for Adobe Photoshop httpwwwdrjohnrusscomindexhtml httpwwwdrjohnrusscombookshtml httpwwwreindeergraphicscomfoveaprotutorialhtml Julie Theriot httpcmgmstanfordedutheriot Karl Deisseroth ndash Stanford University ndash CLARITY optical tissue clearing Optogenetics httpclarityresourcecenterorg httpwebstanfordedugroupdlaboptogeneticsindexhtml Karsten Koumlnig (Koenig) - Saarland University and JenLab GmbH - biophotonics httpwwwbltuni-saarlanddeindex_ehtm httpwwwjenlabde httpwwwthelastescape-filmcom Karsten Rodenacker ndash image measurements httpkaro03bplacednetkaroMeMisc_WWWpdfMicrosoftWord-EQUAPATpdf Kevin Eliceiri ndash UW-Madison Open Source Photonics and Software Laboratory for Optical and Computational Instrumentation (LOCI) wwwlociwiscedu Klaus Kemp ndash Microlife Services ndash diatoms and other prepared microscope slides httpwwwdiatomscouk Kurt Thorn UCSF httpthornlabucsfedu httpsnicucsfedublog httpnicucsfeduFPvisualization httpgigapancomgigapans163370 Lihong Wang - WUSTL - Optical Imaging Laboratory photoacoustic tomography

httpoilabseaswustledu httpoilabseaswustleduresearch_0html Loren Looger - HHMI JFRC - iGluSnFr fluorescent protein biosensor httpswwwjaneliaorglablooger-lab Mary-Lou Pardue ndash MIT (first ever in situ hybridization with J Gall) httpsbiologymitedupeoplemary_lou_pardue httpsenwikipediaorgwikiMary-Lou_Pardue Nancy Allbritton - UNC - Chemical cytometry microraft arrays organ-on-a-chip httpswwwbmencsueduindexphpcomponentcomprofileruserprofilenlallbri httpwwwbmeuncedulabsallbritton Navin Varadarajan - UH - single-cell Lab httpwwwcheeuhedufacultyvaradarajan httpsinglecellcheeuheducontacthtml Nicholas Shaner - Scintillon Institute - mNeonGreen httpwwwscintillonorgshaner_lab Rebecca Richards-Kortum httpbioengineeringriceedufacultyrebecca_richards-kortumaspx Robert Campbell - Fluorescent proteins optogenetic proteins httpcampbellwebchemualbertaca httpcampbellwebchemualbertacaprojects-2 Robert Murphy ndash Cell measurements web services httpmurphylabwebcmueduservices Sabine Mai - University of Manitoba - Genomic Centre for Cancer Research and Diagnosis (GCCRD) - httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBPlatformsGCCRDhtml httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBScientistsMaiAwardshtml Sally Ward and Raimund Ober - Texas AampM University - httpwwwwardoberlabcom Simon Watkins - U Pittsburgh Center for Biologic Imaging httpwwwcbppittedufacultywatkinshtml httpwwwcbppittedufacultylabwatkinshtml httpwwwcbipittedu Stefan Hell ndash Deparment Hell NanoBiopohotonics httpwwwmpibpcmpgdehell httpsenwikipediaorgwikiStefan_Hell httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014hell-factshtml Sunney Xie Harvard httpsbernsteinharvardedu Susan Cox ndash 3B microscopy httpwwwcoxphysicscomindexhtml httpwwwcoxphysicscom3b Radim Chmeliacutek - Center for innovative microscopy Experimental biophotonics group httpswwwceiteceuceitec-butexperimental-biophotonicsrg3 httpwwwbiophotczhome Taekjip Ha ndash Johns Hopkins University ndash single molecules httphamedjhmiedu

Thomas Ried ndash NCI NIH SKYM-FISH and CGH Database httpsccrcancergovGenetics-Branchthomas-ried httpsccrcancergovGenetics-Branchthomas-riedqt-staff_profile_tabs=9qt-staff_profile_tabs ftpftpncbinlmnihgovsky-cghDATA httpswwwncbinlmnihgovdbvar Viviana Gradinaru ndash CalTech ndash CLARITYPACT Optogenetics httpwwwbbecaltecheducontentviviana-gradinaru httpglabcaltechedu Vladislav Verkhusha - near infrared fluorescent proteins httpwwweinsteinyuedulabsvlad-verkhushadefaultaspx httpwwweinsteinyueduresearchfacilitiesfluorescent WE Moerner ndash Stanford University httpwebstanfordedugroupmoerner Willard Wiggans ndash micro gallery httpwwwwillard-wigancomgallery Wolf Frommer ndash Molecular sensors httpbiosensordpbcarnegiescienceedu (fluorescent protein biosensors table) Xiaowei Zhuang = Harvard httpzhuangharvardedu Yuval Garini - Bar-Ilan University - Nano-Bio-Photonics laboratory httpgarinilabbiuacil Microscopy Magazines Imaging amp Microscopy httpwwwimaging-gitcommagazine Laser Focus World httpwwwlaserfocusworldcomindexhtml Microscopy amp Analysis httpwwwmicroscopy-analysiscom Microscopy Today httpwwwmicroscopy-todaycom Microscopy-UK httpwwwmicroscopy-ukorguk Photonics Spectra Biophotonics httpwwwphotonicscomPublicationsaspx The Microscope Journal httpmcriorgv72the-microscope-journal RMS Infocus Magazine httpwwwrmsorgukstudy-readinfocus-magazinehtml Nobel Prizes in Light Microscopy and Related Fields Chemistry 1925 colloids (light sheet) Zsigmondy (Siedentopf Zsigmondy 1902) httpswwwnobelprizeorgnobel_prizeschemistrylaureates1925

Chemistry 2000 conductive polymers Heeger MacDiarmid Shirakawa (Brilliant Violets Ultraviolets Blues) httpwwwnobelprizeorgnobel_prizeschemistrylaureates2000 Chemistry 2008 green fluorescent protein GFP Shimomura Chalfie Tsien httpwwwnobelprizeorgnobel_prizeschemistrylaureates2008 Chemistry 2014 super-resolved fluorescence microscopy Betzig Hell Moerner httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014 Physics 1953 Phase Contrast Zernike httpswwwnobelprizeorgnobel_prizesphysicslaureates1953 Physics 2009 invention of an imaging semiconductor circuit ndash the CCD sensor Kao Boyle Smith httpwwwnobelprizeorgnobel_prizesphysicslaureates2009 Physics 2014 efficient blue light emitting diodes Akasaki Amano Nakamura httpwwwnobelprizeorgnobel_prizesphysicslaureates2014 Physiology or Medicine 2006 Fire and Mello RNA interference ndash gene silencing by double stranded RNA httpwwwnobelprizeorgnobel_prizesmedicinelaureates2006 Physiology or Medicine 2006 Capecchi Evans Smithies specific gene modifications in mice by the use of embryonic stem cells httpwwwnobelprizeorgnobel_prizesmedicinelaureates2007 Physiology or Medicine 2009 Blackburn Greider Szostak how chromosomes are protected by telomeres and telomerase httpwwwnobelprizeorgnobel_prizesmedicinelaureates2009 Physiology or Medicine 2012 Gurdon Yamamanka matured cells can be reprogrammed to become pluripotent httpwwwnobelprizeorgnobel_prizesmedicinelaureates2012

Table 442 Fluorophores Photophysics Data

Fluorophore Abs or Ex max (nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Acridine orange 271 520 27000 020 5

Alexa Fluor 430 431 541 16000 055 9

Alexa Fluor 488 495 519 71000 094 67

Alexa Fluor 532 532 553 81000 080 65

Alexa Fluor 546 556 573 104000 096 100

Alexa Fluor 568 578 603 91300 075 69

Alexa Fluor 594 590 617 73000 064 47

Allophycocyanin (APC) 650 660 700000 068 476

Atto 390 390 479 24000 090 22

Atto 425 436 484 45000 065 29

Atto 430LS 433 547 32000 065 21

Atto 465 453 508 75000 075 56

Atto 490LS 496 661 40000 030 12

Atto 520 525 547 105000 095 100

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 13: McNamara 20161006 revised draft tables for CPHG Light ...

Glencoe Software ndash OMERO Plus enterprise data management for scientific images and any associated metadata (OME = Open Microscopy Environment) DataViewer PathViewer httpsglencoesoftwarecomomeroplushtml httpsglencoesoftwarecomdataviewerhtml httpsglencoesoftwarecompathviewerhtml Gooch amp Housego ndash spectral imager httpsgoochandhousegocomminiature-spectral-imaging-camera httpwwwghinstrumentscomproductsspectral-imaging-synthesishsi-440c-hyperspectral-imaging-system Hindsight Imaging ndash spectral imaging httphindsight-imagingcom Horiba Scientific - SWIFT ultra-fast Raman confocal imaging Raman spectroscopy httpwwwhoribacomscientificproductsraman-spectroscopyraman-imagingswift httpwwwhoribacomscientificproductsraman-spectroscopyraman-imaging httpwwwhoribacomscientificproductsraman-spectroscopy IATIA Ultima Capital ndash QPm (quantitative phase microscopy) httpwwwultimacapitalnetiatiaimagingPublicationsIatia20ImagingapplicationNotesqpmApplicationWithConfocalMicroscopespdf Ibidi - heating and incubation systems optical O2 measurement systems Nanolive 3D Cell Explorer pump system gas incubation system httpibidicomxtproductsenInstruments-AccessoriesHeating-Incubation-Systems httpibidicomxtproductsenInstruments-Accessoriesibidi-OPAL-Optical-O2-Measurement-System httpibidicomxtproductsenInstruments-AccessoriesNanolive-3D-Cell-Explorer httpibidicomxtproductsenInstruments-Accessoriesibidi-Pump-System httpibidicomxtproductsenInstruments-AccessoriesHeating-Incubation-Systemsibidi-Gas-Incubation-System iLAbSolutions (Agilent Technologies) - Instrument management and scheduling software (cores and labs) httpwwwilabsolutionscominstrument-access-control ImageJ - Fiji ImageJ NIH ImageJ ImageJ ndash Fiji (Fiji is just ImageJ) is the main download site httpfijisc httpsimagejnihgovij wwwimagejnet Inscopix ndash nVista in vivo mouse brain imaging miniature microscope httpswwwinscopixcomproducts Intelligent Imaging Innovations Inc (3i) ndash Slidebook imaging software Lattice light sheet (high speed gentle to cells high resolution imaging) Dual-view Inverted Selective Plane Illumination (diSPIM) VIVO 2-Photon (VIVO 2P) multiphoton microscopy Everest intravital imaging Marianas 3D real-time deconvolution timelapse spinning disk FRAP TIRF FLIM single molecule environmental control Phasor - optogenetic photostimulation using digital holography Yokogawa spinning disk confocal units wwwintelligent-imagingcom httpswwwintelligent-imagingcomslidebookphp httpswwwintelligent-imagingcomsystemsphplattice httpswwwintelligent-imagingcomsystemsphpdispim httpswwwintelligent-imagingcomsystemsphptwophoton httpswwwintelligent-imagingcomsystemsphpeverest httpswwwintelligent-imagingcomsystemsphpmarianas httpswwwintelligent-imagingcomoptogeneticsphp httpswwwintelligent-imagingcomsdcphp ISS Inc ndash fluorescence lifetime imaging microscopy fluorescence correlation spectroscopy (FCS) confocal imaging httpwwwisscommicroscopyindexhtml JenLab GmbH cyto-microscopy multiphoton tomography httpwwwjenlabdeproducts250html httpwwwjenlabde2PM-Cryo1330html

httpwwwjenlabdeMultiphoton-Tomography680html Jenoptik - microscope cameras httpswwwjenoptikcomproductscameras-and-imaging-modulesmicroscope-cameras JPK Instruments - integrated atomic force microscope (AFM) force sensing optical tweezers optical trapping single cell force spectroscopy (SCFS) httpwwwjpkcomindex2enhtml httpusajpkcomoptical-tweezers-optical-trapping29ushtml httpusajpkcomcellular-adhesion-cytomechanics30ushtml Keyence ndash VK-X confocal (upright) BZ-X700 widefield (inverted) httpwwwkeyencecomssproductsmicroscopevkx httpwwwkeyencecomssproductsmicroscopebz-x700indexjsp KK Technology - CapiScope HVCS Handheld Video Capillaroscopy System (CytoScan) httpwwwkktechnologycomhvcshtml LaVision BioTec ndash TriMscope Multiphoton TriM Scope II Adaptive Optics UltraMicroscope II light sheet httpwwwlavisionbiotecde httpwwwlavisionbiotecdetrim-scope-overviewhtml httpwwwlavisionbiotecdetrim-scope-ii-adaptive-opticshtml httpwwwlavisionbiotecdeultramicroscope-ii-introductionhtml Laxco ndash upright and inverted microscopes httpwwwlaxcoinccomMICROSCOPES Lego ndash Lego Idea Microscopes httpsideaslegocomprojects44370 httpwwwnico71frlego-working-microscope Li-Cor ndash near-infared fluorescent dyes and in vivo imaging agents in vivo and Western blot imaging systems httpswwwlicorcombioproductsreagents httpswwwlicorcombioproductsreagentsirdyebrightsite_imaging_agents httpswwwlicorcombioproductsimaging_systemsodyssey_familyhtml httpswwwlicorcombioproductsimaging_systemspearl httpswwwlicorcombioproductsimaging_systemscdigit Life Imaging Services - ldquothe Ludin chamberrsquo ldquothe cube amp the boxrdquo httpwwwlischthechamberhtml httpwwwlischtheboxhtml Lightform Inc ndash PARISS imaging spectrometer httplightforminccom LMU Bioimaging httpwwwbioimagingbmcmeduni-muenchendelinkswebsitesindexhtml httpwwwbioimagingbmcmeduni-muenchendelearneduwebsitesindexhtml Ludl Electronic Products Ltd ndash automated XY stages focus motors filter wheels httpwwwludlcom

LumaCyte ndash Laser force Cytology (laser trap meets microfluidics to suspend and manipulate single cells) httpwwwlumacytecomabouttechnology Lumencor ndash LEDs fluorescence light sources httplumencorcomproducts Luxcel ndash mitochondrial and cellular functions O2 sensor reagents httpluxcelcomproduct+list Luxendo GmbH ndash light sheet imager

wwwluxendoeu Lyncee tec - digital holography microscopy (DHM) high content screening by DHM httpwwwlynceeteccom httpwwwlynceeteccomhigh-content-screening Mad City Labs Inc - nanopositioning wwwmadcitylabscom Mauna Kea Technologies ndash CellVizio confocal laser endomicroscopy httpwwwmaunakeatechcomenhealthcare-professionalscellvizio-endomicroscopy-0 MBF Bioscience - stereology and neuron morphology quantitative imaging httpwwwmbfbiosciencecom McCrone Group wwwmccronecominstrument-sales Media Cybernetics Inc ndash Image Premier 3D AutoQuant X3 deconvolution httpwwwmediacycom Meiji Techno America wwwmeijitechnocom MesoLens Ltd httpwwwmesolenscomproducttechnical-specifications httpwwwmesolenscomimages httpswwwbiophotonicsstrathacukresearch_1htm Meyer Instruments ndash Pathscan Enabler GigaMacro digital pathology telepathology httpmeyerinstcom httpmeyerinstcompathscan-enabler-5 httpmeyerinstcomgigamacro-gigapixel-macro-imaging httpmeyerinstcomhomescanners httprealtimetelepathologycom Microarrays - Large-Scale Gene Expression and Microarray Links and Resources httpswwwebiacukarrayexpress Micro-Manager ndash Device Support ndash tabulates many microscope cameras and motorized accessories every new camera and accessory should have a uManager driver to enable simple use with Fiji ImageJ httpsmicro-managerorg httpsmicro-managerorgwikiDevice_Support httpsopen-imagingcom Microvolution ndash (near) instant gratification spatial deconvolution using NVidia GPU card(s) httpmicrovolutioncom Mightex Systems ndash optogenetics DMDDLP illuminator (digital micro-mirror device digital light processing) httpwwwmightexsystemscomindexphpcPath=245 Millipore-Sigma Merck KGaA (Amnis Corp CellASIC EMD Millipore) ndash ImageStreamX and FlowSight imaging flow cytometers ONIX2 Microperfusion System for microscopes httpswwwemdmilliporecom httpswwwemdmilliporecomUSenlife-science-researchcell-analysisamnis-imaging-flow-cytometersQ6ubqBm3UAAAFLCKIpygJnav httpwwwemdmilliporecomUSenlife-science-researchcell-culture-systemscellASIC-live-cell-analysisd1CbqBw58AAAE_0j13MnAnav Mitutoyo America Corp wwwmitutoyocom httpecatalogmitutoyocomMF-U-Series-176-High-power-Multi-function-Measuring-Microscopes-C1413aspx

Molecular Devices Corporation Universal Imaging Corporation (Danaher) ndash MetaMorph MetaFluor high content systems (HCS) httpswwwmoleculardevicescomsystemsmetamorph-research-imaging httpmdccusthelpcomappanswersdetaila_id19319 httpswwwmoleculardevicescomsystemshigh-content-imaging Molecular Machines amp Industries - laser microdissection and tweezer systems httpwwwmolecular-machinescomhome MUSE Microscopy Inc ndash Deep UV illumination for shallow depth of field imaging httpwwwmusemicrocom Micro Video Instruments Inc - DarkLite illuminator httpwwwmvi-inccom NanoEnTek ndash JuLI Stage (imager inside incubator or on lab bench) httpwwwjulistagecom National Instruments ndash LabView software httpwwwnicomen-ushtml Navitar - Hoffman Modulation Contrast (HMC alternative to differential interference contrast phase contrast) custom lens design UVDUVNUV imaging lenses httpsnavitarcommarketsmicroscopy httpsnavitarcomproductsimaging-opticscustom-microscope-objectivescustom-microscope-objectives httpsnavitarcomproductsimaging-opticsuv-imaging National Center for X-ray Tomography (NCXT) ndash soft X-ray tomography (CT of hydrated cells) XM-2 dedicated biological SXT microscope Prof Carolyn Larabell Director (see also SiriusXT) httpncxtlblgov httpncxtlblgovsxt httpncxtlblgovmanual httpncxtlblgovq=carolyn Neogenomics (Clarient) ndash MultiOmyx immunofluorescence or DNA FISH (ldquo60plexrdquo) httpneogenomicscomPharma-ServicesLab-ServicesMultiOmyxTechnologyMultiOmyx-IF-Assay-DNA-FISH-assay-NGS-from-ROI Nexcelom ndash Celigo imaging cytometer Cellometer cell counters httpwwwnexcelomcomCeligoindexphp httpwwwnexcelomcomProducts Nikon ndash Ti-LAPP modular illumination system (for Nikon Ti series microscopes) TIRF Optogenetics httpswwwnikoninstrumentscomProductsPhotostimulation-and-TIRFTi-LAPP Nirmidas Biotech httpwwwnirmidascomtechnologynir httpwwwnirmidascomproductsniriidye NVidia ndash Pascal 10+ Gbps GPU cards for instant gratification deconvolution (software from Microvolutioncom SVInl) httpwwwgeforcecomhardware10seriesgeforce-gtx-1080 httpwwwgeforcecomhardware10seriestitan-x-pascal httpwwwnvidiacomobjectquadro-graphics-with-pascalhtml Ocean Optics ndash spectrometers httpoceanopticscomproduct-categorymodular-spectrometers Oko-Lab stage top incubator httpwwwoko-labcomstage-top Open Microscopy Environment (OME) ndash OMERO (see also Glencoe Software) Bio-Formats LOCI

httpswwwopenmicroscopyorgsite httpswwwopenmicroscopyorgsiteproductsomero httpswwwopenmicroscopyorgsiteproductsbio-formats httpswwwopenmicroscopyorgsitesupportbio-formats52supported-formatshtml httpswwwopenmicroscopyorgsiteaboutdevelopment-teamskevin OpenSPIM ndash do-it-yourself selective plane illumination microscopy (light sheet imaging) httpopenspimorgWelcome_to_the_OpenSPIM_Wiki OpenSpinMicroscopy ndash do-it-yourself SPIMDSLMOPT microscopes httpssitesgooglecomsiteopenspinmicroscopy Ovizio ndash differential digital holography (similar to quantitative phase imaging) httpwwwoviziocomenHome httpwwwoviziocomenMicroscopesQMod Oxford Gene Technologies ndash microarrays ndash cytogenetics molecule genetics cancer research pre-implantation genetic diagnosis httpwwwogtcomclinical_genetics Oxford Nanoimaging ndash single molecule(s) localization fluorescence resonance energy transfer (FRET) (Kapanidis) wwwoxfordnicom Pathology Devices ndash LiveCell stage top incubator amp controller tissue microarrayers (TMA makers) httpwwwpathologydevicescomLiveCellhtm httpwwwpathologydevicescomTMArrayerhtm PeCon GmbH ndash microscope incubators httpwwwpeconbiz Pembroke Instruments ndash spectrometers mini-lasers httppembrokeinstrumentscomqmini-spectrometer httppembrokeinstrumentscommini-lasers PerkinElmer ndash in vivo imaging systems (bioluminescence NIR fluorescence) Vectra digital slide scanner httpwwwperkinelmercomcategoryin-vivo-imaging-instruments httpwwwperkinelmercomcategoryquantitative-pathology-imaging-instruments Phi Optics ndash CellVista SLIM Pro (quantitative phase microscopy) httpphiopticscom Photometrics (Roper Scientific) ndash DualView QuadView httpwwwphotometricscom httpwwwphotometricscomproductsmultichannel Photon Technology International httpwwwpti-njcomindexhtml

PicoQuant GmbH ndash fluorescence lifetime imaging microscopes (FLIM) STED 3D-EasySTED httpswwwpicoquantcomproductscategoryfluorescence-microscopes httpswwwpicoquantcomapplicationscategorylife-sciencested httpwwweasystedorg Physik Instrumente GmbH amp Co KG (PI) - Nanopositioning Applications for Microscopy Neuroscience and Metrology httpswwwphysikinstrumentecomen httpwwwpi-usausindexphp PreSens Prescision Sensing GmbH - VisiSens measure and visualize Oxygen pH or carbon dioxide distributions httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-biological-researchhtml httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-life-science-researchhtml Prior Scientific

httpwwwprior-uscom Profusa Inc - Lumee tissue-integrated biosensors scaffolds httpprofusacomtechnology Reindeer Graphics Inc ndash OptiPix Fovea Pro 9plugins for Adobe Photoshop 6 and CS series) httpwwwreindeergraphicscom Renishaw - StreamLine fast chemical imaging Raman spectroscopy httpwwwrenishawcomenstreamline-generate-chemical-images-rapidly--9449 httpwwwrenishawcomenraman-spectroscopy--6150 Sanford Burnham Prebys ndash High Content Screening httpwwwsbpdiscoveryorgtechnologysrPagesLaJolla_HighContentScreeningaspx ScopeM - Scientific Center for Optical and Electron Microscopy - ETH Zurich httpwwwscopemethzch SiriusXT - soft X-ray tomography (SXT) microscope (CT scan hydrated cell) httpsiriusxtcom SpectraGenetics - Fluorogen Activating Peptides (FAPs) new genetically encoded ldquobinaryrdquo reporters httpspectrageneticscomproductsvectors-for-expressing-fluorogen-activating-proteinsfap-technology-overview Spirochrome - Silicon Rhodamine (SiR) and other fluorescent reagents probes for bioimaging httpspirochromecom Stanford Photonics Inc httpwwwstanfordphotonicscom httpwwwstanfordphotonicscomLife20SciencesLifeScihtm

Stream Technologies Inc ndash ColorFlow lens (multi-wavelength emission onto a camera) httpwwwstreamtechinccomproducts Sutter Instrument Company httpwwwsuttercom httpwwwsuttercomMICROSCOPESindexhtml httpwwwsuttercomIMAGINGindexhtml SVI Huygens ndash Professional (general image analysis) deconvolution NVidia GPU deconvolution httpssvinlHuygensProfessional httpssvinlHuygensDeconvolution httpssvinlHuygensGPU Sysmex Partex ndash CyScope httpwwwsysmex-parteccomproductsmicroscopyhtml httpwwwsysmex-parteccomproductsprdouct-detailviewcyscopeR-malaria-3238html Technical Instruments httpwwwtechinstcomproductsphp TESCAN Brno sro - Tescan Q-PHASE multimodal holographic quantitative phase imaging system (QPi) optional fluorescence httpwwwtescancomenproductsq-phaseq-phase httpq-phasetescancom httpq-phasetescancomindexphptechnologyspecifications Ted Pella Inc ndash specialty light microscopy and electron microscopy supplies httpswwwtedpellacom Texas Instruments ndash DLP 4100 development kit (digital light processingrsquo DMD digital micromirror device) httpwwwticomtooldlpd4x00kit

ThorLabs ndash iCyte imaging cytometer multiphoton confocal EnVista digital slide scanning microscopes httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7473 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7494 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=5696 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=6570 TIRF Labs lightguide TIRF prism TIRF TIRF-Electrochemistry httpwwwtirf-labscom httpwwwtirf-labscomtechnologieshtml TissueVision - Serial Two Photon Tomography (image volume ablate imaged volume with multiphoton laser repeat) httpwwwtissuevisioncomtechnology Tokai Hit - stage top incubator httpwwwtokaihitcomenglishproduct_guidanceoptionhtml TopoNomos Ltd ndash Toponome Imaging Cycler ndash immunofluorescence (100plex) httpwwwtoposnomoscomtechnologyhtml Ultivue Inc ndash DNA-PAINT ndash reagents data processing service httpwwwultivuecom httpwwwultivuecomproducts UMech Technologies ndash Cytovar HCS up to 16 excitation wavelengths httpcloudumechcomproducts httpcloudumechcomproductsmodelC16 Visitech ndash vt-iSIM instant super-resolution microscopy up to 1000 frames per second confocal scanners and light engines httpwwwvisitechcoukvt-isimhtml httpwwwvisitechcoukproductshtml Visitron Systems GmbH - high speed imaging systems httpwwwvisitronde Visualsonics (Fujifilm) - photoacoustic imaging httpwwwvisualsonicscomproductstechnology-overview Wicked Lasers httpwwwwickedlaserscom httpwwwwickedlaserscomarctic WITec Wissenschaftliche Instrumente und Technologie GmbH - imaging systems for FLIM Raman AFM and SNOM analysis httpwitecdeproducts httpwwwwitec-instrumentscom WM Keck Center for Adaptive Optical Microscopy (CfAOM) at UC Santa Cruz httpscfaomsoeucscedu httpcfaoucolickorgpgallery Yokogawa Corp ndash spinning disk confocal scanner live cell imager high content screener confocal quantitative cytometer httpwwwyokogawacomsolutionsproducts-platformslife-science httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-scanner-unit-csu httpwwwyokogawacomsolutionsproducts-platformslife-scienceall-in-one-live-cell-imaging-solution httpwwwyokogawacomsolutionsproducts-platformslife-sciencehigh-throughput-cytological-discovery-system httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-quantitative-image-cytometer Zellkraftwerk (ChipCytometry) ndash immunofluorescence (80plex) httpwwwzellkraftwerkcomProducts2phtml httpwwwzellkraftwerkcomZKWOnephtmlSoftware

httpwwwchipcytometrycomtechnologyphtml Fluorescence Spectra Data and Graphing Sites PubSpectra ndash Excel file data download httpsworksbepresscomgmcnamara9 BD Biosciences ndash spectrum viewer Brilliant fluorophores httpwwwbdbiosciencescomussspectrumviewer httpwwwbdbiosciencescomusapplicationssspectrumguidepage BioLegend ndash spectra analyzer Brilliant Violet fluorophores httpwwwbiolegendcomspectraanalyzer httpwwwbiolegendcombrilliantviolet Chroma Technology httpswwwchromacomspectra-viewer eBioscience (Affymetrix ThermoFisher) ndash fluorPlan ndash a multi-laser spectra viewer httpwwwebiosciencecomresourcesfluorplan-spectra-viewerhtm Spectra Viewer (requires Java) Evrogen ndash Spectrum Viewer httpevrogencomspectra-viewerflashviewerhtml Fluorophoresorg ndash Fluorescent Substances httpwwwfluorophorestugrazatsubstance I Love GFP httpssitesgooglecomsiteilovegfpHomefps Lambert and Thorn UCSF Fluorescent protein properties httpnicucsfeduFPvisualization Leica Microsystem - ldquoFluoScoutrdquo httpwwwleica-microsystemscomfluoscout

Molecular Probes Invitrogen Thermo Fisher ndash Fluorescence SpectraViewer httpwwwthermofishercomusenhomelife-sciencecell-analysislabeling-chemistryfluorescence-spectraviewerhtml httpsitunesapplecomusappfluorescence-spectraviewerid421031826 (iTunes App) Nightsea - Compendium of spectra web sites httpwwwnightseacomsfa-sharingfluorescence-spectra-viewers Omega Optical ldquoCurvomatricrdquo httpswwwomegafilterscomcurvomatic

PhotoChemCAD 20 (Jonathan S Lindsey) dye spectra database and chemistry calculator NIRvana Sciences httpwwwphotochemcadcom httpnirvanasciencescompage_id=3088 UCSF (Lambert Thorn 2016) - Fluorescent protein properties httpnicucsfeduFPvisualization University of Arizona - Fluorescent Spectra Database httpwwwspectraarizonaedu Semrock - Searchlight httpssearchlightsemrockcom Spectroscopy Ninja ndash links to spectral and fluorescence data Spekwin32 spectroscopy software httpwwweffemm2deinfoinfo_specdatahtml

httpwwweffemm2deindexhtml Zeiss ndash interactive fluorescence dye and filter database overview dyes overview filter sets httpswwwmicro-shopzeisscoms=50479761ad21e5ampl=enampp=usampf=fampa=i httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=d httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=f Researcher Labs Alby Diaspro ndash IIT httpwwwlambsitindexphppage=People Alice Ting ndash MIT httpwwwtinglaborgresearch Allen Institute for Brain Science httpwwwalleninstituteorgwhat-we-dobrain-science Allen Institute for Cell Science httpwwwalleninstituteorgwhat-we-docell-science Amina Qutub - Rice University - How are human cells designed lab httpsqutublaborgqutub-lab Amy Herr UC Berkeley ndash Single cell Westerns httpherrlabberkeleyedu Amy Palmer ndash UC Boulder httpspalmerlabcoloradoedu Andrew York ndash Calico Life Sciences httpswwwcalicolabscomteam-memberandrew-york Anne Carpenter ndash Broad Institute CellProfiler httpspersonalbroadinstituteorganne Arjun Raj UPenn single molecule RNA FISH quantitative understanding cellular functions httprajlabseasupenneduindexhtml httpwwwpopscicomsciencearticle2013-09arjun-raj Atsuko Miyawaki - Laboratory for Cell Function Dynamics (CFDS) Fucci2 fluorescent proteins cell cycle indicator httpwwwbrainrikenjpenfacultydetails30 httpcfdsbrainrikenjp httpcfdsbrainrikenjpFuccihtml Aydogan Ozcan - UCLA - new imaging and sensing architectures httpinnovateeeuclaeduwelcomehtml httpwwwhhmiorgscientistsaydogan-ozcan Badri Roysam - UH - FARSIGHT Toolkit httpwwweeuhedufacultyroysam httpwwwfarsight-toolkitorgwikiMain_Page Brian J Ford ndash microscopist and popularizer httpsuklinkedincominprofbrianjford Carolyn Larabell ndashNational Center for X-ray Tomography (LBNL) UCSF httpncxtlblgovq=carolyn httpprofilesucsfeducarolynlarabell Clare Waterman ndash NHLBI NIH

httpswwwnhlbinihgovresearchintramuralresearcherspiwaterman-clare Dana Peer - Columbia University - Computational Systems Biology viSNE and more software httpwwwc2b2columbiaedudanapeerlabhtml httpwwwc2b2columbiaedudanapeerlabhtmlcythtml David Mayerich - UH - STIM Laboratory Scalable Tissue Imaging and Modeling httpwwweeuhedufacultymayerich httpstimeeuhedu David Piston WUSTL httpwwwcellbiologywustledufacultytenureddavid-w-piston-phd Diane Lidke and Keith Lidke - University of New Mexico httppathologyunmeduresearchfaculty-laboratoriesthe-lidke-laboratoryindexhtml httppanda3physunmedu~klidke Donna Arndt-Jovin and Thomas Jovin - Max Planck Institute for Biophysical Chemistry Laboratory of Cellular Dynamics httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsDonnaArdndt-JovinResearchAreasAndProjects httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsChairmanThomasJovinResearchAreasAndProjects Ed Boyden ndash MIT Media Lab ndash expansion microscopy (ExM) optogenetics httpsyntheticneurobiologyorg httpsyntheticneurobiologyorgprotocols httpsyntheticneurobiologyorgpublications httpwwwtedcomtalksed_boyden_baby_diapers_inspired_this_new_way_to_study_the_brain httpwwwextbiocombuycell Elizabeth Blackburn ndash Salk Institute - Telomeres httpswwwsalkeduscientistelizabeth-blackburn httpsenwikipediaorgwikiElizabeth_Blackburn httpswwwnobelprizeorgnobel_prizesmedicinelaureates2009blackburn-factshtml Elizabeth Hillman - Columbia university - SCAPE (Swept Confocally-Aligned Planar Excitation) high speed 3D microscopy DyCE (dynamic contrast enhancement to image and segment small animal organs live) Neuroimaging amp Neurovascular Coupling httporionbmecolumbiaedu~hillmanInstrumentationhtml httporionbmecolumbiaedu~hillmanSCAPEhtml httporionbmecolumbiaedu~hillmanMolecularhtml httporionbmecolumbiaedu~hillmanBrain_Imaginghtml Eric Betzig ndash UCSF (moving from HHMI Janelia Farm in 2016) httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014betzig-factshtml Eva Sevick-Muraca ndash UT Health Science Center at Houston molecular imaging clinical NIR fluoresceince imaging httpswwwutheduimmprofilehtmid=1005459 httpswwwutheduimmcentersmolecular-imaginghtm Evelin Schrock - Technische Universitaumlt Dresden spectral karyotyping cytogenetics httpswwwresearchgatenetprofileEvelin_Schrock Garry Nolan Stanford University ndash Mass cytometry MIBI-ToF high throughput imaging mass cytometry (42plex) httpwebstanfordedugroupnolanresourceshtml httpwebstanfordedugroupnolantechnologieshtml George McNamara ndash Cell Morphometry (41) Figure 1 right top two panels (55) The Chase (2016 temporal area maps lsquodynamic morphologyrsquo) (76) newsletter series on ldquoThe Chaserdquo (73) direct Vimeo movie of ldquoThe Chaserdquo Tiki_Goddess linkedin 10+plex blog httpsworksbepresscomgmcnamara41 httpsworksbepresscomgmcnamara55 httpsworksbepresscomgmcnamara76

httpsworksbepresscomgmcnamara73 httpsvimeocom175151196 httphomeearthlinknet~tiki_goddess httpswwwlinkedincomingeorgemcnamara httpswwwlinkedincompulsebd-biosciences-listed-tandems-horizon-brilliant-violets-mcnamara Gillian Griffiths - University of Cambridge - T-cell immunological synapse httpwwwcimrcamacukresearchprincipal-investigatorsprincipal-investigators-a-hgriffiths Hari Shroff NIBIB NIH httpswwwnibibnihgovlabs-at-nibibsection-high-resolution-optical-imaging-hroi HHMI Janelia Farm Research Campus (JFRC) - Advanced Imaging Center Open Science httpswwwjaneliaorgopen-scienceadvanced-imaging-center-aic httpswwwjaneliaorgopen-science Jeanne Lawrence University of Massachussetts Medical School httpwwwumassmededucellbiolabslawrencepersonnelprincipal-investigator Jennifer Lippincott-Schwartz ndash HHMI Janelia Farm httpswwwjaneliaorgpeoplejennifer-lippincott-schwartz Jin Zhang ndash UCSD httpprofilesucsdedujinzhang Joe DeRisi - UCSF - 3D printable lab stuff httpderisilabucsfeduindexphppage=3D John Russ Chris Russ Fovea Pro plugins for Adobe Photoshop httpwwwdrjohnrusscomindexhtml httpwwwdrjohnrusscombookshtml httpwwwreindeergraphicscomfoveaprotutorialhtml Julie Theriot httpcmgmstanfordedutheriot Karl Deisseroth ndash Stanford University ndash CLARITY optical tissue clearing Optogenetics httpclarityresourcecenterorg httpwebstanfordedugroupdlaboptogeneticsindexhtml Karsten Koumlnig (Koenig) - Saarland University and JenLab GmbH - biophotonics httpwwwbltuni-saarlanddeindex_ehtm httpwwwjenlabde httpwwwthelastescape-filmcom Karsten Rodenacker ndash image measurements httpkaro03bplacednetkaroMeMisc_WWWpdfMicrosoftWord-EQUAPATpdf Kevin Eliceiri ndash UW-Madison Open Source Photonics and Software Laboratory for Optical and Computational Instrumentation (LOCI) wwwlociwiscedu Klaus Kemp ndash Microlife Services ndash diatoms and other prepared microscope slides httpwwwdiatomscouk Kurt Thorn UCSF httpthornlabucsfedu httpsnicucsfedublog httpnicucsfeduFPvisualization httpgigapancomgigapans163370 Lihong Wang - WUSTL - Optical Imaging Laboratory photoacoustic tomography

httpoilabseaswustledu httpoilabseaswustleduresearch_0html Loren Looger - HHMI JFRC - iGluSnFr fluorescent protein biosensor httpswwwjaneliaorglablooger-lab Mary-Lou Pardue ndash MIT (first ever in situ hybridization with J Gall) httpsbiologymitedupeoplemary_lou_pardue httpsenwikipediaorgwikiMary-Lou_Pardue Nancy Allbritton - UNC - Chemical cytometry microraft arrays organ-on-a-chip httpswwwbmencsueduindexphpcomponentcomprofileruserprofilenlallbri httpwwwbmeuncedulabsallbritton Navin Varadarajan - UH - single-cell Lab httpwwwcheeuhedufacultyvaradarajan httpsinglecellcheeuheducontacthtml Nicholas Shaner - Scintillon Institute - mNeonGreen httpwwwscintillonorgshaner_lab Rebecca Richards-Kortum httpbioengineeringriceedufacultyrebecca_richards-kortumaspx Robert Campbell - Fluorescent proteins optogenetic proteins httpcampbellwebchemualbertaca httpcampbellwebchemualbertacaprojects-2 Robert Murphy ndash Cell measurements web services httpmurphylabwebcmueduservices Sabine Mai - University of Manitoba - Genomic Centre for Cancer Research and Diagnosis (GCCRD) - httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBPlatformsGCCRDhtml httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBScientistsMaiAwardshtml Sally Ward and Raimund Ober - Texas AampM University - httpwwwwardoberlabcom Simon Watkins - U Pittsburgh Center for Biologic Imaging httpwwwcbppittedufacultywatkinshtml httpwwwcbppittedufacultylabwatkinshtml httpwwwcbipittedu Stefan Hell ndash Deparment Hell NanoBiopohotonics httpwwwmpibpcmpgdehell httpsenwikipediaorgwikiStefan_Hell httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014hell-factshtml Sunney Xie Harvard httpsbernsteinharvardedu Susan Cox ndash 3B microscopy httpwwwcoxphysicscomindexhtml httpwwwcoxphysicscom3b Radim Chmeliacutek - Center for innovative microscopy Experimental biophotonics group httpswwwceiteceuceitec-butexperimental-biophotonicsrg3 httpwwwbiophotczhome Taekjip Ha ndash Johns Hopkins University ndash single molecules httphamedjhmiedu

Thomas Ried ndash NCI NIH SKYM-FISH and CGH Database httpsccrcancergovGenetics-Branchthomas-ried httpsccrcancergovGenetics-Branchthomas-riedqt-staff_profile_tabs=9qt-staff_profile_tabs ftpftpncbinlmnihgovsky-cghDATA httpswwwncbinlmnihgovdbvar Viviana Gradinaru ndash CalTech ndash CLARITYPACT Optogenetics httpwwwbbecaltecheducontentviviana-gradinaru httpglabcaltechedu Vladislav Verkhusha - near infrared fluorescent proteins httpwwweinsteinyuedulabsvlad-verkhushadefaultaspx httpwwweinsteinyueduresearchfacilitiesfluorescent WE Moerner ndash Stanford University httpwebstanfordedugroupmoerner Willard Wiggans ndash micro gallery httpwwwwillard-wigancomgallery Wolf Frommer ndash Molecular sensors httpbiosensordpbcarnegiescienceedu (fluorescent protein biosensors table) Xiaowei Zhuang = Harvard httpzhuangharvardedu Yuval Garini - Bar-Ilan University - Nano-Bio-Photonics laboratory httpgarinilabbiuacil Microscopy Magazines Imaging amp Microscopy httpwwwimaging-gitcommagazine Laser Focus World httpwwwlaserfocusworldcomindexhtml Microscopy amp Analysis httpwwwmicroscopy-analysiscom Microscopy Today httpwwwmicroscopy-todaycom Microscopy-UK httpwwwmicroscopy-ukorguk Photonics Spectra Biophotonics httpwwwphotonicscomPublicationsaspx The Microscope Journal httpmcriorgv72the-microscope-journal RMS Infocus Magazine httpwwwrmsorgukstudy-readinfocus-magazinehtml Nobel Prizes in Light Microscopy and Related Fields Chemistry 1925 colloids (light sheet) Zsigmondy (Siedentopf Zsigmondy 1902) httpswwwnobelprizeorgnobel_prizeschemistrylaureates1925

Chemistry 2000 conductive polymers Heeger MacDiarmid Shirakawa (Brilliant Violets Ultraviolets Blues) httpwwwnobelprizeorgnobel_prizeschemistrylaureates2000 Chemistry 2008 green fluorescent protein GFP Shimomura Chalfie Tsien httpwwwnobelprizeorgnobel_prizeschemistrylaureates2008 Chemistry 2014 super-resolved fluorescence microscopy Betzig Hell Moerner httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014 Physics 1953 Phase Contrast Zernike httpswwwnobelprizeorgnobel_prizesphysicslaureates1953 Physics 2009 invention of an imaging semiconductor circuit ndash the CCD sensor Kao Boyle Smith httpwwwnobelprizeorgnobel_prizesphysicslaureates2009 Physics 2014 efficient blue light emitting diodes Akasaki Amano Nakamura httpwwwnobelprizeorgnobel_prizesphysicslaureates2014 Physiology or Medicine 2006 Fire and Mello RNA interference ndash gene silencing by double stranded RNA httpwwwnobelprizeorgnobel_prizesmedicinelaureates2006 Physiology or Medicine 2006 Capecchi Evans Smithies specific gene modifications in mice by the use of embryonic stem cells httpwwwnobelprizeorgnobel_prizesmedicinelaureates2007 Physiology or Medicine 2009 Blackburn Greider Szostak how chromosomes are protected by telomeres and telomerase httpwwwnobelprizeorgnobel_prizesmedicinelaureates2009 Physiology or Medicine 2012 Gurdon Yamamanka matured cells can be reprogrammed to become pluripotent httpwwwnobelprizeorgnobel_prizesmedicinelaureates2012

Table 442 Fluorophores Photophysics Data

Fluorophore Abs or Ex max (nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Acridine orange 271 520 27000 020 5

Alexa Fluor 430 431 541 16000 055 9

Alexa Fluor 488 495 519 71000 094 67

Alexa Fluor 532 532 553 81000 080 65

Alexa Fluor 546 556 573 104000 096 100

Alexa Fluor 568 578 603 91300 075 69

Alexa Fluor 594 590 617 73000 064 47

Allophycocyanin (APC) 650 660 700000 068 476

Atto 390 390 479 24000 090 22

Atto 425 436 484 45000 065 29

Atto 430LS 433 547 32000 065 21

Atto 465 453 508 75000 075 56

Atto 490LS 496 661 40000 030 12

Atto 520 525 547 105000 095 100

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 14: McNamara 20161006 revised draft tables for CPHG Light ...

httpwwwjenlabdeMultiphoton-Tomography680html Jenoptik - microscope cameras httpswwwjenoptikcomproductscameras-and-imaging-modulesmicroscope-cameras JPK Instruments - integrated atomic force microscope (AFM) force sensing optical tweezers optical trapping single cell force spectroscopy (SCFS) httpwwwjpkcomindex2enhtml httpusajpkcomoptical-tweezers-optical-trapping29ushtml httpusajpkcomcellular-adhesion-cytomechanics30ushtml Keyence ndash VK-X confocal (upright) BZ-X700 widefield (inverted) httpwwwkeyencecomssproductsmicroscopevkx httpwwwkeyencecomssproductsmicroscopebz-x700indexjsp KK Technology - CapiScope HVCS Handheld Video Capillaroscopy System (CytoScan) httpwwwkktechnologycomhvcshtml LaVision BioTec ndash TriMscope Multiphoton TriM Scope II Adaptive Optics UltraMicroscope II light sheet httpwwwlavisionbiotecde httpwwwlavisionbiotecdetrim-scope-overviewhtml httpwwwlavisionbiotecdetrim-scope-ii-adaptive-opticshtml httpwwwlavisionbiotecdeultramicroscope-ii-introductionhtml Laxco ndash upright and inverted microscopes httpwwwlaxcoinccomMICROSCOPES Lego ndash Lego Idea Microscopes httpsideaslegocomprojects44370 httpwwwnico71frlego-working-microscope Li-Cor ndash near-infared fluorescent dyes and in vivo imaging agents in vivo and Western blot imaging systems httpswwwlicorcombioproductsreagents httpswwwlicorcombioproductsreagentsirdyebrightsite_imaging_agents httpswwwlicorcombioproductsimaging_systemsodyssey_familyhtml httpswwwlicorcombioproductsimaging_systemspearl httpswwwlicorcombioproductsimaging_systemscdigit Life Imaging Services - ldquothe Ludin chamberrsquo ldquothe cube amp the boxrdquo httpwwwlischthechamberhtml httpwwwlischtheboxhtml Lightform Inc ndash PARISS imaging spectrometer httplightforminccom LMU Bioimaging httpwwwbioimagingbmcmeduni-muenchendelinkswebsitesindexhtml httpwwwbioimagingbmcmeduni-muenchendelearneduwebsitesindexhtml Ludl Electronic Products Ltd ndash automated XY stages focus motors filter wheels httpwwwludlcom

LumaCyte ndash Laser force Cytology (laser trap meets microfluidics to suspend and manipulate single cells) httpwwwlumacytecomabouttechnology Lumencor ndash LEDs fluorescence light sources httplumencorcomproducts Luxcel ndash mitochondrial and cellular functions O2 sensor reagents httpluxcelcomproduct+list Luxendo GmbH ndash light sheet imager

wwwluxendoeu Lyncee tec - digital holography microscopy (DHM) high content screening by DHM httpwwwlynceeteccom httpwwwlynceeteccomhigh-content-screening Mad City Labs Inc - nanopositioning wwwmadcitylabscom Mauna Kea Technologies ndash CellVizio confocal laser endomicroscopy httpwwwmaunakeatechcomenhealthcare-professionalscellvizio-endomicroscopy-0 MBF Bioscience - stereology and neuron morphology quantitative imaging httpwwwmbfbiosciencecom McCrone Group wwwmccronecominstrument-sales Media Cybernetics Inc ndash Image Premier 3D AutoQuant X3 deconvolution httpwwwmediacycom Meiji Techno America wwwmeijitechnocom MesoLens Ltd httpwwwmesolenscomproducttechnical-specifications httpwwwmesolenscomimages httpswwwbiophotonicsstrathacukresearch_1htm Meyer Instruments ndash Pathscan Enabler GigaMacro digital pathology telepathology httpmeyerinstcom httpmeyerinstcompathscan-enabler-5 httpmeyerinstcomgigamacro-gigapixel-macro-imaging httpmeyerinstcomhomescanners httprealtimetelepathologycom Microarrays - Large-Scale Gene Expression and Microarray Links and Resources httpswwwebiacukarrayexpress Micro-Manager ndash Device Support ndash tabulates many microscope cameras and motorized accessories every new camera and accessory should have a uManager driver to enable simple use with Fiji ImageJ httpsmicro-managerorg httpsmicro-managerorgwikiDevice_Support httpsopen-imagingcom Microvolution ndash (near) instant gratification spatial deconvolution using NVidia GPU card(s) httpmicrovolutioncom Mightex Systems ndash optogenetics DMDDLP illuminator (digital micro-mirror device digital light processing) httpwwwmightexsystemscomindexphpcPath=245 Millipore-Sigma Merck KGaA (Amnis Corp CellASIC EMD Millipore) ndash ImageStreamX and FlowSight imaging flow cytometers ONIX2 Microperfusion System for microscopes httpswwwemdmilliporecom httpswwwemdmilliporecomUSenlife-science-researchcell-analysisamnis-imaging-flow-cytometersQ6ubqBm3UAAAFLCKIpygJnav httpwwwemdmilliporecomUSenlife-science-researchcell-culture-systemscellASIC-live-cell-analysisd1CbqBw58AAAE_0j13MnAnav Mitutoyo America Corp wwwmitutoyocom httpecatalogmitutoyocomMF-U-Series-176-High-power-Multi-function-Measuring-Microscopes-C1413aspx

Molecular Devices Corporation Universal Imaging Corporation (Danaher) ndash MetaMorph MetaFluor high content systems (HCS) httpswwwmoleculardevicescomsystemsmetamorph-research-imaging httpmdccusthelpcomappanswersdetaila_id19319 httpswwwmoleculardevicescomsystemshigh-content-imaging Molecular Machines amp Industries - laser microdissection and tweezer systems httpwwwmolecular-machinescomhome MUSE Microscopy Inc ndash Deep UV illumination for shallow depth of field imaging httpwwwmusemicrocom Micro Video Instruments Inc - DarkLite illuminator httpwwwmvi-inccom NanoEnTek ndash JuLI Stage (imager inside incubator or on lab bench) httpwwwjulistagecom National Instruments ndash LabView software httpwwwnicomen-ushtml Navitar - Hoffman Modulation Contrast (HMC alternative to differential interference contrast phase contrast) custom lens design UVDUVNUV imaging lenses httpsnavitarcommarketsmicroscopy httpsnavitarcomproductsimaging-opticscustom-microscope-objectivescustom-microscope-objectives httpsnavitarcomproductsimaging-opticsuv-imaging National Center for X-ray Tomography (NCXT) ndash soft X-ray tomography (CT of hydrated cells) XM-2 dedicated biological SXT microscope Prof Carolyn Larabell Director (see also SiriusXT) httpncxtlblgov httpncxtlblgovsxt httpncxtlblgovmanual httpncxtlblgovq=carolyn Neogenomics (Clarient) ndash MultiOmyx immunofluorescence or DNA FISH (ldquo60plexrdquo) httpneogenomicscomPharma-ServicesLab-ServicesMultiOmyxTechnologyMultiOmyx-IF-Assay-DNA-FISH-assay-NGS-from-ROI Nexcelom ndash Celigo imaging cytometer Cellometer cell counters httpwwwnexcelomcomCeligoindexphp httpwwwnexcelomcomProducts Nikon ndash Ti-LAPP modular illumination system (for Nikon Ti series microscopes) TIRF Optogenetics httpswwwnikoninstrumentscomProductsPhotostimulation-and-TIRFTi-LAPP Nirmidas Biotech httpwwwnirmidascomtechnologynir httpwwwnirmidascomproductsniriidye NVidia ndash Pascal 10+ Gbps GPU cards for instant gratification deconvolution (software from Microvolutioncom SVInl) httpwwwgeforcecomhardware10seriesgeforce-gtx-1080 httpwwwgeforcecomhardware10seriestitan-x-pascal httpwwwnvidiacomobjectquadro-graphics-with-pascalhtml Ocean Optics ndash spectrometers httpoceanopticscomproduct-categorymodular-spectrometers Oko-Lab stage top incubator httpwwwoko-labcomstage-top Open Microscopy Environment (OME) ndash OMERO (see also Glencoe Software) Bio-Formats LOCI

httpswwwopenmicroscopyorgsite httpswwwopenmicroscopyorgsiteproductsomero httpswwwopenmicroscopyorgsiteproductsbio-formats httpswwwopenmicroscopyorgsitesupportbio-formats52supported-formatshtml httpswwwopenmicroscopyorgsiteaboutdevelopment-teamskevin OpenSPIM ndash do-it-yourself selective plane illumination microscopy (light sheet imaging) httpopenspimorgWelcome_to_the_OpenSPIM_Wiki OpenSpinMicroscopy ndash do-it-yourself SPIMDSLMOPT microscopes httpssitesgooglecomsiteopenspinmicroscopy Ovizio ndash differential digital holography (similar to quantitative phase imaging) httpwwwoviziocomenHome httpwwwoviziocomenMicroscopesQMod Oxford Gene Technologies ndash microarrays ndash cytogenetics molecule genetics cancer research pre-implantation genetic diagnosis httpwwwogtcomclinical_genetics Oxford Nanoimaging ndash single molecule(s) localization fluorescence resonance energy transfer (FRET) (Kapanidis) wwwoxfordnicom Pathology Devices ndash LiveCell stage top incubator amp controller tissue microarrayers (TMA makers) httpwwwpathologydevicescomLiveCellhtm httpwwwpathologydevicescomTMArrayerhtm PeCon GmbH ndash microscope incubators httpwwwpeconbiz Pembroke Instruments ndash spectrometers mini-lasers httppembrokeinstrumentscomqmini-spectrometer httppembrokeinstrumentscommini-lasers PerkinElmer ndash in vivo imaging systems (bioluminescence NIR fluorescence) Vectra digital slide scanner httpwwwperkinelmercomcategoryin-vivo-imaging-instruments httpwwwperkinelmercomcategoryquantitative-pathology-imaging-instruments Phi Optics ndash CellVista SLIM Pro (quantitative phase microscopy) httpphiopticscom Photometrics (Roper Scientific) ndash DualView QuadView httpwwwphotometricscom httpwwwphotometricscomproductsmultichannel Photon Technology International httpwwwpti-njcomindexhtml

PicoQuant GmbH ndash fluorescence lifetime imaging microscopes (FLIM) STED 3D-EasySTED httpswwwpicoquantcomproductscategoryfluorescence-microscopes httpswwwpicoquantcomapplicationscategorylife-sciencested httpwwweasystedorg Physik Instrumente GmbH amp Co KG (PI) - Nanopositioning Applications for Microscopy Neuroscience and Metrology httpswwwphysikinstrumentecomen httpwwwpi-usausindexphp PreSens Prescision Sensing GmbH - VisiSens measure and visualize Oxygen pH or carbon dioxide distributions httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-biological-researchhtml httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-life-science-researchhtml Prior Scientific

httpwwwprior-uscom Profusa Inc - Lumee tissue-integrated biosensors scaffolds httpprofusacomtechnology Reindeer Graphics Inc ndash OptiPix Fovea Pro 9plugins for Adobe Photoshop 6 and CS series) httpwwwreindeergraphicscom Renishaw - StreamLine fast chemical imaging Raman spectroscopy httpwwwrenishawcomenstreamline-generate-chemical-images-rapidly--9449 httpwwwrenishawcomenraman-spectroscopy--6150 Sanford Burnham Prebys ndash High Content Screening httpwwwsbpdiscoveryorgtechnologysrPagesLaJolla_HighContentScreeningaspx ScopeM - Scientific Center for Optical and Electron Microscopy - ETH Zurich httpwwwscopemethzch SiriusXT - soft X-ray tomography (SXT) microscope (CT scan hydrated cell) httpsiriusxtcom SpectraGenetics - Fluorogen Activating Peptides (FAPs) new genetically encoded ldquobinaryrdquo reporters httpspectrageneticscomproductsvectors-for-expressing-fluorogen-activating-proteinsfap-technology-overview Spirochrome - Silicon Rhodamine (SiR) and other fluorescent reagents probes for bioimaging httpspirochromecom Stanford Photonics Inc httpwwwstanfordphotonicscom httpwwwstanfordphotonicscomLife20SciencesLifeScihtm

Stream Technologies Inc ndash ColorFlow lens (multi-wavelength emission onto a camera) httpwwwstreamtechinccomproducts Sutter Instrument Company httpwwwsuttercom httpwwwsuttercomMICROSCOPESindexhtml httpwwwsuttercomIMAGINGindexhtml SVI Huygens ndash Professional (general image analysis) deconvolution NVidia GPU deconvolution httpssvinlHuygensProfessional httpssvinlHuygensDeconvolution httpssvinlHuygensGPU Sysmex Partex ndash CyScope httpwwwsysmex-parteccomproductsmicroscopyhtml httpwwwsysmex-parteccomproductsprdouct-detailviewcyscopeR-malaria-3238html Technical Instruments httpwwwtechinstcomproductsphp TESCAN Brno sro - Tescan Q-PHASE multimodal holographic quantitative phase imaging system (QPi) optional fluorescence httpwwwtescancomenproductsq-phaseq-phase httpq-phasetescancom httpq-phasetescancomindexphptechnologyspecifications Ted Pella Inc ndash specialty light microscopy and electron microscopy supplies httpswwwtedpellacom Texas Instruments ndash DLP 4100 development kit (digital light processingrsquo DMD digital micromirror device) httpwwwticomtooldlpd4x00kit

ThorLabs ndash iCyte imaging cytometer multiphoton confocal EnVista digital slide scanning microscopes httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7473 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7494 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=5696 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=6570 TIRF Labs lightguide TIRF prism TIRF TIRF-Electrochemistry httpwwwtirf-labscom httpwwwtirf-labscomtechnologieshtml TissueVision - Serial Two Photon Tomography (image volume ablate imaged volume with multiphoton laser repeat) httpwwwtissuevisioncomtechnology Tokai Hit - stage top incubator httpwwwtokaihitcomenglishproduct_guidanceoptionhtml TopoNomos Ltd ndash Toponome Imaging Cycler ndash immunofluorescence (100plex) httpwwwtoposnomoscomtechnologyhtml Ultivue Inc ndash DNA-PAINT ndash reagents data processing service httpwwwultivuecom httpwwwultivuecomproducts UMech Technologies ndash Cytovar HCS up to 16 excitation wavelengths httpcloudumechcomproducts httpcloudumechcomproductsmodelC16 Visitech ndash vt-iSIM instant super-resolution microscopy up to 1000 frames per second confocal scanners and light engines httpwwwvisitechcoukvt-isimhtml httpwwwvisitechcoukproductshtml Visitron Systems GmbH - high speed imaging systems httpwwwvisitronde Visualsonics (Fujifilm) - photoacoustic imaging httpwwwvisualsonicscomproductstechnology-overview Wicked Lasers httpwwwwickedlaserscom httpwwwwickedlaserscomarctic WITec Wissenschaftliche Instrumente und Technologie GmbH - imaging systems for FLIM Raman AFM and SNOM analysis httpwitecdeproducts httpwwwwitec-instrumentscom WM Keck Center for Adaptive Optical Microscopy (CfAOM) at UC Santa Cruz httpscfaomsoeucscedu httpcfaoucolickorgpgallery Yokogawa Corp ndash spinning disk confocal scanner live cell imager high content screener confocal quantitative cytometer httpwwwyokogawacomsolutionsproducts-platformslife-science httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-scanner-unit-csu httpwwwyokogawacomsolutionsproducts-platformslife-scienceall-in-one-live-cell-imaging-solution httpwwwyokogawacomsolutionsproducts-platformslife-sciencehigh-throughput-cytological-discovery-system httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-quantitative-image-cytometer Zellkraftwerk (ChipCytometry) ndash immunofluorescence (80plex) httpwwwzellkraftwerkcomProducts2phtml httpwwwzellkraftwerkcomZKWOnephtmlSoftware

httpwwwchipcytometrycomtechnologyphtml Fluorescence Spectra Data and Graphing Sites PubSpectra ndash Excel file data download httpsworksbepresscomgmcnamara9 BD Biosciences ndash spectrum viewer Brilliant fluorophores httpwwwbdbiosciencescomussspectrumviewer httpwwwbdbiosciencescomusapplicationssspectrumguidepage BioLegend ndash spectra analyzer Brilliant Violet fluorophores httpwwwbiolegendcomspectraanalyzer httpwwwbiolegendcombrilliantviolet Chroma Technology httpswwwchromacomspectra-viewer eBioscience (Affymetrix ThermoFisher) ndash fluorPlan ndash a multi-laser spectra viewer httpwwwebiosciencecomresourcesfluorplan-spectra-viewerhtm Spectra Viewer (requires Java) Evrogen ndash Spectrum Viewer httpevrogencomspectra-viewerflashviewerhtml Fluorophoresorg ndash Fluorescent Substances httpwwwfluorophorestugrazatsubstance I Love GFP httpssitesgooglecomsiteilovegfpHomefps Lambert and Thorn UCSF Fluorescent protein properties httpnicucsfeduFPvisualization Leica Microsystem - ldquoFluoScoutrdquo httpwwwleica-microsystemscomfluoscout

Molecular Probes Invitrogen Thermo Fisher ndash Fluorescence SpectraViewer httpwwwthermofishercomusenhomelife-sciencecell-analysislabeling-chemistryfluorescence-spectraviewerhtml httpsitunesapplecomusappfluorescence-spectraviewerid421031826 (iTunes App) Nightsea - Compendium of spectra web sites httpwwwnightseacomsfa-sharingfluorescence-spectra-viewers Omega Optical ldquoCurvomatricrdquo httpswwwomegafilterscomcurvomatic

PhotoChemCAD 20 (Jonathan S Lindsey) dye spectra database and chemistry calculator NIRvana Sciences httpwwwphotochemcadcom httpnirvanasciencescompage_id=3088 UCSF (Lambert Thorn 2016) - Fluorescent protein properties httpnicucsfeduFPvisualization University of Arizona - Fluorescent Spectra Database httpwwwspectraarizonaedu Semrock - Searchlight httpssearchlightsemrockcom Spectroscopy Ninja ndash links to spectral and fluorescence data Spekwin32 spectroscopy software httpwwweffemm2deinfoinfo_specdatahtml

httpwwweffemm2deindexhtml Zeiss ndash interactive fluorescence dye and filter database overview dyes overview filter sets httpswwwmicro-shopzeisscoms=50479761ad21e5ampl=enampp=usampf=fampa=i httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=d httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=f Researcher Labs Alby Diaspro ndash IIT httpwwwlambsitindexphppage=People Alice Ting ndash MIT httpwwwtinglaborgresearch Allen Institute for Brain Science httpwwwalleninstituteorgwhat-we-dobrain-science Allen Institute for Cell Science httpwwwalleninstituteorgwhat-we-docell-science Amina Qutub - Rice University - How are human cells designed lab httpsqutublaborgqutub-lab Amy Herr UC Berkeley ndash Single cell Westerns httpherrlabberkeleyedu Amy Palmer ndash UC Boulder httpspalmerlabcoloradoedu Andrew York ndash Calico Life Sciences httpswwwcalicolabscomteam-memberandrew-york Anne Carpenter ndash Broad Institute CellProfiler httpspersonalbroadinstituteorganne Arjun Raj UPenn single molecule RNA FISH quantitative understanding cellular functions httprajlabseasupenneduindexhtml httpwwwpopscicomsciencearticle2013-09arjun-raj Atsuko Miyawaki - Laboratory for Cell Function Dynamics (CFDS) Fucci2 fluorescent proteins cell cycle indicator httpwwwbrainrikenjpenfacultydetails30 httpcfdsbrainrikenjp httpcfdsbrainrikenjpFuccihtml Aydogan Ozcan - UCLA - new imaging and sensing architectures httpinnovateeeuclaeduwelcomehtml httpwwwhhmiorgscientistsaydogan-ozcan Badri Roysam - UH - FARSIGHT Toolkit httpwwweeuhedufacultyroysam httpwwwfarsight-toolkitorgwikiMain_Page Brian J Ford ndash microscopist and popularizer httpsuklinkedincominprofbrianjford Carolyn Larabell ndashNational Center for X-ray Tomography (LBNL) UCSF httpncxtlblgovq=carolyn httpprofilesucsfeducarolynlarabell Clare Waterman ndash NHLBI NIH

httpswwwnhlbinihgovresearchintramuralresearcherspiwaterman-clare Dana Peer - Columbia University - Computational Systems Biology viSNE and more software httpwwwc2b2columbiaedudanapeerlabhtml httpwwwc2b2columbiaedudanapeerlabhtmlcythtml David Mayerich - UH - STIM Laboratory Scalable Tissue Imaging and Modeling httpwwweeuhedufacultymayerich httpstimeeuhedu David Piston WUSTL httpwwwcellbiologywustledufacultytenureddavid-w-piston-phd Diane Lidke and Keith Lidke - University of New Mexico httppathologyunmeduresearchfaculty-laboratoriesthe-lidke-laboratoryindexhtml httppanda3physunmedu~klidke Donna Arndt-Jovin and Thomas Jovin - Max Planck Institute for Biophysical Chemistry Laboratory of Cellular Dynamics httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsDonnaArdndt-JovinResearchAreasAndProjects httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsChairmanThomasJovinResearchAreasAndProjects Ed Boyden ndash MIT Media Lab ndash expansion microscopy (ExM) optogenetics httpsyntheticneurobiologyorg httpsyntheticneurobiologyorgprotocols httpsyntheticneurobiologyorgpublications httpwwwtedcomtalksed_boyden_baby_diapers_inspired_this_new_way_to_study_the_brain httpwwwextbiocombuycell Elizabeth Blackburn ndash Salk Institute - Telomeres httpswwwsalkeduscientistelizabeth-blackburn httpsenwikipediaorgwikiElizabeth_Blackburn httpswwwnobelprizeorgnobel_prizesmedicinelaureates2009blackburn-factshtml Elizabeth Hillman - Columbia university - SCAPE (Swept Confocally-Aligned Planar Excitation) high speed 3D microscopy DyCE (dynamic contrast enhancement to image and segment small animal organs live) Neuroimaging amp Neurovascular Coupling httporionbmecolumbiaedu~hillmanInstrumentationhtml httporionbmecolumbiaedu~hillmanSCAPEhtml httporionbmecolumbiaedu~hillmanMolecularhtml httporionbmecolumbiaedu~hillmanBrain_Imaginghtml Eric Betzig ndash UCSF (moving from HHMI Janelia Farm in 2016) httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014betzig-factshtml Eva Sevick-Muraca ndash UT Health Science Center at Houston molecular imaging clinical NIR fluoresceince imaging httpswwwutheduimmprofilehtmid=1005459 httpswwwutheduimmcentersmolecular-imaginghtm Evelin Schrock - Technische Universitaumlt Dresden spectral karyotyping cytogenetics httpswwwresearchgatenetprofileEvelin_Schrock Garry Nolan Stanford University ndash Mass cytometry MIBI-ToF high throughput imaging mass cytometry (42plex) httpwebstanfordedugroupnolanresourceshtml httpwebstanfordedugroupnolantechnologieshtml George McNamara ndash Cell Morphometry (41) Figure 1 right top two panels (55) The Chase (2016 temporal area maps lsquodynamic morphologyrsquo) (76) newsletter series on ldquoThe Chaserdquo (73) direct Vimeo movie of ldquoThe Chaserdquo Tiki_Goddess linkedin 10+plex blog httpsworksbepresscomgmcnamara41 httpsworksbepresscomgmcnamara55 httpsworksbepresscomgmcnamara76

httpsworksbepresscomgmcnamara73 httpsvimeocom175151196 httphomeearthlinknet~tiki_goddess httpswwwlinkedincomingeorgemcnamara httpswwwlinkedincompulsebd-biosciences-listed-tandems-horizon-brilliant-violets-mcnamara Gillian Griffiths - University of Cambridge - T-cell immunological synapse httpwwwcimrcamacukresearchprincipal-investigatorsprincipal-investigators-a-hgriffiths Hari Shroff NIBIB NIH httpswwwnibibnihgovlabs-at-nibibsection-high-resolution-optical-imaging-hroi HHMI Janelia Farm Research Campus (JFRC) - Advanced Imaging Center Open Science httpswwwjaneliaorgopen-scienceadvanced-imaging-center-aic httpswwwjaneliaorgopen-science Jeanne Lawrence University of Massachussetts Medical School httpwwwumassmededucellbiolabslawrencepersonnelprincipal-investigator Jennifer Lippincott-Schwartz ndash HHMI Janelia Farm httpswwwjaneliaorgpeoplejennifer-lippincott-schwartz Jin Zhang ndash UCSD httpprofilesucsdedujinzhang Joe DeRisi - UCSF - 3D printable lab stuff httpderisilabucsfeduindexphppage=3D John Russ Chris Russ Fovea Pro plugins for Adobe Photoshop httpwwwdrjohnrusscomindexhtml httpwwwdrjohnrusscombookshtml httpwwwreindeergraphicscomfoveaprotutorialhtml Julie Theriot httpcmgmstanfordedutheriot Karl Deisseroth ndash Stanford University ndash CLARITY optical tissue clearing Optogenetics httpclarityresourcecenterorg httpwebstanfordedugroupdlaboptogeneticsindexhtml Karsten Koumlnig (Koenig) - Saarland University and JenLab GmbH - biophotonics httpwwwbltuni-saarlanddeindex_ehtm httpwwwjenlabde httpwwwthelastescape-filmcom Karsten Rodenacker ndash image measurements httpkaro03bplacednetkaroMeMisc_WWWpdfMicrosoftWord-EQUAPATpdf Kevin Eliceiri ndash UW-Madison Open Source Photonics and Software Laboratory for Optical and Computational Instrumentation (LOCI) wwwlociwiscedu Klaus Kemp ndash Microlife Services ndash diatoms and other prepared microscope slides httpwwwdiatomscouk Kurt Thorn UCSF httpthornlabucsfedu httpsnicucsfedublog httpnicucsfeduFPvisualization httpgigapancomgigapans163370 Lihong Wang - WUSTL - Optical Imaging Laboratory photoacoustic tomography

httpoilabseaswustledu httpoilabseaswustleduresearch_0html Loren Looger - HHMI JFRC - iGluSnFr fluorescent protein biosensor httpswwwjaneliaorglablooger-lab Mary-Lou Pardue ndash MIT (first ever in situ hybridization with J Gall) httpsbiologymitedupeoplemary_lou_pardue httpsenwikipediaorgwikiMary-Lou_Pardue Nancy Allbritton - UNC - Chemical cytometry microraft arrays organ-on-a-chip httpswwwbmencsueduindexphpcomponentcomprofileruserprofilenlallbri httpwwwbmeuncedulabsallbritton Navin Varadarajan - UH - single-cell Lab httpwwwcheeuhedufacultyvaradarajan httpsinglecellcheeuheducontacthtml Nicholas Shaner - Scintillon Institute - mNeonGreen httpwwwscintillonorgshaner_lab Rebecca Richards-Kortum httpbioengineeringriceedufacultyrebecca_richards-kortumaspx Robert Campbell - Fluorescent proteins optogenetic proteins httpcampbellwebchemualbertaca httpcampbellwebchemualbertacaprojects-2 Robert Murphy ndash Cell measurements web services httpmurphylabwebcmueduservices Sabine Mai - University of Manitoba - Genomic Centre for Cancer Research and Diagnosis (GCCRD) - httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBPlatformsGCCRDhtml httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBScientistsMaiAwardshtml Sally Ward and Raimund Ober - Texas AampM University - httpwwwwardoberlabcom Simon Watkins - U Pittsburgh Center for Biologic Imaging httpwwwcbppittedufacultywatkinshtml httpwwwcbppittedufacultylabwatkinshtml httpwwwcbipittedu Stefan Hell ndash Deparment Hell NanoBiopohotonics httpwwwmpibpcmpgdehell httpsenwikipediaorgwikiStefan_Hell httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014hell-factshtml Sunney Xie Harvard httpsbernsteinharvardedu Susan Cox ndash 3B microscopy httpwwwcoxphysicscomindexhtml httpwwwcoxphysicscom3b Radim Chmeliacutek - Center for innovative microscopy Experimental biophotonics group httpswwwceiteceuceitec-butexperimental-biophotonicsrg3 httpwwwbiophotczhome Taekjip Ha ndash Johns Hopkins University ndash single molecules httphamedjhmiedu

Thomas Ried ndash NCI NIH SKYM-FISH and CGH Database httpsccrcancergovGenetics-Branchthomas-ried httpsccrcancergovGenetics-Branchthomas-riedqt-staff_profile_tabs=9qt-staff_profile_tabs ftpftpncbinlmnihgovsky-cghDATA httpswwwncbinlmnihgovdbvar Viviana Gradinaru ndash CalTech ndash CLARITYPACT Optogenetics httpwwwbbecaltecheducontentviviana-gradinaru httpglabcaltechedu Vladislav Verkhusha - near infrared fluorescent proteins httpwwweinsteinyuedulabsvlad-verkhushadefaultaspx httpwwweinsteinyueduresearchfacilitiesfluorescent WE Moerner ndash Stanford University httpwebstanfordedugroupmoerner Willard Wiggans ndash micro gallery httpwwwwillard-wigancomgallery Wolf Frommer ndash Molecular sensors httpbiosensordpbcarnegiescienceedu (fluorescent protein biosensors table) Xiaowei Zhuang = Harvard httpzhuangharvardedu Yuval Garini - Bar-Ilan University - Nano-Bio-Photonics laboratory httpgarinilabbiuacil Microscopy Magazines Imaging amp Microscopy httpwwwimaging-gitcommagazine Laser Focus World httpwwwlaserfocusworldcomindexhtml Microscopy amp Analysis httpwwwmicroscopy-analysiscom Microscopy Today httpwwwmicroscopy-todaycom Microscopy-UK httpwwwmicroscopy-ukorguk Photonics Spectra Biophotonics httpwwwphotonicscomPublicationsaspx The Microscope Journal httpmcriorgv72the-microscope-journal RMS Infocus Magazine httpwwwrmsorgukstudy-readinfocus-magazinehtml Nobel Prizes in Light Microscopy and Related Fields Chemistry 1925 colloids (light sheet) Zsigmondy (Siedentopf Zsigmondy 1902) httpswwwnobelprizeorgnobel_prizeschemistrylaureates1925

Chemistry 2000 conductive polymers Heeger MacDiarmid Shirakawa (Brilliant Violets Ultraviolets Blues) httpwwwnobelprizeorgnobel_prizeschemistrylaureates2000 Chemistry 2008 green fluorescent protein GFP Shimomura Chalfie Tsien httpwwwnobelprizeorgnobel_prizeschemistrylaureates2008 Chemistry 2014 super-resolved fluorescence microscopy Betzig Hell Moerner httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014 Physics 1953 Phase Contrast Zernike httpswwwnobelprizeorgnobel_prizesphysicslaureates1953 Physics 2009 invention of an imaging semiconductor circuit ndash the CCD sensor Kao Boyle Smith httpwwwnobelprizeorgnobel_prizesphysicslaureates2009 Physics 2014 efficient blue light emitting diodes Akasaki Amano Nakamura httpwwwnobelprizeorgnobel_prizesphysicslaureates2014 Physiology or Medicine 2006 Fire and Mello RNA interference ndash gene silencing by double stranded RNA httpwwwnobelprizeorgnobel_prizesmedicinelaureates2006 Physiology or Medicine 2006 Capecchi Evans Smithies specific gene modifications in mice by the use of embryonic stem cells httpwwwnobelprizeorgnobel_prizesmedicinelaureates2007 Physiology or Medicine 2009 Blackburn Greider Szostak how chromosomes are protected by telomeres and telomerase httpwwwnobelprizeorgnobel_prizesmedicinelaureates2009 Physiology or Medicine 2012 Gurdon Yamamanka matured cells can be reprogrammed to become pluripotent httpwwwnobelprizeorgnobel_prizesmedicinelaureates2012

Table 442 Fluorophores Photophysics Data

Fluorophore Abs or Ex max (nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Acridine orange 271 520 27000 020 5

Alexa Fluor 430 431 541 16000 055 9

Alexa Fluor 488 495 519 71000 094 67

Alexa Fluor 532 532 553 81000 080 65

Alexa Fluor 546 556 573 104000 096 100

Alexa Fluor 568 578 603 91300 075 69

Alexa Fluor 594 590 617 73000 064 47

Allophycocyanin (APC) 650 660 700000 068 476

Atto 390 390 479 24000 090 22

Atto 425 436 484 45000 065 29

Atto 430LS 433 547 32000 065 21

Atto 465 453 508 75000 075 56

Atto 490LS 496 661 40000 030 12

Atto 520 525 547 105000 095 100

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 15: McNamara 20161006 revised draft tables for CPHG Light ...

wwwluxendoeu Lyncee tec - digital holography microscopy (DHM) high content screening by DHM httpwwwlynceeteccom httpwwwlynceeteccomhigh-content-screening Mad City Labs Inc - nanopositioning wwwmadcitylabscom Mauna Kea Technologies ndash CellVizio confocal laser endomicroscopy httpwwwmaunakeatechcomenhealthcare-professionalscellvizio-endomicroscopy-0 MBF Bioscience - stereology and neuron morphology quantitative imaging httpwwwmbfbiosciencecom McCrone Group wwwmccronecominstrument-sales Media Cybernetics Inc ndash Image Premier 3D AutoQuant X3 deconvolution httpwwwmediacycom Meiji Techno America wwwmeijitechnocom MesoLens Ltd httpwwwmesolenscomproducttechnical-specifications httpwwwmesolenscomimages httpswwwbiophotonicsstrathacukresearch_1htm Meyer Instruments ndash Pathscan Enabler GigaMacro digital pathology telepathology httpmeyerinstcom httpmeyerinstcompathscan-enabler-5 httpmeyerinstcomgigamacro-gigapixel-macro-imaging httpmeyerinstcomhomescanners httprealtimetelepathologycom Microarrays - Large-Scale Gene Expression and Microarray Links and Resources httpswwwebiacukarrayexpress Micro-Manager ndash Device Support ndash tabulates many microscope cameras and motorized accessories every new camera and accessory should have a uManager driver to enable simple use with Fiji ImageJ httpsmicro-managerorg httpsmicro-managerorgwikiDevice_Support httpsopen-imagingcom Microvolution ndash (near) instant gratification spatial deconvolution using NVidia GPU card(s) httpmicrovolutioncom Mightex Systems ndash optogenetics DMDDLP illuminator (digital micro-mirror device digital light processing) httpwwwmightexsystemscomindexphpcPath=245 Millipore-Sigma Merck KGaA (Amnis Corp CellASIC EMD Millipore) ndash ImageStreamX and FlowSight imaging flow cytometers ONIX2 Microperfusion System for microscopes httpswwwemdmilliporecom httpswwwemdmilliporecomUSenlife-science-researchcell-analysisamnis-imaging-flow-cytometersQ6ubqBm3UAAAFLCKIpygJnav httpwwwemdmilliporecomUSenlife-science-researchcell-culture-systemscellASIC-live-cell-analysisd1CbqBw58AAAE_0j13MnAnav Mitutoyo America Corp wwwmitutoyocom httpecatalogmitutoyocomMF-U-Series-176-High-power-Multi-function-Measuring-Microscopes-C1413aspx

Molecular Devices Corporation Universal Imaging Corporation (Danaher) ndash MetaMorph MetaFluor high content systems (HCS) httpswwwmoleculardevicescomsystemsmetamorph-research-imaging httpmdccusthelpcomappanswersdetaila_id19319 httpswwwmoleculardevicescomsystemshigh-content-imaging Molecular Machines amp Industries - laser microdissection and tweezer systems httpwwwmolecular-machinescomhome MUSE Microscopy Inc ndash Deep UV illumination for shallow depth of field imaging httpwwwmusemicrocom Micro Video Instruments Inc - DarkLite illuminator httpwwwmvi-inccom NanoEnTek ndash JuLI Stage (imager inside incubator or on lab bench) httpwwwjulistagecom National Instruments ndash LabView software httpwwwnicomen-ushtml Navitar - Hoffman Modulation Contrast (HMC alternative to differential interference contrast phase contrast) custom lens design UVDUVNUV imaging lenses httpsnavitarcommarketsmicroscopy httpsnavitarcomproductsimaging-opticscustom-microscope-objectivescustom-microscope-objectives httpsnavitarcomproductsimaging-opticsuv-imaging National Center for X-ray Tomography (NCXT) ndash soft X-ray tomography (CT of hydrated cells) XM-2 dedicated biological SXT microscope Prof Carolyn Larabell Director (see also SiriusXT) httpncxtlblgov httpncxtlblgovsxt httpncxtlblgovmanual httpncxtlblgovq=carolyn Neogenomics (Clarient) ndash MultiOmyx immunofluorescence or DNA FISH (ldquo60plexrdquo) httpneogenomicscomPharma-ServicesLab-ServicesMultiOmyxTechnologyMultiOmyx-IF-Assay-DNA-FISH-assay-NGS-from-ROI Nexcelom ndash Celigo imaging cytometer Cellometer cell counters httpwwwnexcelomcomCeligoindexphp httpwwwnexcelomcomProducts Nikon ndash Ti-LAPP modular illumination system (for Nikon Ti series microscopes) TIRF Optogenetics httpswwwnikoninstrumentscomProductsPhotostimulation-and-TIRFTi-LAPP Nirmidas Biotech httpwwwnirmidascomtechnologynir httpwwwnirmidascomproductsniriidye NVidia ndash Pascal 10+ Gbps GPU cards for instant gratification deconvolution (software from Microvolutioncom SVInl) httpwwwgeforcecomhardware10seriesgeforce-gtx-1080 httpwwwgeforcecomhardware10seriestitan-x-pascal httpwwwnvidiacomobjectquadro-graphics-with-pascalhtml Ocean Optics ndash spectrometers httpoceanopticscomproduct-categorymodular-spectrometers Oko-Lab stage top incubator httpwwwoko-labcomstage-top Open Microscopy Environment (OME) ndash OMERO (see also Glencoe Software) Bio-Formats LOCI

httpswwwopenmicroscopyorgsite httpswwwopenmicroscopyorgsiteproductsomero httpswwwopenmicroscopyorgsiteproductsbio-formats httpswwwopenmicroscopyorgsitesupportbio-formats52supported-formatshtml httpswwwopenmicroscopyorgsiteaboutdevelopment-teamskevin OpenSPIM ndash do-it-yourself selective plane illumination microscopy (light sheet imaging) httpopenspimorgWelcome_to_the_OpenSPIM_Wiki OpenSpinMicroscopy ndash do-it-yourself SPIMDSLMOPT microscopes httpssitesgooglecomsiteopenspinmicroscopy Ovizio ndash differential digital holography (similar to quantitative phase imaging) httpwwwoviziocomenHome httpwwwoviziocomenMicroscopesQMod Oxford Gene Technologies ndash microarrays ndash cytogenetics molecule genetics cancer research pre-implantation genetic diagnosis httpwwwogtcomclinical_genetics Oxford Nanoimaging ndash single molecule(s) localization fluorescence resonance energy transfer (FRET) (Kapanidis) wwwoxfordnicom Pathology Devices ndash LiveCell stage top incubator amp controller tissue microarrayers (TMA makers) httpwwwpathologydevicescomLiveCellhtm httpwwwpathologydevicescomTMArrayerhtm PeCon GmbH ndash microscope incubators httpwwwpeconbiz Pembroke Instruments ndash spectrometers mini-lasers httppembrokeinstrumentscomqmini-spectrometer httppembrokeinstrumentscommini-lasers PerkinElmer ndash in vivo imaging systems (bioluminescence NIR fluorescence) Vectra digital slide scanner httpwwwperkinelmercomcategoryin-vivo-imaging-instruments httpwwwperkinelmercomcategoryquantitative-pathology-imaging-instruments Phi Optics ndash CellVista SLIM Pro (quantitative phase microscopy) httpphiopticscom Photometrics (Roper Scientific) ndash DualView QuadView httpwwwphotometricscom httpwwwphotometricscomproductsmultichannel Photon Technology International httpwwwpti-njcomindexhtml

PicoQuant GmbH ndash fluorescence lifetime imaging microscopes (FLIM) STED 3D-EasySTED httpswwwpicoquantcomproductscategoryfluorescence-microscopes httpswwwpicoquantcomapplicationscategorylife-sciencested httpwwweasystedorg Physik Instrumente GmbH amp Co KG (PI) - Nanopositioning Applications for Microscopy Neuroscience and Metrology httpswwwphysikinstrumentecomen httpwwwpi-usausindexphp PreSens Prescision Sensing GmbH - VisiSens measure and visualize Oxygen pH or carbon dioxide distributions httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-biological-researchhtml httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-life-science-researchhtml Prior Scientific

httpwwwprior-uscom Profusa Inc - Lumee tissue-integrated biosensors scaffolds httpprofusacomtechnology Reindeer Graphics Inc ndash OptiPix Fovea Pro 9plugins for Adobe Photoshop 6 and CS series) httpwwwreindeergraphicscom Renishaw - StreamLine fast chemical imaging Raman spectroscopy httpwwwrenishawcomenstreamline-generate-chemical-images-rapidly--9449 httpwwwrenishawcomenraman-spectroscopy--6150 Sanford Burnham Prebys ndash High Content Screening httpwwwsbpdiscoveryorgtechnologysrPagesLaJolla_HighContentScreeningaspx ScopeM - Scientific Center for Optical and Electron Microscopy - ETH Zurich httpwwwscopemethzch SiriusXT - soft X-ray tomography (SXT) microscope (CT scan hydrated cell) httpsiriusxtcom SpectraGenetics - Fluorogen Activating Peptides (FAPs) new genetically encoded ldquobinaryrdquo reporters httpspectrageneticscomproductsvectors-for-expressing-fluorogen-activating-proteinsfap-technology-overview Spirochrome - Silicon Rhodamine (SiR) and other fluorescent reagents probes for bioimaging httpspirochromecom Stanford Photonics Inc httpwwwstanfordphotonicscom httpwwwstanfordphotonicscomLife20SciencesLifeScihtm

Stream Technologies Inc ndash ColorFlow lens (multi-wavelength emission onto a camera) httpwwwstreamtechinccomproducts Sutter Instrument Company httpwwwsuttercom httpwwwsuttercomMICROSCOPESindexhtml httpwwwsuttercomIMAGINGindexhtml SVI Huygens ndash Professional (general image analysis) deconvolution NVidia GPU deconvolution httpssvinlHuygensProfessional httpssvinlHuygensDeconvolution httpssvinlHuygensGPU Sysmex Partex ndash CyScope httpwwwsysmex-parteccomproductsmicroscopyhtml httpwwwsysmex-parteccomproductsprdouct-detailviewcyscopeR-malaria-3238html Technical Instruments httpwwwtechinstcomproductsphp TESCAN Brno sro - Tescan Q-PHASE multimodal holographic quantitative phase imaging system (QPi) optional fluorescence httpwwwtescancomenproductsq-phaseq-phase httpq-phasetescancom httpq-phasetescancomindexphptechnologyspecifications Ted Pella Inc ndash specialty light microscopy and electron microscopy supplies httpswwwtedpellacom Texas Instruments ndash DLP 4100 development kit (digital light processingrsquo DMD digital micromirror device) httpwwwticomtooldlpd4x00kit

ThorLabs ndash iCyte imaging cytometer multiphoton confocal EnVista digital slide scanning microscopes httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7473 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7494 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=5696 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=6570 TIRF Labs lightguide TIRF prism TIRF TIRF-Electrochemistry httpwwwtirf-labscom httpwwwtirf-labscomtechnologieshtml TissueVision - Serial Two Photon Tomography (image volume ablate imaged volume with multiphoton laser repeat) httpwwwtissuevisioncomtechnology Tokai Hit - stage top incubator httpwwwtokaihitcomenglishproduct_guidanceoptionhtml TopoNomos Ltd ndash Toponome Imaging Cycler ndash immunofluorescence (100plex) httpwwwtoposnomoscomtechnologyhtml Ultivue Inc ndash DNA-PAINT ndash reagents data processing service httpwwwultivuecom httpwwwultivuecomproducts UMech Technologies ndash Cytovar HCS up to 16 excitation wavelengths httpcloudumechcomproducts httpcloudumechcomproductsmodelC16 Visitech ndash vt-iSIM instant super-resolution microscopy up to 1000 frames per second confocal scanners and light engines httpwwwvisitechcoukvt-isimhtml httpwwwvisitechcoukproductshtml Visitron Systems GmbH - high speed imaging systems httpwwwvisitronde Visualsonics (Fujifilm) - photoacoustic imaging httpwwwvisualsonicscomproductstechnology-overview Wicked Lasers httpwwwwickedlaserscom httpwwwwickedlaserscomarctic WITec Wissenschaftliche Instrumente und Technologie GmbH - imaging systems for FLIM Raman AFM and SNOM analysis httpwitecdeproducts httpwwwwitec-instrumentscom WM Keck Center for Adaptive Optical Microscopy (CfAOM) at UC Santa Cruz httpscfaomsoeucscedu httpcfaoucolickorgpgallery Yokogawa Corp ndash spinning disk confocal scanner live cell imager high content screener confocal quantitative cytometer httpwwwyokogawacomsolutionsproducts-platformslife-science httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-scanner-unit-csu httpwwwyokogawacomsolutionsproducts-platformslife-scienceall-in-one-live-cell-imaging-solution httpwwwyokogawacomsolutionsproducts-platformslife-sciencehigh-throughput-cytological-discovery-system httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-quantitative-image-cytometer Zellkraftwerk (ChipCytometry) ndash immunofluorescence (80plex) httpwwwzellkraftwerkcomProducts2phtml httpwwwzellkraftwerkcomZKWOnephtmlSoftware

httpwwwchipcytometrycomtechnologyphtml Fluorescence Spectra Data and Graphing Sites PubSpectra ndash Excel file data download httpsworksbepresscomgmcnamara9 BD Biosciences ndash spectrum viewer Brilliant fluorophores httpwwwbdbiosciencescomussspectrumviewer httpwwwbdbiosciencescomusapplicationssspectrumguidepage BioLegend ndash spectra analyzer Brilliant Violet fluorophores httpwwwbiolegendcomspectraanalyzer httpwwwbiolegendcombrilliantviolet Chroma Technology httpswwwchromacomspectra-viewer eBioscience (Affymetrix ThermoFisher) ndash fluorPlan ndash a multi-laser spectra viewer httpwwwebiosciencecomresourcesfluorplan-spectra-viewerhtm Spectra Viewer (requires Java) Evrogen ndash Spectrum Viewer httpevrogencomspectra-viewerflashviewerhtml Fluorophoresorg ndash Fluorescent Substances httpwwwfluorophorestugrazatsubstance I Love GFP httpssitesgooglecomsiteilovegfpHomefps Lambert and Thorn UCSF Fluorescent protein properties httpnicucsfeduFPvisualization Leica Microsystem - ldquoFluoScoutrdquo httpwwwleica-microsystemscomfluoscout

Molecular Probes Invitrogen Thermo Fisher ndash Fluorescence SpectraViewer httpwwwthermofishercomusenhomelife-sciencecell-analysislabeling-chemistryfluorescence-spectraviewerhtml httpsitunesapplecomusappfluorescence-spectraviewerid421031826 (iTunes App) Nightsea - Compendium of spectra web sites httpwwwnightseacomsfa-sharingfluorescence-spectra-viewers Omega Optical ldquoCurvomatricrdquo httpswwwomegafilterscomcurvomatic

PhotoChemCAD 20 (Jonathan S Lindsey) dye spectra database and chemistry calculator NIRvana Sciences httpwwwphotochemcadcom httpnirvanasciencescompage_id=3088 UCSF (Lambert Thorn 2016) - Fluorescent protein properties httpnicucsfeduFPvisualization University of Arizona - Fluorescent Spectra Database httpwwwspectraarizonaedu Semrock - Searchlight httpssearchlightsemrockcom Spectroscopy Ninja ndash links to spectral and fluorescence data Spekwin32 spectroscopy software httpwwweffemm2deinfoinfo_specdatahtml

httpwwweffemm2deindexhtml Zeiss ndash interactive fluorescence dye and filter database overview dyes overview filter sets httpswwwmicro-shopzeisscoms=50479761ad21e5ampl=enampp=usampf=fampa=i httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=d httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=f Researcher Labs Alby Diaspro ndash IIT httpwwwlambsitindexphppage=People Alice Ting ndash MIT httpwwwtinglaborgresearch Allen Institute for Brain Science httpwwwalleninstituteorgwhat-we-dobrain-science Allen Institute for Cell Science httpwwwalleninstituteorgwhat-we-docell-science Amina Qutub - Rice University - How are human cells designed lab httpsqutublaborgqutub-lab Amy Herr UC Berkeley ndash Single cell Westerns httpherrlabberkeleyedu Amy Palmer ndash UC Boulder httpspalmerlabcoloradoedu Andrew York ndash Calico Life Sciences httpswwwcalicolabscomteam-memberandrew-york Anne Carpenter ndash Broad Institute CellProfiler httpspersonalbroadinstituteorganne Arjun Raj UPenn single molecule RNA FISH quantitative understanding cellular functions httprajlabseasupenneduindexhtml httpwwwpopscicomsciencearticle2013-09arjun-raj Atsuko Miyawaki - Laboratory for Cell Function Dynamics (CFDS) Fucci2 fluorescent proteins cell cycle indicator httpwwwbrainrikenjpenfacultydetails30 httpcfdsbrainrikenjp httpcfdsbrainrikenjpFuccihtml Aydogan Ozcan - UCLA - new imaging and sensing architectures httpinnovateeeuclaeduwelcomehtml httpwwwhhmiorgscientistsaydogan-ozcan Badri Roysam - UH - FARSIGHT Toolkit httpwwweeuhedufacultyroysam httpwwwfarsight-toolkitorgwikiMain_Page Brian J Ford ndash microscopist and popularizer httpsuklinkedincominprofbrianjford Carolyn Larabell ndashNational Center for X-ray Tomography (LBNL) UCSF httpncxtlblgovq=carolyn httpprofilesucsfeducarolynlarabell Clare Waterman ndash NHLBI NIH

httpswwwnhlbinihgovresearchintramuralresearcherspiwaterman-clare Dana Peer - Columbia University - Computational Systems Biology viSNE and more software httpwwwc2b2columbiaedudanapeerlabhtml httpwwwc2b2columbiaedudanapeerlabhtmlcythtml David Mayerich - UH - STIM Laboratory Scalable Tissue Imaging and Modeling httpwwweeuhedufacultymayerich httpstimeeuhedu David Piston WUSTL httpwwwcellbiologywustledufacultytenureddavid-w-piston-phd Diane Lidke and Keith Lidke - University of New Mexico httppathologyunmeduresearchfaculty-laboratoriesthe-lidke-laboratoryindexhtml httppanda3physunmedu~klidke Donna Arndt-Jovin and Thomas Jovin - Max Planck Institute for Biophysical Chemistry Laboratory of Cellular Dynamics httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsDonnaArdndt-JovinResearchAreasAndProjects httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsChairmanThomasJovinResearchAreasAndProjects Ed Boyden ndash MIT Media Lab ndash expansion microscopy (ExM) optogenetics httpsyntheticneurobiologyorg httpsyntheticneurobiologyorgprotocols httpsyntheticneurobiologyorgpublications httpwwwtedcomtalksed_boyden_baby_diapers_inspired_this_new_way_to_study_the_brain httpwwwextbiocombuycell Elizabeth Blackburn ndash Salk Institute - Telomeres httpswwwsalkeduscientistelizabeth-blackburn httpsenwikipediaorgwikiElizabeth_Blackburn httpswwwnobelprizeorgnobel_prizesmedicinelaureates2009blackburn-factshtml Elizabeth Hillman - Columbia university - SCAPE (Swept Confocally-Aligned Planar Excitation) high speed 3D microscopy DyCE (dynamic contrast enhancement to image and segment small animal organs live) Neuroimaging amp Neurovascular Coupling httporionbmecolumbiaedu~hillmanInstrumentationhtml httporionbmecolumbiaedu~hillmanSCAPEhtml httporionbmecolumbiaedu~hillmanMolecularhtml httporionbmecolumbiaedu~hillmanBrain_Imaginghtml Eric Betzig ndash UCSF (moving from HHMI Janelia Farm in 2016) httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014betzig-factshtml Eva Sevick-Muraca ndash UT Health Science Center at Houston molecular imaging clinical NIR fluoresceince imaging httpswwwutheduimmprofilehtmid=1005459 httpswwwutheduimmcentersmolecular-imaginghtm Evelin Schrock - Technische Universitaumlt Dresden spectral karyotyping cytogenetics httpswwwresearchgatenetprofileEvelin_Schrock Garry Nolan Stanford University ndash Mass cytometry MIBI-ToF high throughput imaging mass cytometry (42plex) httpwebstanfordedugroupnolanresourceshtml httpwebstanfordedugroupnolantechnologieshtml George McNamara ndash Cell Morphometry (41) Figure 1 right top two panels (55) The Chase (2016 temporal area maps lsquodynamic morphologyrsquo) (76) newsletter series on ldquoThe Chaserdquo (73) direct Vimeo movie of ldquoThe Chaserdquo Tiki_Goddess linkedin 10+plex blog httpsworksbepresscomgmcnamara41 httpsworksbepresscomgmcnamara55 httpsworksbepresscomgmcnamara76

httpsworksbepresscomgmcnamara73 httpsvimeocom175151196 httphomeearthlinknet~tiki_goddess httpswwwlinkedincomingeorgemcnamara httpswwwlinkedincompulsebd-biosciences-listed-tandems-horizon-brilliant-violets-mcnamara Gillian Griffiths - University of Cambridge - T-cell immunological synapse httpwwwcimrcamacukresearchprincipal-investigatorsprincipal-investigators-a-hgriffiths Hari Shroff NIBIB NIH httpswwwnibibnihgovlabs-at-nibibsection-high-resolution-optical-imaging-hroi HHMI Janelia Farm Research Campus (JFRC) - Advanced Imaging Center Open Science httpswwwjaneliaorgopen-scienceadvanced-imaging-center-aic httpswwwjaneliaorgopen-science Jeanne Lawrence University of Massachussetts Medical School httpwwwumassmededucellbiolabslawrencepersonnelprincipal-investigator Jennifer Lippincott-Schwartz ndash HHMI Janelia Farm httpswwwjaneliaorgpeoplejennifer-lippincott-schwartz Jin Zhang ndash UCSD httpprofilesucsdedujinzhang Joe DeRisi - UCSF - 3D printable lab stuff httpderisilabucsfeduindexphppage=3D John Russ Chris Russ Fovea Pro plugins for Adobe Photoshop httpwwwdrjohnrusscomindexhtml httpwwwdrjohnrusscombookshtml httpwwwreindeergraphicscomfoveaprotutorialhtml Julie Theriot httpcmgmstanfordedutheriot Karl Deisseroth ndash Stanford University ndash CLARITY optical tissue clearing Optogenetics httpclarityresourcecenterorg httpwebstanfordedugroupdlaboptogeneticsindexhtml Karsten Koumlnig (Koenig) - Saarland University and JenLab GmbH - biophotonics httpwwwbltuni-saarlanddeindex_ehtm httpwwwjenlabde httpwwwthelastescape-filmcom Karsten Rodenacker ndash image measurements httpkaro03bplacednetkaroMeMisc_WWWpdfMicrosoftWord-EQUAPATpdf Kevin Eliceiri ndash UW-Madison Open Source Photonics and Software Laboratory for Optical and Computational Instrumentation (LOCI) wwwlociwiscedu Klaus Kemp ndash Microlife Services ndash diatoms and other prepared microscope slides httpwwwdiatomscouk Kurt Thorn UCSF httpthornlabucsfedu httpsnicucsfedublog httpnicucsfeduFPvisualization httpgigapancomgigapans163370 Lihong Wang - WUSTL - Optical Imaging Laboratory photoacoustic tomography

httpoilabseaswustledu httpoilabseaswustleduresearch_0html Loren Looger - HHMI JFRC - iGluSnFr fluorescent protein biosensor httpswwwjaneliaorglablooger-lab Mary-Lou Pardue ndash MIT (first ever in situ hybridization with J Gall) httpsbiologymitedupeoplemary_lou_pardue httpsenwikipediaorgwikiMary-Lou_Pardue Nancy Allbritton - UNC - Chemical cytometry microraft arrays organ-on-a-chip httpswwwbmencsueduindexphpcomponentcomprofileruserprofilenlallbri httpwwwbmeuncedulabsallbritton Navin Varadarajan - UH - single-cell Lab httpwwwcheeuhedufacultyvaradarajan httpsinglecellcheeuheducontacthtml Nicholas Shaner - Scintillon Institute - mNeonGreen httpwwwscintillonorgshaner_lab Rebecca Richards-Kortum httpbioengineeringriceedufacultyrebecca_richards-kortumaspx Robert Campbell - Fluorescent proteins optogenetic proteins httpcampbellwebchemualbertaca httpcampbellwebchemualbertacaprojects-2 Robert Murphy ndash Cell measurements web services httpmurphylabwebcmueduservices Sabine Mai - University of Manitoba - Genomic Centre for Cancer Research and Diagnosis (GCCRD) - httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBPlatformsGCCRDhtml httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBScientistsMaiAwardshtml Sally Ward and Raimund Ober - Texas AampM University - httpwwwwardoberlabcom Simon Watkins - U Pittsburgh Center for Biologic Imaging httpwwwcbppittedufacultywatkinshtml httpwwwcbppittedufacultylabwatkinshtml httpwwwcbipittedu Stefan Hell ndash Deparment Hell NanoBiopohotonics httpwwwmpibpcmpgdehell httpsenwikipediaorgwikiStefan_Hell httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014hell-factshtml Sunney Xie Harvard httpsbernsteinharvardedu Susan Cox ndash 3B microscopy httpwwwcoxphysicscomindexhtml httpwwwcoxphysicscom3b Radim Chmeliacutek - Center for innovative microscopy Experimental biophotonics group httpswwwceiteceuceitec-butexperimental-biophotonicsrg3 httpwwwbiophotczhome Taekjip Ha ndash Johns Hopkins University ndash single molecules httphamedjhmiedu

Thomas Ried ndash NCI NIH SKYM-FISH and CGH Database httpsccrcancergovGenetics-Branchthomas-ried httpsccrcancergovGenetics-Branchthomas-riedqt-staff_profile_tabs=9qt-staff_profile_tabs ftpftpncbinlmnihgovsky-cghDATA httpswwwncbinlmnihgovdbvar Viviana Gradinaru ndash CalTech ndash CLARITYPACT Optogenetics httpwwwbbecaltecheducontentviviana-gradinaru httpglabcaltechedu Vladislav Verkhusha - near infrared fluorescent proteins httpwwweinsteinyuedulabsvlad-verkhushadefaultaspx httpwwweinsteinyueduresearchfacilitiesfluorescent WE Moerner ndash Stanford University httpwebstanfordedugroupmoerner Willard Wiggans ndash micro gallery httpwwwwillard-wigancomgallery Wolf Frommer ndash Molecular sensors httpbiosensordpbcarnegiescienceedu (fluorescent protein biosensors table) Xiaowei Zhuang = Harvard httpzhuangharvardedu Yuval Garini - Bar-Ilan University - Nano-Bio-Photonics laboratory httpgarinilabbiuacil Microscopy Magazines Imaging amp Microscopy httpwwwimaging-gitcommagazine Laser Focus World httpwwwlaserfocusworldcomindexhtml Microscopy amp Analysis httpwwwmicroscopy-analysiscom Microscopy Today httpwwwmicroscopy-todaycom Microscopy-UK httpwwwmicroscopy-ukorguk Photonics Spectra Biophotonics httpwwwphotonicscomPublicationsaspx The Microscope Journal httpmcriorgv72the-microscope-journal RMS Infocus Magazine httpwwwrmsorgukstudy-readinfocus-magazinehtml Nobel Prizes in Light Microscopy and Related Fields Chemistry 1925 colloids (light sheet) Zsigmondy (Siedentopf Zsigmondy 1902) httpswwwnobelprizeorgnobel_prizeschemistrylaureates1925

Chemistry 2000 conductive polymers Heeger MacDiarmid Shirakawa (Brilliant Violets Ultraviolets Blues) httpwwwnobelprizeorgnobel_prizeschemistrylaureates2000 Chemistry 2008 green fluorescent protein GFP Shimomura Chalfie Tsien httpwwwnobelprizeorgnobel_prizeschemistrylaureates2008 Chemistry 2014 super-resolved fluorescence microscopy Betzig Hell Moerner httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014 Physics 1953 Phase Contrast Zernike httpswwwnobelprizeorgnobel_prizesphysicslaureates1953 Physics 2009 invention of an imaging semiconductor circuit ndash the CCD sensor Kao Boyle Smith httpwwwnobelprizeorgnobel_prizesphysicslaureates2009 Physics 2014 efficient blue light emitting diodes Akasaki Amano Nakamura httpwwwnobelprizeorgnobel_prizesphysicslaureates2014 Physiology or Medicine 2006 Fire and Mello RNA interference ndash gene silencing by double stranded RNA httpwwwnobelprizeorgnobel_prizesmedicinelaureates2006 Physiology or Medicine 2006 Capecchi Evans Smithies specific gene modifications in mice by the use of embryonic stem cells httpwwwnobelprizeorgnobel_prizesmedicinelaureates2007 Physiology or Medicine 2009 Blackburn Greider Szostak how chromosomes are protected by telomeres and telomerase httpwwwnobelprizeorgnobel_prizesmedicinelaureates2009 Physiology or Medicine 2012 Gurdon Yamamanka matured cells can be reprogrammed to become pluripotent httpwwwnobelprizeorgnobel_prizesmedicinelaureates2012

Table 442 Fluorophores Photophysics Data

Fluorophore Abs or Ex max (nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Acridine orange 271 520 27000 020 5

Alexa Fluor 430 431 541 16000 055 9

Alexa Fluor 488 495 519 71000 094 67

Alexa Fluor 532 532 553 81000 080 65

Alexa Fluor 546 556 573 104000 096 100

Alexa Fluor 568 578 603 91300 075 69

Alexa Fluor 594 590 617 73000 064 47

Allophycocyanin (APC) 650 660 700000 068 476

Atto 390 390 479 24000 090 22

Atto 425 436 484 45000 065 29

Atto 430LS 433 547 32000 065 21

Atto 465 453 508 75000 075 56

Atto 490LS 496 661 40000 030 12

Atto 520 525 547 105000 095 100

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 16: McNamara 20161006 revised draft tables for CPHG Light ...

Molecular Devices Corporation Universal Imaging Corporation (Danaher) ndash MetaMorph MetaFluor high content systems (HCS) httpswwwmoleculardevicescomsystemsmetamorph-research-imaging httpmdccusthelpcomappanswersdetaila_id19319 httpswwwmoleculardevicescomsystemshigh-content-imaging Molecular Machines amp Industries - laser microdissection and tweezer systems httpwwwmolecular-machinescomhome MUSE Microscopy Inc ndash Deep UV illumination for shallow depth of field imaging httpwwwmusemicrocom Micro Video Instruments Inc - DarkLite illuminator httpwwwmvi-inccom NanoEnTek ndash JuLI Stage (imager inside incubator or on lab bench) httpwwwjulistagecom National Instruments ndash LabView software httpwwwnicomen-ushtml Navitar - Hoffman Modulation Contrast (HMC alternative to differential interference contrast phase contrast) custom lens design UVDUVNUV imaging lenses httpsnavitarcommarketsmicroscopy httpsnavitarcomproductsimaging-opticscustom-microscope-objectivescustom-microscope-objectives httpsnavitarcomproductsimaging-opticsuv-imaging National Center for X-ray Tomography (NCXT) ndash soft X-ray tomography (CT of hydrated cells) XM-2 dedicated biological SXT microscope Prof Carolyn Larabell Director (see also SiriusXT) httpncxtlblgov httpncxtlblgovsxt httpncxtlblgovmanual httpncxtlblgovq=carolyn Neogenomics (Clarient) ndash MultiOmyx immunofluorescence or DNA FISH (ldquo60plexrdquo) httpneogenomicscomPharma-ServicesLab-ServicesMultiOmyxTechnologyMultiOmyx-IF-Assay-DNA-FISH-assay-NGS-from-ROI Nexcelom ndash Celigo imaging cytometer Cellometer cell counters httpwwwnexcelomcomCeligoindexphp httpwwwnexcelomcomProducts Nikon ndash Ti-LAPP modular illumination system (for Nikon Ti series microscopes) TIRF Optogenetics httpswwwnikoninstrumentscomProductsPhotostimulation-and-TIRFTi-LAPP Nirmidas Biotech httpwwwnirmidascomtechnologynir httpwwwnirmidascomproductsniriidye NVidia ndash Pascal 10+ Gbps GPU cards for instant gratification deconvolution (software from Microvolutioncom SVInl) httpwwwgeforcecomhardware10seriesgeforce-gtx-1080 httpwwwgeforcecomhardware10seriestitan-x-pascal httpwwwnvidiacomobjectquadro-graphics-with-pascalhtml Ocean Optics ndash spectrometers httpoceanopticscomproduct-categorymodular-spectrometers Oko-Lab stage top incubator httpwwwoko-labcomstage-top Open Microscopy Environment (OME) ndash OMERO (see also Glencoe Software) Bio-Formats LOCI

httpswwwopenmicroscopyorgsite httpswwwopenmicroscopyorgsiteproductsomero httpswwwopenmicroscopyorgsiteproductsbio-formats httpswwwopenmicroscopyorgsitesupportbio-formats52supported-formatshtml httpswwwopenmicroscopyorgsiteaboutdevelopment-teamskevin OpenSPIM ndash do-it-yourself selective plane illumination microscopy (light sheet imaging) httpopenspimorgWelcome_to_the_OpenSPIM_Wiki OpenSpinMicroscopy ndash do-it-yourself SPIMDSLMOPT microscopes httpssitesgooglecomsiteopenspinmicroscopy Ovizio ndash differential digital holography (similar to quantitative phase imaging) httpwwwoviziocomenHome httpwwwoviziocomenMicroscopesQMod Oxford Gene Technologies ndash microarrays ndash cytogenetics molecule genetics cancer research pre-implantation genetic diagnosis httpwwwogtcomclinical_genetics Oxford Nanoimaging ndash single molecule(s) localization fluorescence resonance energy transfer (FRET) (Kapanidis) wwwoxfordnicom Pathology Devices ndash LiveCell stage top incubator amp controller tissue microarrayers (TMA makers) httpwwwpathologydevicescomLiveCellhtm httpwwwpathologydevicescomTMArrayerhtm PeCon GmbH ndash microscope incubators httpwwwpeconbiz Pembroke Instruments ndash spectrometers mini-lasers httppembrokeinstrumentscomqmini-spectrometer httppembrokeinstrumentscommini-lasers PerkinElmer ndash in vivo imaging systems (bioluminescence NIR fluorescence) Vectra digital slide scanner httpwwwperkinelmercomcategoryin-vivo-imaging-instruments httpwwwperkinelmercomcategoryquantitative-pathology-imaging-instruments Phi Optics ndash CellVista SLIM Pro (quantitative phase microscopy) httpphiopticscom Photometrics (Roper Scientific) ndash DualView QuadView httpwwwphotometricscom httpwwwphotometricscomproductsmultichannel Photon Technology International httpwwwpti-njcomindexhtml

PicoQuant GmbH ndash fluorescence lifetime imaging microscopes (FLIM) STED 3D-EasySTED httpswwwpicoquantcomproductscategoryfluorescence-microscopes httpswwwpicoquantcomapplicationscategorylife-sciencested httpwwweasystedorg Physik Instrumente GmbH amp Co KG (PI) - Nanopositioning Applications for Microscopy Neuroscience and Metrology httpswwwphysikinstrumentecomen httpwwwpi-usausindexphp PreSens Prescision Sensing GmbH - VisiSens measure and visualize Oxygen pH or carbon dioxide distributions httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-biological-researchhtml httpwwwpresensdeproductsbrochurescategoryimagingbrochureimaging-solutions-life-science-researchhtml Prior Scientific

httpwwwprior-uscom Profusa Inc - Lumee tissue-integrated biosensors scaffolds httpprofusacomtechnology Reindeer Graphics Inc ndash OptiPix Fovea Pro 9plugins for Adobe Photoshop 6 and CS series) httpwwwreindeergraphicscom Renishaw - StreamLine fast chemical imaging Raman spectroscopy httpwwwrenishawcomenstreamline-generate-chemical-images-rapidly--9449 httpwwwrenishawcomenraman-spectroscopy--6150 Sanford Burnham Prebys ndash High Content Screening httpwwwsbpdiscoveryorgtechnologysrPagesLaJolla_HighContentScreeningaspx ScopeM - Scientific Center for Optical and Electron Microscopy - ETH Zurich httpwwwscopemethzch SiriusXT - soft X-ray tomography (SXT) microscope (CT scan hydrated cell) httpsiriusxtcom SpectraGenetics - Fluorogen Activating Peptides (FAPs) new genetically encoded ldquobinaryrdquo reporters httpspectrageneticscomproductsvectors-for-expressing-fluorogen-activating-proteinsfap-technology-overview Spirochrome - Silicon Rhodamine (SiR) and other fluorescent reagents probes for bioimaging httpspirochromecom Stanford Photonics Inc httpwwwstanfordphotonicscom httpwwwstanfordphotonicscomLife20SciencesLifeScihtm

Stream Technologies Inc ndash ColorFlow lens (multi-wavelength emission onto a camera) httpwwwstreamtechinccomproducts Sutter Instrument Company httpwwwsuttercom httpwwwsuttercomMICROSCOPESindexhtml httpwwwsuttercomIMAGINGindexhtml SVI Huygens ndash Professional (general image analysis) deconvolution NVidia GPU deconvolution httpssvinlHuygensProfessional httpssvinlHuygensDeconvolution httpssvinlHuygensGPU Sysmex Partex ndash CyScope httpwwwsysmex-parteccomproductsmicroscopyhtml httpwwwsysmex-parteccomproductsprdouct-detailviewcyscopeR-malaria-3238html Technical Instruments httpwwwtechinstcomproductsphp TESCAN Brno sro - Tescan Q-PHASE multimodal holographic quantitative phase imaging system (QPi) optional fluorescence httpwwwtescancomenproductsq-phaseq-phase httpq-phasetescancom httpq-phasetescancomindexphptechnologyspecifications Ted Pella Inc ndash specialty light microscopy and electron microscopy supplies httpswwwtedpellacom Texas Instruments ndash DLP 4100 development kit (digital light processingrsquo DMD digital micromirror device) httpwwwticomtooldlpd4x00kit

ThorLabs ndash iCyte imaging cytometer multiphoton confocal EnVista digital slide scanning microscopes httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7473 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7494 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=5696 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=6570 TIRF Labs lightguide TIRF prism TIRF TIRF-Electrochemistry httpwwwtirf-labscom httpwwwtirf-labscomtechnologieshtml TissueVision - Serial Two Photon Tomography (image volume ablate imaged volume with multiphoton laser repeat) httpwwwtissuevisioncomtechnology Tokai Hit - stage top incubator httpwwwtokaihitcomenglishproduct_guidanceoptionhtml TopoNomos Ltd ndash Toponome Imaging Cycler ndash immunofluorescence (100plex) httpwwwtoposnomoscomtechnologyhtml Ultivue Inc ndash DNA-PAINT ndash reagents data processing service httpwwwultivuecom httpwwwultivuecomproducts UMech Technologies ndash Cytovar HCS up to 16 excitation wavelengths httpcloudumechcomproducts httpcloudumechcomproductsmodelC16 Visitech ndash vt-iSIM instant super-resolution microscopy up to 1000 frames per second confocal scanners and light engines httpwwwvisitechcoukvt-isimhtml httpwwwvisitechcoukproductshtml Visitron Systems GmbH - high speed imaging systems httpwwwvisitronde Visualsonics (Fujifilm) - photoacoustic imaging httpwwwvisualsonicscomproductstechnology-overview Wicked Lasers httpwwwwickedlaserscom httpwwwwickedlaserscomarctic WITec Wissenschaftliche Instrumente und Technologie GmbH - imaging systems for FLIM Raman AFM and SNOM analysis httpwitecdeproducts httpwwwwitec-instrumentscom WM Keck Center for Adaptive Optical Microscopy (CfAOM) at UC Santa Cruz httpscfaomsoeucscedu httpcfaoucolickorgpgallery Yokogawa Corp ndash spinning disk confocal scanner live cell imager high content screener confocal quantitative cytometer httpwwwyokogawacomsolutionsproducts-platformslife-science httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-scanner-unit-csu httpwwwyokogawacomsolutionsproducts-platformslife-scienceall-in-one-live-cell-imaging-solution httpwwwyokogawacomsolutionsproducts-platformslife-sciencehigh-throughput-cytological-discovery-system httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-quantitative-image-cytometer Zellkraftwerk (ChipCytometry) ndash immunofluorescence (80plex) httpwwwzellkraftwerkcomProducts2phtml httpwwwzellkraftwerkcomZKWOnephtmlSoftware

httpwwwchipcytometrycomtechnologyphtml Fluorescence Spectra Data and Graphing Sites PubSpectra ndash Excel file data download httpsworksbepresscomgmcnamara9 BD Biosciences ndash spectrum viewer Brilliant fluorophores httpwwwbdbiosciencescomussspectrumviewer httpwwwbdbiosciencescomusapplicationssspectrumguidepage BioLegend ndash spectra analyzer Brilliant Violet fluorophores httpwwwbiolegendcomspectraanalyzer httpwwwbiolegendcombrilliantviolet Chroma Technology httpswwwchromacomspectra-viewer eBioscience (Affymetrix ThermoFisher) ndash fluorPlan ndash a multi-laser spectra viewer httpwwwebiosciencecomresourcesfluorplan-spectra-viewerhtm Spectra Viewer (requires Java) Evrogen ndash Spectrum Viewer httpevrogencomspectra-viewerflashviewerhtml Fluorophoresorg ndash Fluorescent Substances httpwwwfluorophorestugrazatsubstance I Love GFP httpssitesgooglecomsiteilovegfpHomefps Lambert and Thorn UCSF Fluorescent protein properties httpnicucsfeduFPvisualization Leica Microsystem - ldquoFluoScoutrdquo httpwwwleica-microsystemscomfluoscout

Molecular Probes Invitrogen Thermo Fisher ndash Fluorescence SpectraViewer httpwwwthermofishercomusenhomelife-sciencecell-analysislabeling-chemistryfluorescence-spectraviewerhtml httpsitunesapplecomusappfluorescence-spectraviewerid421031826 (iTunes App) Nightsea - Compendium of spectra web sites httpwwwnightseacomsfa-sharingfluorescence-spectra-viewers Omega Optical ldquoCurvomatricrdquo httpswwwomegafilterscomcurvomatic

PhotoChemCAD 20 (Jonathan S Lindsey) dye spectra database and chemistry calculator NIRvana Sciences httpwwwphotochemcadcom httpnirvanasciencescompage_id=3088 UCSF (Lambert Thorn 2016) - Fluorescent protein properties httpnicucsfeduFPvisualization University of Arizona - Fluorescent Spectra Database httpwwwspectraarizonaedu Semrock - Searchlight httpssearchlightsemrockcom Spectroscopy Ninja ndash links to spectral and fluorescence data Spekwin32 spectroscopy software httpwwweffemm2deinfoinfo_specdatahtml

httpwwweffemm2deindexhtml Zeiss ndash interactive fluorescence dye and filter database overview dyes overview filter sets httpswwwmicro-shopzeisscoms=50479761ad21e5ampl=enampp=usampf=fampa=i httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=d httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=f Researcher Labs Alby Diaspro ndash IIT httpwwwlambsitindexphppage=People Alice Ting ndash MIT httpwwwtinglaborgresearch Allen Institute for Brain Science httpwwwalleninstituteorgwhat-we-dobrain-science Allen Institute for Cell Science httpwwwalleninstituteorgwhat-we-docell-science Amina Qutub - Rice University - How are human cells designed lab httpsqutublaborgqutub-lab Amy Herr UC Berkeley ndash Single cell Westerns httpherrlabberkeleyedu Amy Palmer ndash UC Boulder httpspalmerlabcoloradoedu Andrew York ndash Calico Life Sciences httpswwwcalicolabscomteam-memberandrew-york Anne Carpenter ndash Broad Institute CellProfiler httpspersonalbroadinstituteorganne Arjun Raj UPenn single molecule RNA FISH quantitative understanding cellular functions httprajlabseasupenneduindexhtml httpwwwpopscicomsciencearticle2013-09arjun-raj Atsuko Miyawaki - Laboratory for Cell Function Dynamics (CFDS) Fucci2 fluorescent proteins cell cycle indicator httpwwwbrainrikenjpenfacultydetails30 httpcfdsbrainrikenjp httpcfdsbrainrikenjpFuccihtml Aydogan Ozcan - UCLA - new imaging and sensing architectures httpinnovateeeuclaeduwelcomehtml httpwwwhhmiorgscientistsaydogan-ozcan Badri Roysam - UH - FARSIGHT Toolkit httpwwweeuhedufacultyroysam httpwwwfarsight-toolkitorgwikiMain_Page Brian J Ford ndash microscopist and popularizer httpsuklinkedincominprofbrianjford Carolyn Larabell ndashNational Center for X-ray Tomography (LBNL) UCSF httpncxtlblgovq=carolyn httpprofilesucsfeducarolynlarabell Clare Waterman ndash NHLBI NIH

httpswwwnhlbinihgovresearchintramuralresearcherspiwaterman-clare Dana Peer - Columbia University - Computational Systems Biology viSNE and more software httpwwwc2b2columbiaedudanapeerlabhtml httpwwwc2b2columbiaedudanapeerlabhtmlcythtml David Mayerich - UH - STIM Laboratory Scalable Tissue Imaging and Modeling httpwwweeuhedufacultymayerich httpstimeeuhedu David Piston WUSTL httpwwwcellbiologywustledufacultytenureddavid-w-piston-phd Diane Lidke and Keith Lidke - University of New Mexico httppathologyunmeduresearchfaculty-laboratoriesthe-lidke-laboratoryindexhtml httppanda3physunmedu~klidke Donna Arndt-Jovin and Thomas Jovin - Max Planck Institute for Biophysical Chemistry Laboratory of Cellular Dynamics httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsDonnaArdndt-JovinResearchAreasAndProjects httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsChairmanThomasJovinResearchAreasAndProjects Ed Boyden ndash MIT Media Lab ndash expansion microscopy (ExM) optogenetics httpsyntheticneurobiologyorg httpsyntheticneurobiologyorgprotocols httpsyntheticneurobiologyorgpublications httpwwwtedcomtalksed_boyden_baby_diapers_inspired_this_new_way_to_study_the_brain httpwwwextbiocombuycell Elizabeth Blackburn ndash Salk Institute - Telomeres httpswwwsalkeduscientistelizabeth-blackburn httpsenwikipediaorgwikiElizabeth_Blackburn httpswwwnobelprizeorgnobel_prizesmedicinelaureates2009blackburn-factshtml Elizabeth Hillman - Columbia university - SCAPE (Swept Confocally-Aligned Planar Excitation) high speed 3D microscopy DyCE (dynamic contrast enhancement to image and segment small animal organs live) Neuroimaging amp Neurovascular Coupling httporionbmecolumbiaedu~hillmanInstrumentationhtml httporionbmecolumbiaedu~hillmanSCAPEhtml httporionbmecolumbiaedu~hillmanMolecularhtml httporionbmecolumbiaedu~hillmanBrain_Imaginghtml Eric Betzig ndash UCSF (moving from HHMI Janelia Farm in 2016) httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014betzig-factshtml Eva Sevick-Muraca ndash UT Health Science Center at Houston molecular imaging clinical NIR fluoresceince imaging httpswwwutheduimmprofilehtmid=1005459 httpswwwutheduimmcentersmolecular-imaginghtm Evelin Schrock - Technische Universitaumlt Dresden spectral karyotyping cytogenetics httpswwwresearchgatenetprofileEvelin_Schrock Garry Nolan Stanford University ndash Mass cytometry MIBI-ToF high throughput imaging mass cytometry (42plex) httpwebstanfordedugroupnolanresourceshtml httpwebstanfordedugroupnolantechnologieshtml George McNamara ndash Cell Morphometry (41) Figure 1 right top two panels (55) The Chase (2016 temporal area maps lsquodynamic morphologyrsquo) (76) newsletter series on ldquoThe Chaserdquo (73) direct Vimeo movie of ldquoThe Chaserdquo Tiki_Goddess linkedin 10+plex blog httpsworksbepresscomgmcnamara41 httpsworksbepresscomgmcnamara55 httpsworksbepresscomgmcnamara76

httpsworksbepresscomgmcnamara73 httpsvimeocom175151196 httphomeearthlinknet~tiki_goddess httpswwwlinkedincomingeorgemcnamara httpswwwlinkedincompulsebd-biosciences-listed-tandems-horizon-brilliant-violets-mcnamara Gillian Griffiths - University of Cambridge - T-cell immunological synapse httpwwwcimrcamacukresearchprincipal-investigatorsprincipal-investigators-a-hgriffiths Hari Shroff NIBIB NIH httpswwwnibibnihgovlabs-at-nibibsection-high-resolution-optical-imaging-hroi HHMI Janelia Farm Research Campus (JFRC) - Advanced Imaging Center Open Science httpswwwjaneliaorgopen-scienceadvanced-imaging-center-aic httpswwwjaneliaorgopen-science Jeanne Lawrence University of Massachussetts Medical School httpwwwumassmededucellbiolabslawrencepersonnelprincipal-investigator Jennifer Lippincott-Schwartz ndash HHMI Janelia Farm httpswwwjaneliaorgpeoplejennifer-lippincott-schwartz Jin Zhang ndash UCSD httpprofilesucsdedujinzhang Joe DeRisi - UCSF - 3D printable lab stuff httpderisilabucsfeduindexphppage=3D John Russ Chris Russ Fovea Pro plugins for Adobe Photoshop httpwwwdrjohnrusscomindexhtml httpwwwdrjohnrusscombookshtml httpwwwreindeergraphicscomfoveaprotutorialhtml Julie Theriot httpcmgmstanfordedutheriot Karl Deisseroth ndash Stanford University ndash CLARITY optical tissue clearing Optogenetics httpclarityresourcecenterorg httpwebstanfordedugroupdlaboptogeneticsindexhtml Karsten Koumlnig (Koenig) - Saarland University and JenLab GmbH - biophotonics httpwwwbltuni-saarlanddeindex_ehtm httpwwwjenlabde httpwwwthelastescape-filmcom Karsten Rodenacker ndash image measurements httpkaro03bplacednetkaroMeMisc_WWWpdfMicrosoftWord-EQUAPATpdf Kevin Eliceiri ndash UW-Madison Open Source Photonics and Software Laboratory for Optical and Computational Instrumentation (LOCI) wwwlociwiscedu Klaus Kemp ndash Microlife Services ndash diatoms and other prepared microscope slides httpwwwdiatomscouk Kurt Thorn UCSF httpthornlabucsfedu httpsnicucsfedublog httpnicucsfeduFPvisualization httpgigapancomgigapans163370 Lihong Wang - WUSTL - Optical Imaging Laboratory photoacoustic tomography

httpoilabseaswustledu httpoilabseaswustleduresearch_0html Loren Looger - HHMI JFRC - iGluSnFr fluorescent protein biosensor httpswwwjaneliaorglablooger-lab Mary-Lou Pardue ndash MIT (first ever in situ hybridization with J Gall) httpsbiologymitedupeoplemary_lou_pardue httpsenwikipediaorgwikiMary-Lou_Pardue Nancy Allbritton - UNC - Chemical cytometry microraft arrays organ-on-a-chip httpswwwbmencsueduindexphpcomponentcomprofileruserprofilenlallbri httpwwwbmeuncedulabsallbritton Navin Varadarajan - UH - single-cell Lab httpwwwcheeuhedufacultyvaradarajan httpsinglecellcheeuheducontacthtml Nicholas Shaner - Scintillon Institute - mNeonGreen httpwwwscintillonorgshaner_lab Rebecca Richards-Kortum httpbioengineeringriceedufacultyrebecca_richards-kortumaspx Robert Campbell - Fluorescent proteins optogenetic proteins httpcampbellwebchemualbertaca httpcampbellwebchemualbertacaprojects-2 Robert Murphy ndash Cell measurements web services httpmurphylabwebcmueduservices Sabine Mai - University of Manitoba - Genomic Centre for Cancer Research and Diagnosis (GCCRD) - httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBPlatformsGCCRDhtml httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBScientistsMaiAwardshtml Sally Ward and Raimund Ober - Texas AampM University - httpwwwwardoberlabcom Simon Watkins - U Pittsburgh Center for Biologic Imaging httpwwwcbppittedufacultywatkinshtml httpwwwcbppittedufacultylabwatkinshtml httpwwwcbipittedu Stefan Hell ndash Deparment Hell NanoBiopohotonics httpwwwmpibpcmpgdehell httpsenwikipediaorgwikiStefan_Hell httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014hell-factshtml Sunney Xie Harvard httpsbernsteinharvardedu Susan Cox ndash 3B microscopy httpwwwcoxphysicscomindexhtml httpwwwcoxphysicscom3b Radim Chmeliacutek - Center for innovative microscopy Experimental biophotonics group httpswwwceiteceuceitec-butexperimental-biophotonicsrg3 httpwwwbiophotczhome Taekjip Ha ndash Johns Hopkins University ndash single molecules httphamedjhmiedu

Thomas Ried ndash NCI NIH SKYM-FISH and CGH Database httpsccrcancergovGenetics-Branchthomas-ried httpsccrcancergovGenetics-Branchthomas-riedqt-staff_profile_tabs=9qt-staff_profile_tabs ftpftpncbinlmnihgovsky-cghDATA httpswwwncbinlmnihgovdbvar Viviana Gradinaru ndash CalTech ndash CLARITYPACT Optogenetics httpwwwbbecaltecheducontentviviana-gradinaru httpglabcaltechedu Vladislav Verkhusha - near infrared fluorescent proteins httpwwweinsteinyuedulabsvlad-verkhushadefaultaspx httpwwweinsteinyueduresearchfacilitiesfluorescent WE Moerner ndash Stanford University httpwebstanfordedugroupmoerner Willard Wiggans ndash micro gallery httpwwwwillard-wigancomgallery Wolf Frommer ndash Molecular sensors httpbiosensordpbcarnegiescienceedu (fluorescent protein biosensors table) Xiaowei Zhuang = Harvard httpzhuangharvardedu Yuval Garini - Bar-Ilan University - Nano-Bio-Photonics laboratory httpgarinilabbiuacil Microscopy Magazines Imaging amp Microscopy httpwwwimaging-gitcommagazine Laser Focus World httpwwwlaserfocusworldcomindexhtml Microscopy amp Analysis httpwwwmicroscopy-analysiscom Microscopy Today httpwwwmicroscopy-todaycom Microscopy-UK httpwwwmicroscopy-ukorguk Photonics Spectra Biophotonics httpwwwphotonicscomPublicationsaspx The Microscope Journal httpmcriorgv72the-microscope-journal RMS Infocus Magazine httpwwwrmsorgukstudy-readinfocus-magazinehtml Nobel Prizes in Light Microscopy and Related Fields Chemistry 1925 colloids (light sheet) Zsigmondy (Siedentopf Zsigmondy 1902) httpswwwnobelprizeorgnobel_prizeschemistrylaureates1925

Chemistry 2000 conductive polymers Heeger MacDiarmid Shirakawa (Brilliant Violets Ultraviolets Blues) httpwwwnobelprizeorgnobel_prizeschemistrylaureates2000 Chemistry 2008 green fluorescent protein GFP Shimomura Chalfie Tsien httpwwwnobelprizeorgnobel_prizeschemistrylaureates2008 Chemistry 2014 super-resolved fluorescence microscopy Betzig Hell Moerner httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014 Physics 1953 Phase Contrast Zernike httpswwwnobelprizeorgnobel_prizesphysicslaureates1953 Physics 2009 invention of an imaging semiconductor circuit ndash the CCD sensor Kao Boyle Smith httpwwwnobelprizeorgnobel_prizesphysicslaureates2009 Physics 2014 efficient blue light emitting diodes Akasaki Amano Nakamura httpwwwnobelprizeorgnobel_prizesphysicslaureates2014 Physiology or Medicine 2006 Fire and Mello RNA interference ndash gene silencing by double stranded RNA httpwwwnobelprizeorgnobel_prizesmedicinelaureates2006 Physiology or Medicine 2006 Capecchi Evans Smithies specific gene modifications in mice by the use of embryonic stem cells httpwwwnobelprizeorgnobel_prizesmedicinelaureates2007 Physiology or Medicine 2009 Blackburn Greider Szostak how chromosomes are protected by telomeres and telomerase httpwwwnobelprizeorgnobel_prizesmedicinelaureates2009 Physiology or Medicine 2012 Gurdon Yamamanka matured cells can be reprogrammed to become pluripotent httpwwwnobelprizeorgnobel_prizesmedicinelaureates2012

Table 442 Fluorophores Photophysics Data

Fluorophore Abs or Ex max (nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Acridine orange 271 520 27000 020 5

Alexa Fluor 430 431 541 16000 055 9

Alexa Fluor 488 495 519 71000 094 67

Alexa Fluor 532 532 553 81000 080 65

Alexa Fluor 546 556 573 104000 096 100

Alexa Fluor 568 578 603 91300 075 69

Alexa Fluor 594 590 617 73000 064 47

Allophycocyanin (APC) 650 660 700000 068 476

Atto 390 390 479 24000 090 22

Atto 425 436 484 45000 065 29

Atto 430LS 433 547 32000 065 21

Atto 465 453 508 75000 075 56

Atto 490LS 496 661 40000 030 12

Atto 520 525 547 105000 095 100

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 17: McNamara 20161006 revised draft tables for CPHG Light ...

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httpwwwprior-uscom Profusa Inc - Lumee tissue-integrated biosensors scaffolds httpprofusacomtechnology Reindeer Graphics Inc ndash OptiPix Fovea Pro 9plugins for Adobe Photoshop 6 and CS series) httpwwwreindeergraphicscom Renishaw - StreamLine fast chemical imaging Raman spectroscopy httpwwwrenishawcomenstreamline-generate-chemical-images-rapidly--9449 httpwwwrenishawcomenraman-spectroscopy--6150 Sanford Burnham Prebys ndash High Content Screening httpwwwsbpdiscoveryorgtechnologysrPagesLaJolla_HighContentScreeningaspx ScopeM - Scientific Center for Optical and Electron Microscopy - ETH Zurich httpwwwscopemethzch SiriusXT - soft X-ray tomography (SXT) microscope (CT scan hydrated cell) httpsiriusxtcom SpectraGenetics - Fluorogen Activating Peptides (FAPs) new genetically encoded ldquobinaryrdquo reporters httpspectrageneticscomproductsvectors-for-expressing-fluorogen-activating-proteinsfap-technology-overview Spirochrome - Silicon Rhodamine (SiR) and other fluorescent reagents probes for bioimaging httpspirochromecom Stanford Photonics Inc httpwwwstanfordphotonicscom httpwwwstanfordphotonicscomLife20SciencesLifeScihtm

Stream Technologies Inc ndash ColorFlow lens (multi-wavelength emission onto a camera) httpwwwstreamtechinccomproducts Sutter Instrument Company httpwwwsuttercom httpwwwsuttercomMICROSCOPESindexhtml httpwwwsuttercomIMAGINGindexhtml SVI Huygens ndash Professional (general image analysis) deconvolution NVidia GPU deconvolution httpssvinlHuygensProfessional httpssvinlHuygensDeconvolution httpssvinlHuygensGPU Sysmex Partex ndash CyScope httpwwwsysmex-parteccomproductsmicroscopyhtml httpwwwsysmex-parteccomproductsprdouct-detailviewcyscopeR-malaria-3238html Technical Instruments httpwwwtechinstcomproductsphp TESCAN Brno sro - Tescan Q-PHASE multimodal holographic quantitative phase imaging system (QPi) optional fluorescence httpwwwtescancomenproductsq-phaseq-phase httpq-phasetescancom httpq-phasetescancomindexphptechnologyspecifications Ted Pella Inc ndash specialty light microscopy and electron microscopy supplies httpswwwtedpellacom Texas Instruments ndash DLP 4100 development kit (digital light processingrsquo DMD digital micromirror device) httpwwwticomtooldlpd4x00kit

ThorLabs ndash iCyte imaging cytometer multiphoton confocal EnVista digital slide scanning microscopes httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7473 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7494 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=5696 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=6570 TIRF Labs lightguide TIRF prism TIRF TIRF-Electrochemistry httpwwwtirf-labscom httpwwwtirf-labscomtechnologieshtml TissueVision - Serial Two Photon Tomography (image volume ablate imaged volume with multiphoton laser repeat) httpwwwtissuevisioncomtechnology Tokai Hit - stage top incubator httpwwwtokaihitcomenglishproduct_guidanceoptionhtml TopoNomos Ltd ndash Toponome Imaging Cycler ndash immunofluorescence (100plex) httpwwwtoposnomoscomtechnologyhtml Ultivue Inc ndash DNA-PAINT ndash reagents data processing service httpwwwultivuecom httpwwwultivuecomproducts UMech Technologies ndash Cytovar HCS up to 16 excitation wavelengths httpcloudumechcomproducts httpcloudumechcomproductsmodelC16 Visitech ndash vt-iSIM instant super-resolution microscopy up to 1000 frames per second confocal scanners and light engines httpwwwvisitechcoukvt-isimhtml httpwwwvisitechcoukproductshtml Visitron Systems GmbH - high speed imaging systems httpwwwvisitronde Visualsonics (Fujifilm) - photoacoustic imaging httpwwwvisualsonicscomproductstechnology-overview Wicked Lasers httpwwwwickedlaserscom httpwwwwickedlaserscomarctic WITec Wissenschaftliche Instrumente und Technologie GmbH - imaging systems for FLIM Raman AFM and SNOM analysis httpwitecdeproducts httpwwwwitec-instrumentscom WM Keck Center for Adaptive Optical Microscopy (CfAOM) at UC Santa Cruz httpscfaomsoeucscedu httpcfaoucolickorgpgallery Yokogawa Corp ndash spinning disk confocal scanner live cell imager high content screener confocal quantitative cytometer httpwwwyokogawacomsolutionsproducts-platformslife-science httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-scanner-unit-csu httpwwwyokogawacomsolutionsproducts-platformslife-scienceall-in-one-live-cell-imaging-solution httpwwwyokogawacomsolutionsproducts-platformslife-sciencehigh-throughput-cytological-discovery-system httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-quantitative-image-cytometer Zellkraftwerk (ChipCytometry) ndash immunofluorescence (80plex) httpwwwzellkraftwerkcomProducts2phtml httpwwwzellkraftwerkcomZKWOnephtmlSoftware

httpwwwchipcytometrycomtechnologyphtml Fluorescence Spectra Data and Graphing Sites PubSpectra ndash Excel file data download httpsworksbepresscomgmcnamara9 BD Biosciences ndash spectrum viewer Brilliant fluorophores httpwwwbdbiosciencescomussspectrumviewer httpwwwbdbiosciencescomusapplicationssspectrumguidepage BioLegend ndash spectra analyzer Brilliant Violet fluorophores httpwwwbiolegendcomspectraanalyzer httpwwwbiolegendcombrilliantviolet Chroma Technology httpswwwchromacomspectra-viewer eBioscience (Affymetrix ThermoFisher) ndash fluorPlan ndash a multi-laser spectra viewer httpwwwebiosciencecomresourcesfluorplan-spectra-viewerhtm Spectra Viewer (requires Java) Evrogen ndash Spectrum Viewer httpevrogencomspectra-viewerflashviewerhtml Fluorophoresorg ndash Fluorescent Substances httpwwwfluorophorestugrazatsubstance I Love GFP httpssitesgooglecomsiteilovegfpHomefps Lambert and Thorn UCSF Fluorescent protein properties httpnicucsfeduFPvisualization Leica Microsystem - ldquoFluoScoutrdquo httpwwwleica-microsystemscomfluoscout

Molecular Probes Invitrogen Thermo Fisher ndash Fluorescence SpectraViewer httpwwwthermofishercomusenhomelife-sciencecell-analysislabeling-chemistryfluorescence-spectraviewerhtml httpsitunesapplecomusappfluorescence-spectraviewerid421031826 (iTunes App) Nightsea - Compendium of spectra web sites httpwwwnightseacomsfa-sharingfluorescence-spectra-viewers Omega Optical ldquoCurvomatricrdquo httpswwwomegafilterscomcurvomatic

PhotoChemCAD 20 (Jonathan S Lindsey) dye spectra database and chemistry calculator NIRvana Sciences httpwwwphotochemcadcom httpnirvanasciencescompage_id=3088 UCSF (Lambert Thorn 2016) - Fluorescent protein properties httpnicucsfeduFPvisualization University of Arizona - Fluorescent Spectra Database httpwwwspectraarizonaedu Semrock - Searchlight httpssearchlightsemrockcom Spectroscopy Ninja ndash links to spectral and fluorescence data Spekwin32 spectroscopy software httpwwweffemm2deinfoinfo_specdatahtml

httpwwweffemm2deindexhtml Zeiss ndash interactive fluorescence dye and filter database overview dyes overview filter sets httpswwwmicro-shopzeisscoms=50479761ad21e5ampl=enampp=usampf=fampa=i httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=d httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=f Researcher Labs Alby Diaspro ndash IIT httpwwwlambsitindexphppage=People Alice Ting ndash MIT httpwwwtinglaborgresearch Allen Institute for Brain Science httpwwwalleninstituteorgwhat-we-dobrain-science Allen Institute for Cell Science httpwwwalleninstituteorgwhat-we-docell-science Amina Qutub - Rice University - How are human cells designed lab httpsqutublaborgqutub-lab Amy Herr UC Berkeley ndash Single cell Westerns httpherrlabberkeleyedu Amy Palmer ndash UC Boulder httpspalmerlabcoloradoedu Andrew York ndash Calico Life Sciences httpswwwcalicolabscomteam-memberandrew-york Anne Carpenter ndash Broad Institute CellProfiler httpspersonalbroadinstituteorganne Arjun Raj UPenn single molecule RNA FISH quantitative understanding cellular functions httprajlabseasupenneduindexhtml httpwwwpopscicomsciencearticle2013-09arjun-raj Atsuko Miyawaki - Laboratory for Cell Function Dynamics (CFDS) Fucci2 fluorescent proteins cell cycle indicator httpwwwbrainrikenjpenfacultydetails30 httpcfdsbrainrikenjp httpcfdsbrainrikenjpFuccihtml Aydogan Ozcan - UCLA - new imaging and sensing architectures httpinnovateeeuclaeduwelcomehtml httpwwwhhmiorgscientistsaydogan-ozcan Badri Roysam - UH - FARSIGHT Toolkit httpwwweeuhedufacultyroysam httpwwwfarsight-toolkitorgwikiMain_Page Brian J Ford ndash microscopist and popularizer httpsuklinkedincominprofbrianjford Carolyn Larabell ndashNational Center for X-ray Tomography (LBNL) UCSF httpncxtlblgovq=carolyn httpprofilesucsfeducarolynlarabell Clare Waterman ndash NHLBI NIH

httpswwwnhlbinihgovresearchintramuralresearcherspiwaterman-clare Dana Peer - Columbia University - Computational Systems Biology viSNE and more software httpwwwc2b2columbiaedudanapeerlabhtml httpwwwc2b2columbiaedudanapeerlabhtmlcythtml David Mayerich - UH - STIM Laboratory Scalable Tissue Imaging and Modeling httpwwweeuhedufacultymayerich httpstimeeuhedu David Piston WUSTL httpwwwcellbiologywustledufacultytenureddavid-w-piston-phd Diane Lidke and Keith Lidke - University of New Mexico httppathologyunmeduresearchfaculty-laboratoriesthe-lidke-laboratoryindexhtml httppanda3physunmedu~klidke Donna Arndt-Jovin and Thomas Jovin - Max Planck Institute for Biophysical Chemistry Laboratory of Cellular Dynamics httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsDonnaArdndt-JovinResearchAreasAndProjects httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsChairmanThomasJovinResearchAreasAndProjects Ed Boyden ndash MIT Media Lab ndash expansion microscopy (ExM) optogenetics httpsyntheticneurobiologyorg httpsyntheticneurobiologyorgprotocols httpsyntheticneurobiologyorgpublications httpwwwtedcomtalksed_boyden_baby_diapers_inspired_this_new_way_to_study_the_brain httpwwwextbiocombuycell Elizabeth Blackburn ndash Salk Institute - Telomeres httpswwwsalkeduscientistelizabeth-blackburn httpsenwikipediaorgwikiElizabeth_Blackburn httpswwwnobelprizeorgnobel_prizesmedicinelaureates2009blackburn-factshtml Elizabeth Hillman - Columbia university - SCAPE (Swept Confocally-Aligned Planar Excitation) high speed 3D microscopy DyCE (dynamic contrast enhancement to image and segment small animal organs live) Neuroimaging amp Neurovascular Coupling httporionbmecolumbiaedu~hillmanInstrumentationhtml httporionbmecolumbiaedu~hillmanSCAPEhtml httporionbmecolumbiaedu~hillmanMolecularhtml httporionbmecolumbiaedu~hillmanBrain_Imaginghtml Eric Betzig ndash UCSF (moving from HHMI Janelia Farm in 2016) httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014betzig-factshtml Eva Sevick-Muraca ndash UT Health Science Center at Houston molecular imaging clinical NIR fluoresceince imaging httpswwwutheduimmprofilehtmid=1005459 httpswwwutheduimmcentersmolecular-imaginghtm Evelin Schrock - Technische Universitaumlt Dresden spectral karyotyping cytogenetics httpswwwresearchgatenetprofileEvelin_Schrock Garry Nolan Stanford University ndash Mass cytometry MIBI-ToF high throughput imaging mass cytometry (42plex) httpwebstanfordedugroupnolanresourceshtml httpwebstanfordedugroupnolantechnologieshtml George McNamara ndash Cell Morphometry (41) Figure 1 right top two panels (55) The Chase (2016 temporal area maps lsquodynamic morphologyrsquo) (76) newsletter series on ldquoThe Chaserdquo (73) direct Vimeo movie of ldquoThe Chaserdquo Tiki_Goddess linkedin 10+plex blog httpsworksbepresscomgmcnamara41 httpsworksbepresscomgmcnamara55 httpsworksbepresscomgmcnamara76

httpsworksbepresscomgmcnamara73 httpsvimeocom175151196 httphomeearthlinknet~tiki_goddess httpswwwlinkedincomingeorgemcnamara httpswwwlinkedincompulsebd-biosciences-listed-tandems-horizon-brilliant-violets-mcnamara Gillian Griffiths - University of Cambridge - T-cell immunological synapse httpwwwcimrcamacukresearchprincipal-investigatorsprincipal-investigators-a-hgriffiths Hari Shroff NIBIB NIH httpswwwnibibnihgovlabs-at-nibibsection-high-resolution-optical-imaging-hroi HHMI Janelia Farm Research Campus (JFRC) - Advanced Imaging Center Open Science httpswwwjaneliaorgopen-scienceadvanced-imaging-center-aic httpswwwjaneliaorgopen-science Jeanne Lawrence University of Massachussetts Medical School httpwwwumassmededucellbiolabslawrencepersonnelprincipal-investigator Jennifer Lippincott-Schwartz ndash HHMI Janelia Farm httpswwwjaneliaorgpeoplejennifer-lippincott-schwartz Jin Zhang ndash UCSD httpprofilesucsdedujinzhang Joe DeRisi - UCSF - 3D printable lab stuff httpderisilabucsfeduindexphppage=3D John Russ Chris Russ Fovea Pro plugins for Adobe Photoshop httpwwwdrjohnrusscomindexhtml httpwwwdrjohnrusscombookshtml httpwwwreindeergraphicscomfoveaprotutorialhtml Julie Theriot httpcmgmstanfordedutheriot Karl Deisseroth ndash Stanford University ndash CLARITY optical tissue clearing Optogenetics httpclarityresourcecenterorg httpwebstanfordedugroupdlaboptogeneticsindexhtml Karsten Koumlnig (Koenig) - Saarland University and JenLab GmbH - biophotonics httpwwwbltuni-saarlanddeindex_ehtm httpwwwjenlabde httpwwwthelastescape-filmcom Karsten Rodenacker ndash image measurements httpkaro03bplacednetkaroMeMisc_WWWpdfMicrosoftWord-EQUAPATpdf Kevin Eliceiri ndash UW-Madison Open Source Photonics and Software Laboratory for Optical and Computational Instrumentation (LOCI) wwwlociwiscedu Klaus Kemp ndash Microlife Services ndash diatoms and other prepared microscope slides httpwwwdiatomscouk Kurt Thorn UCSF httpthornlabucsfedu httpsnicucsfedublog httpnicucsfeduFPvisualization httpgigapancomgigapans163370 Lihong Wang - WUSTL - Optical Imaging Laboratory photoacoustic tomography

httpoilabseaswustledu httpoilabseaswustleduresearch_0html Loren Looger - HHMI JFRC - iGluSnFr fluorescent protein biosensor httpswwwjaneliaorglablooger-lab Mary-Lou Pardue ndash MIT (first ever in situ hybridization with J Gall) httpsbiologymitedupeoplemary_lou_pardue httpsenwikipediaorgwikiMary-Lou_Pardue Nancy Allbritton - UNC - Chemical cytometry microraft arrays organ-on-a-chip httpswwwbmencsueduindexphpcomponentcomprofileruserprofilenlallbri httpwwwbmeuncedulabsallbritton Navin Varadarajan - UH - single-cell Lab httpwwwcheeuhedufacultyvaradarajan httpsinglecellcheeuheducontacthtml Nicholas Shaner - Scintillon Institute - mNeonGreen httpwwwscintillonorgshaner_lab Rebecca Richards-Kortum httpbioengineeringriceedufacultyrebecca_richards-kortumaspx Robert Campbell - Fluorescent proteins optogenetic proteins httpcampbellwebchemualbertaca httpcampbellwebchemualbertacaprojects-2 Robert Murphy ndash Cell measurements web services httpmurphylabwebcmueduservices Sabine Mai - University of Manitoba - Genomic Centre for Cancer Research and Diagnosis (GCCRD) - httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBPlatformsGCCRDhtml httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBScientistsMaiAwardshtml Sally Ward and Raimund Ober - Texas AampM University - httpwwwwardoberlabcom Simon Watkins - U Pittsburgh Center for Biologic Imaging httpwwwcbppittedufacultywatkinshtml httpwwwcbppittedufacultylabwatkinshtml httpwwwcbipittedu Stefan Hell ndash Deparment Hell NanoBiopohotonics httpwwwmpibpcmpgdehell httpsenwikipediaorgwikiStefan_Hell httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014hell-factshtml Sunney Xie Harvard httpsbernsteinharvardedu Susan Cox ndash 3B microscopy httpwwwcoxphysicscomindexhtml httpwwwcoxphysicscom3b Radim Chmeliacutek - Center for innovative microscopy Experimental biophotonics group httpswwwceiteceuceitec-butexperimental-biophotonicsrg3 httpwwwbiophotczhome Taekjip Ha ndash Johns Hopkins University ndash single molecules httphamedjhmiedu

Thomas Ried ndash NCI NIH SKYM-FISH and CGH Database httpsccrcancergovGenetics-Branchthomas-ried httpsccrcancergovGenetics-Branchthomas-riedqt-staff_profile_tabs=9qt-staff_profile_tabs ftpftpncbinlmnihgovsky-cghDATA httpswwwncbinlmnihgovdbvar Viviana Gradinaru ndash CalTech ndash CLARITYPACT Optogenetics httpwwwbbecaltecheducontentviviana-gradinaru httpglabcaltechedu Vladislav Verkhusha - near infrared fluorescent proteins httpwwweinsteinyuedulabsvlad-verkhushadefaultaspx httpwwweinsteinyueduresearchfacilitiesfluorescent WE Moerner ndash Stanford University httpwebstanfordedugroupmoerner Willard Wiggans ndash micro gallery httpwwwwillard-wigancomgallery Wolf Frommer ndash Molecular sensors httpbiosensordpbcarnegiescienceedu (fluorescent protein biosensors table) Xiaowei Zhuang = Harvard httpzhuangharvardedu Yuval Garini - Bar-Ilan University - Nano-Bio-Photonics laboratory httpgarinilabbiuacil Microscopy Magazines Imaging amp Microscopy httpwwwimaging-gitcommagazine Laser Focus World httpwwwlaserfocusworldcomindexhtml Microscopy amp Analysis httpwwwmicroscopy-analysiscom Microscopy Today httpwwwmicroscopy-todaycom Microscopy-UK httpwwwmicroscopy-ukorguk Photonics Spectra Biophotonics httpwwwphotonicscomPublicationsaspx The Microscope Journal httpmcriorgv72the-microscope-journal RMS Infocus Magazine httpwwwrmsorgukstudy-readinfocus-magazinehtml Nobel Prizes in Light Microscopy and Related Fields Chemistry 1925 colloids (light sheet) Zsigmondy (Siedentopf Zsigmondy 1902) httpswwwnobelprizeorgnobel_prizeschemistrylaureates1925

Chemistry 2000 conductive polymers Heeger MacDiarmid Shirakawa (Brilliant Violets Ultraviolets Blues) httpwwwnobelprizeorgnobel_prizeschemistrylaureates2000 Chemistry 2008 green fluorescent protein GFP Shimomura Chalfie Tsien httpwwwnobelprizeorgnobel_prizeschemistrylaureates2008 Chemistry 2014 super-resolved fluorescence microscopy Betzig Hell Moerner httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014 Physics 1953 Phase Contrast Zernike httpswwwnobelprizeorgnobel_prizesphysicslaureates1953 Physics 2009 invention of an imaging semiconductor circuit ndash the CCD sensor Kao Boyle Smith httpwwwnobelprizeorgnobel_prizesphysicslaureates2009 Physics 2014 efficient blue light emitting diodes Akasaki Amano Nakamura httpwwwnobelprizeorgnobel_prizesphysicslaureates2014 Physiology or Medicine 2006 Fire and Mello RNA interference ndash gene silencing by double stranded RNA httpwwwnobelprizeorgnobel_prizesmedicinelaureates2006 Physiology or Medicine 2006 Capecchi Evans Smithies specific gene modifications in mice by the use of embryonic stem cells httpwwwnobelprizeorgnobel_prizesmedicinelaureates2007 Physiology or Medicine 2009 Blackburn Greider Szostak how chromosomes are protected by telomeres and telomerase httpwwwnobelprizeorgnobel_prizesmedicinelaureates2009 Physiology or Medicine 2012 Gurdon Yamamanka matured cells can be reprogrammed to become pluripotent httpwwwnobelprizeorgnobel_prizesmedicinelaureates2012

Table 442 Fluorophores Photophysics Data

Fluorophore Abs or Ex max (nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Acridine orange 271 520 27000 020 5

Alexa Fluor 430 431 541 16000 055 9

Alexa Fluor 488 495 519 71000 094 67

Alexa Fluor 532 532 553 81000 080 65

Alexa Fluor 546 556 573 104000 096 100

Alexa Fluor 568 578 603 91300 075 69

Alexa Fluor 594 590 617 73000 064 47

Allophycocyanin (APC) 650 660 700000 068 476

Atto 390 390 479 24000 090 22

Atto 425 436 484 45000 065 29

Atto 430LS 433 547 32000 065 21

Atto 465 453 508 75000 075 56

Atto 490LS 496 661 40000 030 12

Atto 520 525 547 105000 095 100

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 18: McNamara 20161006 revised draft tables for CPHG Light ...

httpwwwprior-uscom Profusa Inc - Lumee tissue-integrated biosensors scaffolds httpprofusacomtechnology Reindeer Graphics Inc ndash OptiPix Fovea Pro 9plugins for Adobe Photoshop 6 and CS series) httpwwwreindeergraphicscom Renishaw - StreamLine fast chemical imaging Raman spectroscopy httpwwwrenishawcomenstreamline-generate-chemical-images-rapidly--9449 httpwwwrenishawcomenraman-spectroscopy--6150 Sanford Burnham Prebys ndash High Content Screening httpwwwsbpdiscoveryorgtechnologysrPagesLaJolla_HighContentScreeningaspx ScopeM - Scientific Center for Optical and Electron Microscopy - ETH Zurich httpwwwscopemethzch SiriusXT - soft X-ray tomography (SXT) microscope (CT scan hydrated cell) httpsiriusxtcom SpectraGenetics - Fluorogen Activating Peptides (FAPs) new genetically encoded ldquobinaryrdquo reporters httpspectrageneticscomproductsvectors-for-expressing-fluorogen-activating-proteinsfap-technology-overview Spirochrome - Silicon Rhodamine (SiR) and other fluorescent reagents probes for bioimaging httpspirochromecom Stanford Photonics Inc httpwwwstanfordphotonicscom httpwwwstanfordphotonicscomLife20SciencesLifeScihtm

Stream Technologies Inc ndash ColorFlow lens (multi-wavelength emission onto a camera) httpwwwstreamtechinccomproducts Sutter Instrument Company httpwwwsuttercom httpwwwsuttercomMICROSCOPESindexhtml httpwwwsuttercomIMAGINGindexhtml SVI Huygens ndash Professional (general image analysis) deconvolution NVidia GPU deconvolution httpssvinlHuygensProfessional httpssvinlHuygensDeconvolution httpssvinlHuygensGPU Sysmex Partex ndash CyScope httpwwwsysmex-parteccomproductsmicroscopyhtml httpwwwsysmex-parteccomproductsprdouct-detailviewcyscopeR-malaria-3238html Technical Instruments httpwwwtechinstcomproductsphp TESCAN Brno sro - Tescan Q-PHASE multimodal holographic quantitative phase imaging system (QPi) optional fluorescence httpwwwtescancomenproductsq-phaseq-phase httpq-phasetescancom httpq-phasetescancomindexphptechnologyspecifications Ted Pella Inc ndash specialty light microscopy and electron microscopy supplies httpswwwtedpellacom Texas Instruments ndash DLP 4100 development kit (digital light processingrsquo DMD digital micromirror device) httpwwwticomtooldlpd4x00kit

ThorLabs ndash iCyte imaging cytometer multiphoton confocal EnVista digital slide scanning microscopes httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7473 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7494 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=5696 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=6570 TIRF Labs lightguide TIRF prism TIRF TIRF-Electrochemistry httpwwwtirf-labscom httpwwwtirf-labscomtechnologieshtml TissueVision - Serial Two Photon Tomography (image volume ablate imaged volume with multiphoton laser repeat) httpwwwtissuevisioncomtechnology Tokai Hit - stage top incubator httpwwwtokaihitcomenglishproduct_guidanceoptionhtml TopoNomos Ltd ndash Toponome Imaging Cycler ndash immunofluorescence (100plex) httpwwwtoposnomoscomtechnologyhtml Ultivue Inc ndash DNA-PAINT ndash reagents data processing service httpwwwultivuecom httpwwwultivuecomproducts UMech Technologies ndash Cytovar HCS up to 16 excitation wavelengths httpcloudumechcomproducts httpcloudumechcomproductsmodelC16 Visitech ndash vt-iSIM instant super-resolution microscopy up to 1000 frames per second confocal scanners and light engines httpwwwvisitechcoukvt-isimhtml httpwwwvisitechcoukproductshtml Visitron Systems GmbH - high speed imaging systems httpwwwvisitronde Visualsonics (Fujifilm) - photoacoustic imaging httpwwwvisualsonicscomproductstechnology-overview Wicked Lasers httpwwwwickedlaserscom httpwwwwickedlaserscomarctic WITec Wissenschaftliche Instrumente und Technologie GmbH - imaging systems for FLIM Raman AFM and SNOM analysis httpwitecdeproducts httpwwwwitec-instrumentscom WM Keck Center for Adaptive Optical Microscopy (CfAOM) at UC Santa Cruz httpscfaomsoeucscedu httpcfaoucolickorgpgallery Yokogawa Corp ndash spinning disk confocal scanner live cell imager high content screener confocal quantitative cytometer httpwwwyokogawacomsolutionsproducts-platformslife-science httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-scanner-unit-csu httpwwwyokogawacomsolutionsproducts-platformslife-scienceall-in-one-live-cell-imaging-solution httpwwwyokogawacomsolutionsproducts-platformslife-sciencehigh-throughput-cytological-discovery-system httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-quantitative-image-cytometer Zellkraftwerk (ChipCytometry) ndash immunofluorescence (80plex) httpwwwzellkraftwerkcomProducts2phtml httpwwwzellkraftwerkcomZKWOnephtmlSoftware

httpwwwchipcytometrycomtechnologyphtml Fluorescence Spectra Data and Graphing Sites PubSpectra ndash Excel file data download httpsworksbepresscomgmcnamara9 BD Biosciences ndash spectrum viewer Brilliant fluorophores httpwwwbdbiosciencescomussspectrumviewer httpwwwbdbiosciencescomusapplicationssspectrumguidepage BioLegend ndash spectra analyzer Brilliant Violet fluorophores httpwwwbiolegendcomspectraanalyzer httpwwwbiolegendcombrilliantviolet Chroma Technology httpswwwchromacomspectra-viewer eBioscience (Affymetrix ThermoFisher) ndash fluorPlan ndash a multi-laser spectra viewer httpwwwebiosciencecomresourcesfluorplan-spectra-viewerhtm Spectra Viewer (requires Java) Evrogen ndash Spectrum Viewer httpevrogencomspectra-viewerflashviewerhtml Fluorophoresorg ndash Fluorescent Substances httpwwwfluorophorestugrazatsubstance I Love GFP httpssitesgooglecomsiteilovegfpHomefps Lambert and Thorn UCSF Fluorescent protein properties httpnicucsfeduFPvisualization Leica Microsystem - ldquoFluoScoutrdquo httpwwwleica-microsystemscomfluoscout

Molecular Probes Invitrogen Thermo Fisher ndash Fluorescence SpectraViewer httpwwwthermofishercomusenhomelife-sciencecell-analysislabeling-chemistryfluorescence-spectraviewerhtml httpsitunesapplecomusappfluorescence-spectraviewerid421031826 (iTunes App) Nightsea - Compendium of spectra web sites httpwwwnightseacomsfa-sharingfluorescence-spectra-viewers Omega Optical ldquoCurvomatricrdquo httpswwwomegafilterscomcurvomatic

PhotoChemCAD 20 (Jonathan S Lindsey) dye spectra database and chemistry calculator NIRvana Sciences httpwwwphotochemcadcom httpnirvanasciencescompage_id=3088 UCSF (Lambert Thorn 2016) - Fluorescent protein properties httpnicucsfeduFPvisualization University of Arizona - Fluorescent Spectra Database httpwwwspectraarizonaedu Semrock - Searchlight httpssearchlightsemrockcom Spectroscopy Ninja ndash links to spectral and fluorescence data Spekwin32 spectroscopy software httpwwweffemm2deinfoinfo_specdatahtml

httpwwweffemm2deindexhtml Zeiss ndash interactive fluorescence dye and filter database overview dyes overview filter sets httpswwwmicro-shopzeisscoms=50479761ad21e5ampl=enampp=usampf=fampa=i httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=d httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=f Researcher Labs Alby Diaspro ndash IIT httpwwwlambsitindexphppage=People Alice Ting ndash MIT httpwwwtinglaborgresearch Allen Institute for Brain Science httpwwwalleninstituteorgwhat-we-dobrain-science Allen Institute for Cell Science httpwwwalleninstituteorgwhat-we-docell-science Amina Qutub - Rice University - How are human cells designed lab httpsqutublaborgqutub-lab Amy Herr UC Berkeley ndash Single cell Westerns httpherrlabberkeleyedu Amy Palmer ndash UC Boulder httpspalmerlabcoloradoedu Andrew York ndash Calico Life Sciences httpswwwcalicolabscomteam-memberandrew-york Anne Carpenter ndash Broad Institute CellProfiler httpspersonalbroadinstituteorganne Arjun Raj UPenn single molecule RNA FISH quantitative understanding cellular functions httprajlabseasupenneduindexhtml httpwwwpopscicomsciencearticle2013-09arjun-raj Atsuko Miyawaki - Laboratory for Cell Function Dynamics (CFDS) Fucci2 fluorescent proteins cell cycle indicator httpwwwbrainrikenjpenfacultydetails30 httpcfdsbrainrikenjp httpcfdsbrainrikenjpFuccihtml Aydogan Ozcan - UCLA - new imaging and sensing architectures httpinnovateeeuclaeduwelcomehtml httpwwwhhmiorgscientistsaydogan-ozcan Badri Roysam - UH - FARSIGHT Toolkit httpwwweeuhedufacultyroysam httpwwwfarsight-toolkitorgwikiMain_Page Brian J Ford ndash microscopist and popularizer httpsuklinkedincominprofbrianjford Carolyn Larabell ndashNational Center for X-ray Tomography (LBNL) UCSF httpncxtlblgovq=carolyn httpprofilesucsfeducarolynlarabell Clare Waterman ndash NHLBI NIH

httpswwwnhlbinihgovresearchintramuralresearcherspiwaterman-clare Dana Peer - Columbia University - Computational Systems Biology viSNE and more software httpwwwc2b2columbiaedudanapeerlabhtml httpwwwc2b2columbiaedudanapeerlabhtmlcythtml David Mayerich - UH - STIM Laboratory Scalable Tissue Imaging and Modeling httpwwweeuhedufacultymayerich httpstimeeuhedu David Piston WUSTL httpwwwcellbiologywustledufacultytenureddavid-w-piston-phd Diane Lidke and Keith Lidke - University of New Mexico httppathologyunmeduresearchfaculty-laboratoriesthe-lidke-laboratoryindexhtml httppanda3physunmedu~klidke Donna Arndt-Jovin and Thomas Jovin - Max Planck Institute for Biophysical Chemistry Laboratory of Cellular Dynamics httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsDonnaArdndt-JovinResearchAreasAndProjects httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsChairmanThomasJovinResearchAreasAndProjects Ed Boyden ndash MIT Media Lab ndash expansion microscopy (ExM) optogenetics httpsyntheticneurobiologyorg httpsyntheticneurobiologyorgprotocols httpsyntheticneurobiologyorgpublications httpwwwtedcomtalksed_boyden_baby_diapers_inspired_this_new_way_to_study_the_brain httpwwwextbiocombuycell Elizabeth Blackburn ndash Salk Institute - Telomeres httpswwwsalkeduscientistelizabeth-blackburn httpsenwikipediaorgwikiElizabeth_Blackburn httpswwwnobelprizeorgnobel_prizesmedicinelaureates2009blackburn-factshtml Elizabeth Hillman - Columbia university - SCAPE (Swept Confocally-Aligned Planar Excitation) high speed 3D microscopy DyCE (dynamic contrast enhancement to image and segment small animal organs live) Neuroimaging amp Neurovascular Coupling httporionbmecolumbiaedu~hillmanInstrumentationhtml httporionbmecolumbiaedu~hillmanSCAPEhtml httporionbmecolumbiaedu~hillmanMolecularhtml httporionbmecolumbiaedu~hillmanBrain_Imaginghtml Eric Betzig ndash UCSF (moving from HHMI Janelia Farm in 2016) httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014betzig-factshtml Eva Sevick-Muraca ndash UT Health Science Center at Houston molecular imaging clinical NIR fluoresceince imaging httpswwwutheduimmprofilehtmid=1005459 httpswwwutheduimmcentersmolecular-imaginghtm Evelin Schrock - Technische Universitaumlt Dresden spectral karyotyping cytogenetics httpswwwresearchgatenetprofileEvelin_Schrock Garry Nolan Stanford University ndash Mass cytometry MIBI-ToF high throughput imaging mass cytometry (42plex) httpwebstanfordedugroupnolanresourceshtml httpwebstanfordedugroupnolantechnologieshtml George McNamara ndash Cell Morphometry (41) Figure 1 right top two panels (55) The Chase (2016 temporal area maps lsquodynamic morphologyrsquo) (76) newsletter series on ldquoThe Chaserdquo (73) direct Vimeo movie of ldquoThe Chaserdquo Tiki_Goddess linkedin 10+plex blog httpsworksbepresscomgmcnamara41 httpsworksbepresscomgmcnamara55 httpsworksbepresscomgmcnamara76

httpsworksbepresscomgmcnamara73 httpsvimeocom175151196 httphomeearthlinknet~tiki_goddess httpswwwlinkedincomingeorgemcnamara httpswwwlinkedincompulsebd-biosciences-listed-tandems-horizon-brilliant-violets-mcnamara Gillian Griffiths - University of Cambridge - T-cell immunological synapse httpwwwcimrcamacukresearchprincipal-investigatorsprincipal-investigators-a-hgriffiths Hari Shroff NIBIB NIH httpswwwnibibnihgovlabs-at-nibibsection-high-resolution-optical-imaging-hroi HHMI Janelia Farm Research Campus (JFRC) - Advanced Imaging Center Open Science httpswwwjaneliaorgopen-scienceadvanced-imaging-center-aic httpswwwjaneliaorgopen-science Jeanne Lawrence University of Massachussetts Medical School httpwwwumassmededucellbiolabslawrencepersonnelprincipal-investigator Jennifer Lippincott-Schwartz ndash HHMI Janelia Farm httpswwwjaneliaorgpeoplejennifer-lippincott-schwartz Jin Zhang ndash UCSD httpprofilesucsdedujinzhang Joe DeRisi - UCSF - 3D printable lab stuff httpderisilabucsfeduindexphppage=3D John Russ Chris Russ Fovea Pro plugins for Adobe Photoshop httpwwwdrjohnrusscomindexhtml httpwwwdrjohnrusscombookshtml httpwwwreindeergraphicscomfoveaprotutorialhtml Julie Theriot httpcmgmstanfordedutheriot Karl Deisseroth ndash Stanford University ndash CLARITY optical tissue clearing Optogenetics httpclarityresourcecenterorg httpwebstanfordedugroupdlaboptogeneticsindexhtml Karsten Koumlnig (Koenig) - Saarland University and JenLab GmbH - biophotonics httpwwwbltuni-saarlanddeindex_ehtm httpwwwjenlabde httpwwwthelastescape-filmcom Karsten Rodenacker ndash image measurements httpkaro03bplacednetkaroMeMisc_WWWpdfMicrosoftWord-EQUAPATpdf Kevin Eliceiri ndash UW-Madison Open Source Photonics and Software Laboratory for Optical and Computational Instrumentation (LOCI) wwwlociwiscedu Klaus Kemp ndash Microlife Services ndash diatoms and other prepared microscope slides httpwwwdiatomscouk Kurt Thorn UCSF httpthornlabucsfedu httpsnicucsfedublog httpnicucsfeduFPvisualization httpgigapancomgigapans163370 Lihong Wang - WUSTL - Optical Imaging Laboratory photoacoustic tomography

httpoilabseaswustledu httpoilabseaswustleduresearch_0html Loren Looger - HHMI JFRC - iGluSnFr fluorescent protein biosensor httpswwwjaneliaorglablooger-lab Mary-Lou Pardue ndash MIT (first ever in situ hybridization with J Gall) httpsbiologymitedupeoplemary_lou_pardue httpsenwikipediaorgwikiMary-Lou_Pardue Nancy Allbritton - UNC - Chemical cytometry microraft arrays organ-on-a-chip httpswwwbmencsueduindexphpcomponentcomprofileruserprofilenlallbri httpwwwbmeuncedulabsallbritton Navin Varadarajan - UH - single-cell Lab httpwwwcheeuhedufacultyvaradarajan httpsinglecellcheeuheducontacthtml Nicholas Shaner - Scintillon Institute - mNeonGreen httpwwwscintillonorgshaner_lab Rebecca Richards-Kortum httpbioengineeringriceedufacultyrebecca_richards-kortumaspx Robert Campbell - Fluorescent proteins optogenetic proteins httpcampbellwebchemualbertaca httpcampbellwebchemualbertacaprojects-2 Robert Murphy ndash Cell measurements web services httpmurphylabwebcmueduservices Sabine Mai - University of Manitoba - Genomic Centre for Cancer Research and Diagnosis (GCCRD) - httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBPlatformsGCCRDhtml httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBScientistsMaiAwardshtml Sally Ward and Raimund Ober - Texas AampM University - httpwwwwardoberlabcom Simon Watkins - U Pittsburgh Center for Biologic Imaging httpwwwcbppittedufacultywatkinshtml httpwwwcbppittedufacultylabwatkinshtml httpwwwcbipittedu Stefan Hell ndash Deparment Hell NanoBiopohotonics httpwwwmpibpcmpgdehell httpsenwikipediaorgwikiStefan_Hell httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014hell-factshtml Sunney Xie Harvard httpsbernsteinharvardedu Susan Cox ndash 3B microscopy httpwwwcoxphysicscomindexhtml httpwwwcoxphysicscom3b Radim Chmeliacutek - Center for innovative microscopy Experimental biophotonics group httpswwwceiteceuceitec-butexperimental-biophotonicsrg3 httpwwwbiophotczhome Taekjip Ha ndash Johns Hopkins University ndash single molecules httphamedjhmiedu

Thomas Ried ndash NCI NIH SKYM-FISH and CGH Database httpsccrcancergovGenetics-Branchthomas-ried httpsccrcancergovGenetics-Branchthomas-riedqt-staff_profile_tabs=9qt-staff_profile_tabs ftpftpncbinlmnihgovsky-cghDATA httpswwwncbinlmnihgovdbvar Viviana Gradinaru ndash CalTech ndash CLARITYPACT Optogenetics httpwwwbbecaltecheducontentviviana-gradinaru httpglabcaltechedu Vladislav Verkhusha - near infrared fluorescent proteins httpwwweinsteinyuedulabsvlad-verkhushadefaultaspx httpwwweinsteinyueduresearchfacilitiesfluorescent WE Moerner ndash Stanford University httpwebstanfordedugroupmoerner Willard Wiggans ndash micro gallery httpwwwwillard-wigancomgallery Wolf Frommer ndash Molecular sensors httpbiosensordpbcarnegiescienceedu (fluorescent protein biosensors table) Xiaowei Zhuang = Harvard httpzhuangharvardedu Yuval Garini - Bar-Ilan University - Nano-Bio-Photonics laboratory httpgarinilabbiuacil Microscopy Magazines Imaging amp Microscopy httpwwwimaging-gitcommagazine Laser Focus World httpwwwlaserfocusworldcomindexhtml Microscopy amp Analysis httpwwwmicroscopy-analysiscom Microscopy Today httpwwwmicroscopy-todaycom Microscopy-UK httpwwwmicroscopy-ukorguk Photonics Spectra Biophotonics httpwwwphotonicscomPublicationsaspx The Microscope Journal httpmcriorgv72the-microscope-journal RMS Infocus Magazine httpwwwrmsorgukstudy-readinfocus-magazinehtml Nobel Prizes in Light Microscopy and Related Fields Chemistry 1925 colloids (light sheet) Zsigmondy (Siedentopf Zsigmondy 1902) httpswwwnobelprizeorgnobel_prizeschemistrylaureates1925

Chemistry 2000 conductive polymers Heeger MacDiarmid Shirakawa (Brilliant Violets Ultraviolets Blues) httpwwwnobelprizeorgnobel_prizeschemistrylaureates2000 Chemistry 2008 green fluorescent protein GFP Shimomura Chalfie Tsien httpwwwnobelprizeorgnobel_prizeschemistrylaureates2008 Chemistry 2014 super-resolved fluorescence microscopy Betzig Hell Moerner httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014 Physics 1953 Phase Contrast Zernike httpswwwnobelprizeorgnobel_prizesphysicslaureates1953 Physics 2009 invention of an imaging semiconductor circuit ndash the CCD sensor Kao Boyle Smith httpwwwnobelprizeorgnobel_prizesphysicslaureates2009 Physics 2014 efficient blue light emitting diodes Akasaki Amano Nakamura httpwwwnobelprizeorgnobel_prizesphysicslaureates2014 Physiology or Medicine 2006 Fire and Mello RNA interference ndash gene silencing by double stranded RNA httpwwwnobelprizeorgnobel_prizesmedicinelaureates2006 Physiology or Medicine 2006 Capecchi Evans Smithies specific gene modifications in mice by the use of embryonic stem cells httpwwwnobelprizeorgnobel_prizesmedicinelaureates2007 Physiology or Medicine 2009 Blackburn Greider Szostak how chromosomes are protected by telomeres and telomerase httpwwwnobelprizeorgnobel_prizesmedicinelaureates2009 Physiology or Medicine 2012 Gurdon Yamamanka matured cells can be reprogrammed to become pluripotent httpwwwnobelprizeorgnobel_prizesmedicinelaureates2012

Table 442 Fluorophores Photophysics Data

Fluorophore Abs or Ex max (nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Acridine orange 271 520 27000 020 5

Alexa Fluor 430 431 541 16000 055 9

Alexa Fluor 488 495 519 71000 094 67

Alexa Fluor 532 532 553 81000 080 65

Alexa Fluor 546 556 573 104000 096 100

Alexa Fluor 568 578 603 91300 075 69

Alexa Fluor 594 590 617 73000 064 47

Allophycocyanin (APC) 650 660 700000 068 476

Atto 390 390 479 24000 090 22

Atto 425 436 484 45000 065 29

Atto 430LS 433 547 32000 065 21

Atto 465 453 508 75000 075 56

Atto 490LS 496 661 40000 030 12

Atto 520 525 547 105000 095 100

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 19: McNamara 20161006 revised draft tables for CPHG Light ...

ThorLabs ndash iCyte imaging cytometer multiphoton confocal EnVista digital slide scanning microscopes httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7473 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=7494 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=5696 httpswwwthorlabscomnewgrouppage9cfmobjectgroup_id=6570 TIRF Labs lightguide TIRF prism TIRF TIRF-Electrochemistry httpwwwtirf-labscom httpwwwtirf-labscomtechnologieshtml TissueVision - Serial Two Photon Tomography (image volume ablate imaged volume with multiphoton laser repeat) httpwwwtissuevisioncomtechnology Tokai Hit - stage top incubator httpwwwtokaihitcomenglishproduct_guidanceoptionhtml TopoNomos Ltd ndash Toponome Imaging Cycler ndash immunofluorescence (100plex) httpwwwtoposnomoscomtechnologyhtml Ultivue Inc ndash DNA-PAINT ndash reagents data processing service httpwwwultivuecom httpwwwultivuecomproducts UMech Technologies ndash Cytovar HCS up to 16 excitation wavelengths httpcloudumechcomproducts httpcloudumechcomproductsmodelC16 Visitech ndash vt-iSIM instant super-resolution microscopy up to 1000 frames per second confocal scanners and light engines httpwwwvisitechcoukvt-isimhtml httpwwwvisitechcoukproductshtml Visitron Systems GmbH - high speed imaging systems httpwwwvisitronde Visualsonics (Fujifilm) - photoacoustic imaging httpwwwvisualsonicscomproductstechnology-overview Wicked Lasers httpwwwwickedlaserscom httpwwwwickedlaserscomarctic WITec Wissenschaftliche Instrumente und Technologie GmbH - imaging systems for FLIM Raman AFM and SNOM analysis httpwitecdeproducts httpwwwwitec-instrumentscom WM Keck Center for Adaptive Optical Microscopy (CfAOM) at UC Santa Cruz httpscfaomsoeucscedu httpcfaoucolickorgpgallery Yokogawa Corp ndash spinning disk confocal scanner live cell imager high content screener confocal quantitative cytometer httpwwwyokogawacomsolutionsproducts-platformslife-science httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-scanner-unit-csu httpwwwyokogawacomsolutionsproducts-platformslife-scienceall-in-one-live-cell-imaging-solution httpwwwyokogawacomsolutionsproducts-platformslife-sciencehigh-throughput-cytological-discovery-system httpwwwyokogawacomsolutionsproducts-platformslife-scienceconfocal-quantitative-image-cytometer Zellkraftwerk (ChipCytometry) ndash immunofluorescence (80plex) httpwwwzellkraftwerkcomProducts2phtml httpwwwzellkraftwerkcomZKWOnephtmlSoftware

httpwwwchipcytometrycomtechnologyphtml Fluorescence Spectra Data and Graphing Sites PubSpectra ndash Excel file data download httpsworksbepresscomgmcnamara9 BD Biosciences ndash spectrum viewer Brilliant fluorophores httpwwwbdbiosciencescomussspectrumviewer httpwwwbdbiosciencescomusapplicationssspectrumguidepage BioLegend ndash spectra analyzer Brilliant Violet fluorophores httpwwwbiolegendcomspectraanalyzer httpwwwbiolegendcombrilliantviolet Chroma Technology httpswwwchromacomspectra-viewer eBioscience (Affymetrix ThermoFisher) ndash fluorPlan ndash a multi-laser spectra viewer httpwwwebiosciencecomresourcesfluorplan-spectra-viewerhtm Spectra Viewer (requires Java) Evrogen ndash Spectrum Viewer httpevrogencomspectra-viewerflashviewerhtml Fluorophoresorg ndash Fluorescent Substances httpwwwfluorophorestugrazatsubstance I Love GFP httpssitesgooglecomsiteilovegfpHomefps Lambert and Thorn UCSF Fluorescent protein properties httpnicucsfeduFPvisualization Leica Microsystem - ldquoFluoScoutrdquo httpwwwleica-microsystemscomfluoscout

Molecular Probes Invitrogen Thermo Fisher ndash Fluorescence SpectraViewer httpwwwthermofishercomusenhomelife-sciencecell-analysislabeling-chemistryfluorescence-spectraviewerhtml httpsitunesapplecomusappfluorescence-spectraviewerid421031826 (iTunes App) Nightsea - Compendium of spectra web sites httpwwwnightseacomsfa-sharingfluorescence-spectra-viewers Omega Optical ldquoCurvomatricrdquo httpswwwomegafilterscomcurvomatic

PhotoChemCAD 20 (Jonathan S Lindsey) dye spectra database and chemistry calculator NIRvana Sciences httpwwwphotochemcadcom httpnirvanasciencescompage_id=3088 UCSF (Lambert Thorn 2016) - Fluorescent protein properties httpnicucsfeduFPvisualization University of Arizona - Fluorescent Spectra Database httpwwwspectraarizonaedu Semrock - Searchlight httpssearchlightsemrockcom Spectroscopy Ninja ndash links to spectral and fluorescence data Spekwin32 spectroscopy software httpwwweffemm2deinfoinfo_specdatahtml

httpwwweffemm2deindexhtml Zeiss ndash interactive fluorescence dye and filter database overview dyes overview filter sets httpswwwmicro-shopzeisscoms=50479761ad21e5ampl=enampp=usampf=fampa=i httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=d httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=f Researcher Labs Alby Diaspro ndash IIT httpwwwlambsitindexphppage=People Alice Ting ndash MIT httpwwwtinglaborgresearch Allen Institute for Brain Science httpwwwalleninstituteorgwhat-we-dobrain-science Allen Institute for Cell Science httpwwwalleninstituteorgwhat-we-docell-science Amina Qutub - Rice University - How are human cells designed lab httpsqutublaborgqutub-lab Amy Herr UC Berkeley ndash Single cell Westerns httpherrlabberkeleyedu Amy Palmer ndash UC Boulder httpspalmerlabcoloradoedu Andrew York ndash Calico Life Sciences httpswwwcalicolabscomteam-memberandrew-york Anne Carpenter ndash Broad Institute CellProfiler httpspersonalbroadinstituteorganne Arjun Raj UPenn single molecule RNA FISH quantitative understanding cellular functions httprajlabseasupenneduindexhtml httpwwwpopscicomsciencearticle2013-09arjun-raj Atsuko Miyawaki - Laboratory for Cell Function Dynamics (CFDS) Fucci2 fluorescent proteins cell cycle indicator httpwwwbrainrikenjpenfacultydetails30 httpcfdsbrainrikenjp httpcfdsbrainrikenjpFuccihtml Aydogan Ozcan - UCLA - new imaging and sensing architectures httpinnovateeeuclaeduwelcomehtml httpwwwhhmiorgscientistsaydogan-ozcan Badri Roysam - UH - FARSIGHT Toolkit httpwwweeuhedufacultyroysam httpwwwfarsight-toolkitorgwikiMain_Page Brian J Ford ndash microscopist and popularizer httpsuklinkedincominprofbrianjford Carolyn Larabell ndashNational Center for X-ray Tomography (LBNL) UCSF httpncxtlblgovq=carolyn httpprofilesucsfeducarolynlarabell Clare Waterman ndash NHLBI NIH

httpswwwnhlbinihgovresearchintramuralresearcherspiwaterman-clare Dana Peer - Columbia University - Computational Systems Biology viSNE and more software httpwwwc2b2columbiaedudanapeerlabhtml httpwwwc2b2columbiaedudanapeerlabhtmlcythtml David Mayerich - UH - STIM Laboratory Scalable Tissue Imaging and Modeling httpwwweeuhedufacultymayerich httpstimeeuhedu David Piston WUSTL httpwwwcellbiologywustledufacultytenureddavid-w-piston-phd Diane Lidke and Keith Lidke - University of New Mexico httppathologyunmeduresearchfaculty-laboratoriesthe-lidke-laboratoryindexhtml httppanda3physunmedu~klidke Donna Arndt-Jovin and Thomas Jovin - Max Planck Institute for Biophysical Chemistry Laboratory of Cellular Dynamics httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsDonnaArdndt-JovinResearchAreasAndProjects httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsChairmanThomasJovinResearchAreasAndProjects Ed Boyden ndash MIT Media Lab ndash expansion microscopy (ExM) optogenetics httpsyntheticneurobiologyorg httpsyntheticneurobiologyorgprotocols httpsyntheticneurobiologyorgpublications httpwwwtedcomtalksed_boyden_baby_diapers_inspired_this_new_way_to_study_the_brain httpwwwextbiocombuycell Elizabeth Blackburn ndash Salk Institute - Telomeres httpswwwsalkeduscientistelizabeth-blackburn httpsenwikipediaorgwikiElizabeth_Blackburn httpswwwnobelprizeorgnobel_prizesmedicinelaureates2009blackburn-factshtml Elizabeth Hillman - Columbia university - SCAPE (Swept Confocally-Aligned Planar Excitation) high speed 3D microscopy DyCE (dynamic contrast enhancement to image and segment small animal organs live) Neuroimaging amp Neurovascular Coupling httporionbmecolumbiaedu~hillmanInstrumentationhtml httporionbmecolumbiaedu~hillmanSCAPEhtml httporionbmecolumbiaedu~hillmanMolecularhtml httporionbmecolumbiaedu~hillmanBrain_Imaginghtml Eric Betzig ndash UCSF (moving from HHMI Janelia Farm in 2016) httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014betzig-factshtml Eva Sevick-Muraca ndash UT Health Science Center at Houston molecular imaging clinical NIR fluoresceince imaging httpswwwutheduimmprofilehtmid=1005459 httpswwwutheduimmcentersmolecular-imaginghtm Evelin Schrock - Technische Universitaumlt Dresden spectral karyotyping cytogenetics httpswwwresearchgatenetprofileEvelin_Schrock Garry Nolan Stanford University ndash Mass cytometry MIBI-ToF high throughput imaging mass cytometry (42plex) httpwebstanfordedugroupnolanresourceshtml httpwebstanfordedugroupnolantechnologieshtml George McNamara ndash Cell Morphometry (41) Figure 1 right top two panels (55) The Chase (2016 temporal area maps lsquodynamic morphologyrsquo) (76) newsletter series on ldquoThe Chaserdquo (73) direct Vimeo movie of ldquoThe Chaserdquo Tiki_Goddess linkedin 10+plex blog httpsworksbepresscomgmcnamara41 httpsworksbepresscomgmcnamara55 httpsworksbepresscomgmcnamara76

httpsworksbepresscomgmcnamara73 httpsvimeocom175151196 httphomeearthlinknet~tiki_goddess httpswwwlinkedincomingeorgemcnamara httpswwwlinkedincompulsebd-biosciences-listed-tandems-horizon-brilliant-violets-mcnamara Gillian Griffiths - University of Cambridge - T-cell immunological synapse httpwwwcimrcamacukresearchprincipal-investigatorsprincipal-investigators-a-hgriffiths Hari Shroff NIBIB NIH httpswwwnibibnihgovlabs-at-nibibsection-high-resolution-optical-imaging-hroi HHMI Janelia Farm Research Campus (JFRC) - Advanced Imaging Center Open Science httpswwwjaneliaorgopen-scienceadvanced-imaging-center-aic httpswwwjaneliaorgopen-science Jeanne Lawrence University of Massachussetts Medical School httpwwwumassmededucellbiolabslawrencepersonnelprincipal-investigator Jennifer Lippincott-Schwartz ndash HHMI Janelia Farm httpswwwjaneliaorgpeoplejennifer-lippincott-schwartz Jin Zhang ndash UCSD httpprofilesucsdedujinzhang Joe DeRisi - UCSF - 3D printable lab stuff httpderisilabucsfeduindexphppage=3D John Russ Chris Russ Fovea Pro plugins for Adobe Photoshop httpwwwdrjohnrusscomindexhtml httpwwwdrjohnrusscombookshtml httpwwwreindeergraphicscomfoveaprotutorialhtml Julie Theriot httpcmgmstanfordedutheriot Karl Deisseroth ndash Stanford University ndash CLARITY optical tissue clearing Optogenetics httpclarityresourcecenterorg httpwebstanfordedugroupdlaboptogeneticsindexhtml Karsten Koumlnig (Koenig) - Saarland University and JenLab GmbH - biophotonics httpwwwbltuni-saarlanddeindex_ehtm httpwwwjenlabde httpwwwthelastescape-filmcom Karsten Rodenacker ndash image measurements httpkaro03bplacednetkaroMeMisc_WWWpdfMicrosoftWord-EQUAPATpdf Kevin Eliceiri ndash UW-Madison Open Source Photonics and Software Laboratory for Optical and Computational Instrumentation (LOCI) wwwlociwiscedu Klaus Kemp ndash Microlife Services ndash diatoms and other prepared microscope slides httpwwwdiatomscouk Kurt Thorn UCSF httpthornlabucsfedu httpsnicucsfedublog httpnicucsfeduFPvisualization httpgigapancomgigapans163370 Lihong Wang - WUSTL - Optical Imaging Laboratory photoacoustic tomography

httpoilabseaswustledu httpoilabseaswustleduresearch_0html Loren Looger - HHMI JFRC - iGluSnFr fluorescent protein biosensor httpswwwjaneliaorglablooger-lab Mary-Lou Pardue ndash MIT (first ever in situ hybridization with J Gall) httpsbiologymitedupeoplemary_lou_pardue httpsenwikipediaorgwikiMary-Lou_Pardue Nancy Allbritton - UNC - Chemical cytometry microraft arrays organ-on-a-chip httpswwwbmencsueduindexphpcomponentcomprofileruserprofilenlallbri httpwwwbmeuncedulabsallbritton Navin Varadarajan - UH - single-cell Lab httpwwwcheeuhedufacultyvaradarajan httpsinglecellcheeuheducontacthtml Nicholas Shaner - Scintillon Institute - mNeonGreen httpwwwscintillonorgshaner_lab Rebecca Richards-Kortum httpbioengineeringriceedufacultyrebecca_richards-kortumaspx Robert Campbell - Fluorescent proteins optogenetic proteins httpcampbellwebchemualbertaca httpcampbellwebchemualbertacaprojects-2 Robert Murphy ndash Cell measurements web services httpmurphylabwebcmueduservices Sabine Mai - University of Manitoba - Genomic Centre for Cancer Research and Diagnosis (GCCRD) - httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBPlatformsGCCRDhtml httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBScientistsMaiAwardshtml Sally Ward and Raimund Ober - Texas AampM University - httpwwwwardoberlabcom Simon Watkins - U Pittsburgh Center for Biologic Imaging httpwwwcbppittedufacultywatkinshtml httpwwwcbppittedufacultylabwatkinshtml httpwwwcbipittedu Stefan Hell ndash Deparment Hell NanoBiopohotonics httpwwwmpibpcmpgdehell httpsenwikipediaorgwikiStefan_Hell httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014hell-factshtml Sunney Xie Harvard httpsbernsteinharvardedu Susan Cox ndash 3B microscopy httpwwwcoxphysicscomindexhtml httpwwwcoxphysicscom3b Radim Chmeliacutek - Center for innovative microscopy Experimental biophotonics group httpswwwceiteceuceitec-butexperimental-biophotonicsrg3 httpwwwbiophotczhome Taekjip Ha ndash Johns Hopkins University ndash single molecules httphamedjhmiedu

Thomas Ried ndash NCI NIH SKYM-FISH and CGH Database httpsccrcancergovGenetics-Branchthomas-ried httpsccrcancergovGenetics-Branchthomas-riedqt-staff_profile_tabs=9qt-staff_profile_tabs ftpftpncbinlmnihgovsky-cghDATA httpswwwncbinlmnihgovdbvar Viviana Gradinaru ndash CalTech ndash CLARITYPACT Optogenetics httpwwwbbecaltecheducontentviviana-gradinaru httpglabcaltechedu Vladislav Verkhusha - near infrared fluorescent proteins httpwwweinsteinyuedulabsvlad-verkhushadefaultaspx httpwwweinsteinyueduresearchfacilitiesfluorescent WE Moerner ndash Stanford University httpwebstanfordedugroupmoerner Willard Wiggans ndash micro gallery httpwwwwillard-wigancomgallery Wolf Frommer ndash Molecular sensors httpbiosensordpbcarnegiescienceedu (fluorescent protein biosensors table) Xiaowei Zhuang = Harvard httpzhuangharvardedu Yuval Garini - Bar-Ilan University - Nano-Bio-Photonics laboratory httpgarinilabbiuacil Microscopy Magazines Imaging amp Microscopy httpwwwimaging-gitcommagazine Laser Focus World httpwwwlaserfocusworldcomindexhtml Microscopy amp Analysis httpwwwmicroscopy-analysiscom Microscopy Today httpwwwmicroscopy-todaycom Microscopy-UK httpwwwmicroscopy-ukorguk Photonics Spectra Biophotonics httpwwwphotonicscomPublicationsaspx The Microscope Journal httpmcriorgv72the-microscope-journal RMS Infocus Magazine httpwwwrmsorgukstudy-readinfocus-magazinehtml Nobel Prizes in Light Microscopy and Related Fields Chemistry 1925 colloids (light sheet) Zsigmondy (Siedentopf Zsigmondy 1902) httpswwwnobelprizeorgnobel_prizeschemistrylaureates1925

Chemistry 2000 conductive polymers Heeger MacDiarmid Shirakawa (Brilliant Violets Ultraviolets Blues) httpwwwnobelprizeorgnobel_prizeschemistrylaureates2000 Chemistry 2008 green fluorescent protein GFP Shimomura Chalfie Tsien httpwwwnobelprizeorgnobel_prizeschemistrylaureates2008 Chemistry 2014 super-resolved fluorescence microscopy Betzig Hell Moerner httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014 Physics 1953 Phase Contrast Zernike httpswwwnobelprizeorgnobel_prizesphysicslaureates1953 Physics 2009 invention of an imaging semiconductor circuit ndash the CCD sensor Kao Boyle Smith httpwwwnobelprizeorgnobel_prizesphysicslaureates2009 Physics 2014 efficient blue light emitting diodes Akasaki Amano Nakamura httpwwwnobelprizeorgnobel_prizesphysicslaureates2014 Physiology or Medicine 2006 Fire and Mello RNA interference ndash gene silencing by double stranded RNA httpwwwnobelprizeorgnobel_prizesmedicinelaureates2006 Physiology or Medicine 2006 Capecchi Evans Smithies specific gene modifications in mice by the use of embryonic stem cells httpwwwnobelprizeorgnobel_prizesmedicinelaureates2007 Physiology or Medicine 2009 Blackburn Greider Szostak how chromosomes are protected by telomeres and telomerase httpwwwnobelprizeorgnobel_prizesmedicinelaureates2009 Physiology or Medicine 2012 Gurdon Yamamanka matured cells can be reprogrammed to become pluripotent httpwwwnobelprizeorgnobel_prizesmedicinelaureates2012

Table 442 Fluorophores Photophysics Data

Fluorophore Abs or Ex max (nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Acridine orange 271 520 27000 020 5

Alexa Fluor 430 431 541 16000 055 9

Alexa Fluor 488 495 519 71000 094 67

Alexa Fluor 532 532 553 81000 080 65

Alexa Fluor 546 556 573 104000 096 100

Alexa Fluor 568 578 603 91300 075 69

Alexa Fluor 594 590 617 73000 064 47

Allophycocyanin (APC) 650 660 700000 068 476

Atto 390 390 479 24000 090 22

Atto 425 436 484 45000 065 29

Atto 430LS 433 547 32000 065 21

Atto 465 453 508 75000 075 56

Atto 490LS 496 661 40000 030 12

Atto 520 525 547 105000 095 100

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 20: McNamara 20161006 revised draft tables for CPHG Light ...

httpwwwchipcytometrycomtechnologyphtml Fluorescence Spectra Data and Graphing Sites PubSpectra ndash Excel file data download httpsworksbepresscomgmcnamara9 BD Biosciences ndash spectrum viewer Brilliant fluorophores httpwwwbdbiosciencescomussspectrumviewer httpwwwbdbiosciencescomusapplicationssspectrumguidepage BioLegend ndash spectra analyzer Brilliant Violet fluorophores httpwwwbiolegendcomspectraanalyzer httpwwwbiolegendcombrilliantviolet Chroma Technology httpswwwchromacomspectra-viewer eBioscience (Affymetrix ThermoFisher) ndash fluorPlan ndash a multi-laser spectra viewer httpwwwebiosciencecomresourcesfluorplan-spectra-viewerhtm Spectra Viewer (requires Java) Evrogen ndash Spectrum Viewer httpevrogencomspectra-viewerflashviewerhtml Fluorophoresorg ndash Fluorescent Substances httpwwwfluorophorestugrazatsubstance I Love GFP httpssitesgooglecomsiteilovegfpHomefps Lambert and Thorn UCSF Fluorescent protein properties httpnicucsfeduFPvisualization Leica Microsystem - ldquoFluoScoutrdquo httpwwwleica-microsystemscomfluoscout

Molecular Probes Invitrogen Thermo Fisher ndash Fluorescence SpectraViewer httpwwwthermofishercomusenhomelife-sciencecell-analysislabeling-chemistryfluorescence-spectraviewerhtml httpsitunesapplecomusappfluorescence-spectraviewerid421031826 (iTunes App) Nightsea - Compendium of spectra web sites httpwwwnightseacomsfa-sharingfluorescence-spectra-viewers Omega Optical ldquoCurvomatricrdquo httpswwwomegafilterscomcurvomatic

PhotoChemCAD 20 (Jonathan S Lindsey) dye spectra database and chemistry calculator NIRvana Sciences httpwwwphotochemcadcom httpnirvanasciencescompage_id=3088 UCSF (Lambert Thorn 2016) - Fluorescent protein properties httpnicucsfeduFPvisualization University of Arizona - Fluorescent Spectra Database httpwwwspectraarizonaedu Semrock - Searchlight httpssearchlightsemrockcom Spectroscopy Ninja ndash links to spectral and fluorescence data Spekwin32 spectroscopy software httpwwweffemm2deinfoinfo_specdatahtml

httpwwweffemm2deindexhtml Zeiss ndash interactive fluorescence dye and filter database overview dyes overview filter sets httpswwwmicro-shopzeisscoms=50479761ad21e5ampl=enampp=usampf=fampa=i httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=d httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=f Researcher Labs Alby Diaspro ndash IIT httpwwwlambsitindexphppage=People Alice Ting ndash MIT httpwwwtinglaborgresearch Allen Institute for Brain Science httpwwwalleninstituteorgwhat-we-dobrain-science Allen Institute for Cell Science httpwwwalleninstituteorgwhat-we-docell-science Amina Qutub - Rice University - How are human cells designed lab httpsqutublaborgqutub-lab Amy Herr UC Berkeley ndash Single cell Westerns httpherrlabberkeleyedu Amy Palmer ndash UC Boulder httpspalmerlabcoloradoedu Andrew York ndash Calico Life Sciences httpswwwcalicolabscomteam-memberandrew-york Anne Carpenter ndash Broad Institute CellProfiler httpspersonalbroadinstituteorganne Arjun Raj UPenn single molecule RNA FISH quantitative understanding cellular functions httprajlabseasupenneduindexhtml httpwwwpopscicomsciencearticle2013-09arjun-raj Atsuko Miyawaki - Laboratory for Cell Function Dynamics (CFDS) Fucci2 fluorescent proteins cell cycle indicator httpwwwbrainrikenjpenfacultydetails30 httpcfdsbrainrikenjp httpcfdsbrainrikenjpFuccihtml Aydogan Ozcan - UCLA - new imaging and sensing architectures httpinnovateeeuclaeduwelcomehtml httpwwwhhmiorgscientistsaydogan-ozcan Badri Roysam - UH - FARSIGHT Toolkit httpwwweeuhedufacultyroysam httpwwwfarsight-toolkitorgwikiMain_Page Brian J Ford ndash microscopist and popularizer httpsuklinkedincominprofbrianjford Carolyn Larabell ndashNational Center for X-ray Tomography (LBNL) UCSF httpncxtlblgovq=carolyn httpprofilesucsfeducarolynlarabell Clare Waterman ndash NHLBI NIH

httpswwwnhlbinihgovresearchintramuralresearcherspiwaterman-clare Dana Peer - Columbia University - Computational Systems Biology viSNE and more software httpwwwc2b2columbiaedudanapeerlabhtml httpwwwc2b2columbiaedudanapeerlabhtmlcythtml David Mayerich - UH - STIM Laboratory Scalable Tissue Imaging and Modeling httpwwweeuhedufacultymayerich httpstimeeuhedu David Piston WUSTL httpwwwcellbiologywustledufacultytenureddavid-w-piston-phd Diane Lidke and Keith Lidke - University of New Mexico httppathologyunmeduresearchfaculty-laboratoriesthe-lidke-laboratoryindexhtml httppanda3physunmedu~klidke Donna Arndt-Jovin and Thomas Jovin - Max Planck Institute for Biophysical Chemistry Laboratory of Cellular Dynamics httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsDonnaArdndt-JovinResearchAreasAndProjects httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsChairmanThomasJovinResearchAreasAndProjects Ed Boyden ndash MIT Media Lab ndash expansion microscopy (ExM) optogenetics httpsyntheticneurobiologyorg httpsyntheticneurobiologyorgprotocols httpsyntheticneurobiologyorgpublications httpwwwtedcomtalksed_boyden_baby_diapers_inspired_this_new_way_to_study_the_brain httpwwwextbiocombuycell Elizabeth Blackburn ndash Salk Institute - Telomeres httpswwwsalkeduscientistelizabeth-blackburn httpsenwikipediaorgwikiElizabeth_Blackburn httpswwwnobelprizeorgnobel_prizesmedicinelaureates2009blackburn-factshtml Elizabeth Hillman - Columbia university - SCAPE (Swept Confocally-Aligned Planar Excitation) high speed 3D microscopy DyCE (dynamic contrast enhancement to image and segment small animal organs live) Neuroimaging amp Neurovascular Coupling httporionbmecolumbiaedu~hillmanInstrumentationhtml httporionbmecolumbiaedu~hillmanSCAPEhtml httporionbmecolumbiaedu~hillmanMolecularhtml httporionbmecolumbiaedu~hillmanBrain_Imaginghtml Eric Betzig ndash UCSF (moving from HHMI Janelia Farm in 2016) httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014betzig-factshtml Eva Sevick-Muraca ndash UT Health Science Center at Houston molecular imaging clinical NIR fluoresceince imaging httpswwwutheduimmprofilehtmid=1005459 httpswwwutheduimmcentersmolecular-imaginghtm Evelin Schrock - Technische Universitaumlt Dresden spectral karyotyping cytogenetics httpswwwresearchgatenetprofileEvelin_Schrock Garry Nolan Stanford University ndash Mass cytometry MIBI-ToF high throughput imaging mass cytometry (42plex) httpwebstanfordedugroupnolanresourceshtml httpwebstanfordedugroupnolantechnologieshtml George McNamara ndash Cell Morphometry (41) Figure 1 right top two panels (55) The Chase (2016 temporal area maps lsquodynamic morphologyrsquo) (76) newsletter series on ldquoThe Chaserdquo (73) direct Vimeo movie of ldquoThe Chaserdquo Tiki_Goddess linkedin 10+plex blog httpsworksbepresscomgmcnamara41 httpsworksbepresscomgmcnamara55 httpsworksbepresscomgmcnamara76

httpsworksbepresscomgmcnamara73 httpsvimeocom175151196 httphomeearthlinknet~tiki_goddess httpswwwlinkedincomingeorgemcnamara httpswwwlinkedincompulsebd-biosciences-listed-tandems-horizon-brilliant-violets-mcnamara Gillian Griffiths - University of Cambridge - T-cell immunological synapse httpwwwcimrcamacukresearchprincipal-investigatorsprincipal-investigators-a-hgriffiths Hari Shroff NIBIB NIH httpswwwnibibnihgovlabs-at-nibibsection-high-resolution-optical-imaging-hroi HHMI Janelia Farm Research Campus (JFRC) - Advanced Imaging Center Open Science httpswwwjaneliaorgopen-scienceadvanced-imaging-center-aic httpswwwjaneliaorgopen-science Jeanne Lawrence University of Massachussetts Medical School httpwwwumassmededucellbiolabslawrencepersonnelprincipal-investigator Jennifer Lippincott-Schwartz ndash HHMI Janelia Farm httpswwwjaneliaorgpeoplejennifer-lippincott-schwartz Jin Zhang ndash UCSD httpprofilesucsdedujinzhang Joe DeRisi - UCSF - 3D printable lab stuff httpderisilabucsfeduindexphppage=3D John Russ Chris Russ Fovea Pro plugins for Adobe Photoshop httpwwwdrjohnrusscomindexhtml httpwwwdrjohnrusscombookshtml httpwwwreindeergraphicscomfoveaprotutorialhtml Julie Theriot httpcmgmstanfordedutheriot Karl Deisseroth ndash Stanford University ndash CLARITY optical tissue clearing Optogenetics httpclarityresourcecenterorg httpwebstanfordedugroupdlaboptogeneticsindexhtml Karsten Koumlnig (Koenig) - Saarland University and JenLab GmbH - biophotonics httpwwwbltuni-saarlanddeindex_ehtm httpwwwjenlabde httpwwwthelastescape-filmcom Karsten Rodenacker ndash image measurements httpkaro03bplacednetkaroMeMisc_WWWpdfMicrosoftWord-EQUAPATpdf Kevin Eliceiri ndash UW-Madison Open Source Photonics and Software Laboratory for Optical and Computational Instrumentation (LOCI) wwwlociwiscedu Klaus Kemp ndash Microlife Services ndash diatoms and other prepared microscope slides httpwwwdiatomscouk Kurt Thorn UCSF httpthornlabucsfedu httpsnicucsfedublog httpnicucsfeduFPvisualization httpgigapancomgigapans163370 Lihong Wang - WUSTL - Optical Imaging Laboratory photoacoustic tomography

httpoilabseaswustledu httpoilabseaswustleduresearch_0html Loren Looger - HHMI JFRC - iGluSnFr fluorescent protein biosensor httpswwwjaneliaorglablooger-lab Mary-Lou Pardue ndash MIT (first ever in situ hybridization with J Gall) httpsbiologymitedupeoplemary_lou_pardue httpsenwikipediaorgwikiMary-Lou_Pardue Nancy Allbritton - UNC - Chemical cytometry microraft arrays organ-on-a-chip httpswwwbmencsueduindexphpcomponentcomprofileruserprofilenlallbri httpwwwbmeuncedulabsallbritton Navin Varadarajan - UH - single-cell Lab httpwwwcheeuhedufacultyvaradarajan httpsinglecellcheeuheducontacthtml Nicholas Shaner - Scintillon Institute - mNeonGreen httpwwwscintillonorgshaner_lab Rebecca Richards-Kortum httpbioengineeringriceedufacultyrebecca_richards-kortumaspx Robert Campbell - Fluorescent proteins optogenetic proteins httpcampbellwebchemualbertaca httpcampbellwebchemualbertacaprojects-2 Robert Murphy ndash Cell measurements web services httpmurphylabwebcmueduservices Sabine Mai - University of Manitoba - Genomic Centre for Cancer Research and Diagnosis (GCCRD) - httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBPlatformsGCCRDhtml httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBScientistsMaiAwardshtml Sally Ward and Raimund Ober - Texas AampM University - httpwwwwardoberlabcom Simon Watkins - U Pittsburgh Center for Biologic Imaging httpwwwcbppittedufacultywatkinshtml httpwwwcbppittedufacultylabwatkinshtml httpwwwcbipittedu Stefan Hell ndash Deparment Hell NanoBiopohotonics httpwwwmpibpcmpgdehell httpsenwikipediaorgwikiStefan_Hell httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014hell-factshtml Sunney Xie Harvard httpsbernsteinharvardedu Susan Cox ndash 3B microscopy httpwwwcoxphysicscomindexhtml httpwwwcoxphysicscom3b Radim Chmeliacutek - Center for innovative microscopy Experimental biophotonics group httpswwwceiteceuceitec-butexperimental-biophotonicsrg3 httpwwwbiophotczhome Taekjip Ha ndash Johns Hopkins University ndash single molecules httphamedjhmiedu

Thomas Ried ndash NCI NIH SKYM-FISH and CGH Database httpsccrcancergovGenetics-Branchthomas-ried httpsccrcancergovGenetics-Branchthomas-riedqt-staff_profile_tabs=9qt-staff_profile_tabs ftpftpncbinlmnihgovsky-cghDATA httpswwwncbinlmnihgovdbvar Viviana Gradinaru ndash CalTech ndash CLARITYPACT Optogenetics httpwwwbbecaltecheducontentviviana-gradinaru httpglabcaltechedu Vladislav Verkhusha - near infrared fluorescent proteins httpwwweinsteinyuedulabsvlad-verkhushadefaultaspx httpwwweinsteinyueduresearchfacilitiesfluorescent WE Moerner ndash Stanford University httpwebstanfordedugroupmoerner Willard Wiggans ndash micro gallery httpwwwwillard-wigancomgallery Wolf Frommer ndash Molecular sensors httpbiosensordpbcarnegiescienceedu (fluorescent protein biosensors table) Xiaowei Zhuang = Harvard httpzhuangharvardedu Yuval Garini - Bar-Ilan University - Nano-Bio-Photonics laboratory httpgarinilabbiuacil Microscopy Magazines Imaging amp Microscopy httpwwwimaging-gitcommagazine Laser Focus World httpwwwlaserfocusworldcomindexhtml Microscopy amp Analysis httpwwwmicroscopy-analysiscom Microscopy Today httpwwwmicroscopy-todaycom Microscopy-UK httpwwwmicroscopy-ukorguk Photonics Spectra Biophotonics httpwwwphotonicscomPublicationsaspx The Microscope Journal httpmcriorgv72the-microscope-journal RMS Infocus Magazine httpwwwrmsorgukstudy-readinfocus-magazinehtml Nobel Prizes in Light Microscopy and Related Fields Chemistry 1925 colloids (light sheet) Zsigmondy (Siedentopf Zsigmondy 1902) httpswwwnobelprizeorgnobel_prizeschemistrylaureates1925

Chemistry 2000 conductive polymers Heeger MacDiarmid Shirakawa (Brilliant Violets Ultraviolets Blues) httpwwwnobelprizeorgnobel_prizeschemistrylaureates2000 Chemistry 2008 green fluorescent protein GFP Shimomura Chalfie Tsien httpwwwnobelprizeorgnobel_prizeschemistrylaureates2008 Chemistry 2014 super-resolved fluorescence microscopy Betzig Hell Moerner httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014 Physics 1953 Phase Contrast Zernike httpswwwnobelprizeorgnobel_prizesphysicslaureates1953 Physics 2009 invention of an imaging semiconductor circuit ndash the CCD sensor Kao Boyle Smith httpwwwnobelprizeorgnobel_prizesphysicslaureates2009 Physics 2014 efficient blue light emitting diodes Akasaki Amano Nakamura httpwwwnobelprizeorgnobel_prizesphysicslaureates2014 Physiology or Medicine 2006 Fire and Mello RNA interference ndash gene silencing by double stranded RNA httpwwwnobelprizeorgnobel_prizesmedicinelaureates2006 Physiology or Medicine 2006 Capecchi Evans Smithies specific gene modifications in mice by the use of embryonic stem cells httpwwwnobelprizeorgnobel_prizesmedicinelaureates2007 Physiology or Medicine 2009 Blackburn Greider Szostak how chromosomes are protected by telomeres and telomerase httpwwwnobelprizeorgnobel_prizesmedicinelaureates2009 Physiology or Medicine 2012 Gurdon Yamamanka matured cells can be reprogrammed to become pluripotent httpwwwnobelprizeorgnobel_prizesmedicinelaureates2012

Table 442 Fluorophores Photophysics Data

Fluorophore Abs or Ex max (nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Acridine orange 271 520 27000 020 5

Alexa Fluor 430 431 541 16000 055 9

Alexa Fluor 488 495 519 71000 094 67

Alexa Fluor 532 532 553 81000 080 65

Alexa Fluor 546 556 573 104000 096 100

Alexa Fluor 568 578 603 91300 075 69

Alexa Fluor 594 590 617 73000 064 47

Allophycocyanin (APC) 650 660 700000 068 476

Atto 390 390 479 24000 090 22

Atto 425 436 484 45000 065 29

Atto 430LS 433 547 32000 065 21

Atto 465 453 508 75000 075 56

Atto 490LS 496 661 40000 030 12

Atto 520 525 547 105000 095 100

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 21: McNamara 20161006 revised draft tables for CPHG Light ...

httpwwweffemm2deindexhtml Zeiss ndash interactive fluorescence dye and filter database overview dyes overview filter sets httpswwwmicro-shopzeisscoms=50479761ad21e5ampl=enampp=usampf=fampa=i httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=d httpswwwmicro-shopzeisscoms=55721483f91174ampl=enampp=usampf=fampa=f Researcher Labs Alby Diaspro ndash IIT httpwwwlambsitindexphppage=People Alice Ting ndash MIT httpwwwtinglaborgresearch Allen Institute for Brain Science httpwwwalleninstituteorgwhat-we-dobrain-science Allen Institute for Cell Science httpwwwalleninstituteorgwhat-we-docell-science Amina Qutub - Rice University - How are human cells designed lab httpsqutublaborgqutub-lab Amy Herr UC Berkeley ndash Single cell Westerns httpherrlabberkeleyedu Amy Palmer ndash UC Boulder httpspalmerlabcoloradoedu Andrew York ndash Calico Life Sciences httpswwwcalicolabscomteam-memberandrew-york Anne Carpenter ndash Broad Institute CellProfiler httpspersonalbroadinstituteorganne Arjun Raj UPenn single molecule RNA FISH quantitative understanding cellular functions httprajlabseasupenneduindexhtml httpwwwpopscicomsciencearticle2013-09arjun-raj Atsuko Miyawaki - Laboratory for Cell Function Dynamics (CFDS) Fucci2 fluorescent proteins cell cycle indicator httpwwwbrainrikenjpenfacultydetails30 httpcfdsbrainrikenjp httpcfdsbrainrikenjpFuccihtml Aydogan Ozcan - UCLA - new imaging and sensing architectures httpinnovateeeuclaeduwelcomehtml httpwwwhhmiorgscientistsaydogan-ozcan Badri Roysam - UH - FARSIGHT Toolkit httpwwweeuhedufacultyroysam httpwwwfarsight-toolkitorgwikiMain_Page Brian J Ford ndash microscopist and popularizer httpsuklinkedincominprofbrianjford Carolyn Larabell ndashNational Center for X-ray Tomography (LBNL) UCSF httpncxtlblgovq=carolyn httpprofilesucsfeducarolynlarabell Clare Waterman ndash NHLBI NIH

httpswwwnhlbinihgovresearchintramuralresearcherspiwaterman-clare Dana Peer - Columbia University - Computational Systems Biology viSNE and more software httpwwwc2b2columbiaedudanapeerlabhtml httpwwwc2b2columbiaedudanapeerlabhtmlcythtml David Mayerich - UH - STIM Laboratory Scalable Tissue Imaging and Modeling httpwwweeuhedufacultymayerich httpstimeeuhedu David Piston WUSTL httpwwwcellbiologywustledufacultytenureddavid-w-piston-phd Diane Lidke and Keith Lidke - University of New Mexico httppathologyunmeduresearchfaculty-laboratoriesthe-lidke-laboratoryindexhtml httppanda3physunmedu~klidke Donna Arndt-Jovin and Thomas Jovin - Max Planck Institute for Biophysical Chemistry Laboratory of Cellular Dynamics httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsDonnaArdndt-JovinResearchAreasAndProjects httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsChairmanThomasJovinResearchAreasAndProjects Ed Boyden ndash MIT Media Lab ndash expansion microscopy (ExM) optogenetics httpsyntheticneurobiologyorg httpsyntheticneurobiologyorgprotocols httpsyntheticneurobiologyorgpublications httpwwwtedcomtalksed_boyden_baby_diapers_inspired_this_new_way_to_study_the_brain httpwwwextbiocombuycell Elizabeth Blackburn ndash Salk Institute - Telomeres httpswwwsalkeduscientistelizabeth-blackburn httpsenwikipediaorgwikiElizabeth_Blackburn httpswwwnobelprizeorgnobel_prizesmedicinelaureates2009blackburn-factshtml Elizabeth Hillman - Columbia university - SCAPE (Swept Confocally-Aligned Planar Excitation) high speed 3D microscopy DyCE (dynamic contrast enhancement to image and segment small animal organs live) Neuroimaging amp Neurovascular Coupling httporionbmecolumbiaedu~hillmanInstrumentationhtml httporionbmecolumbiaedu~hillmanSCAPEhtml httporionbmecolumbiaedu~hillmanMolecularhtml httporionbmecolumbiaedu~hillmanBrain_Imaginghtml Eric Betzig ndash UCSF (moving from HHMI Janelia Farm in 2016) httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014betzig-factshtml Eva Sevick-Muraca ndash UT Health Science Center at Houston molecular imaging clinical NIR fluoresceince imaging httpswwwutheduimmprofilehtmid=1005459 httpswwwutheduimmcentersmolecular-imaginghtm Evelin Schrock - Technische Universitaumlt Dresden spectral karyotyping cytogenetics httpswwwresearchgatenetprofileEvelin_Schrock Garry Nolan Stanford University ndash Mass cytometry MIBI-ToF high throughput imaging mass cytometry (42plex) httpwebstanfordedugroupnolanresourceshtml httpwebstanfordedugroupnolantechnologieshtml George McNamara ndash Cell Morphometry (41) Figure 1 right top two panels (55) The Chase (2016 temporal area maps lsquodynamic morphologyrsquo) (76) newsletter series on ldquoThe Chaserdquo (73) direct Vimeo movie of ldquoThe Chaserdquo Tiki_Goddess linkedin 10+plex blog httpsworksbepresscomgmcnamara41 httpsworksbepresscomgmcnamara55 httpsworksbepresscomgmcnamara76

httpsworksbepresscomgmcnamara73 httpsvimeocom175151196 httphomeearthlinknet~tiki_goddess httpswwwlinkedincomingeorgemcnamara httpswwwlinkedincompulsebd-biosciences-listed-tandems-horizon-brilliant-violets-mcnamara Gillian Griffiths - University of Cambridge - T-cell immunological synapse httpwwwcimrcamacukresearchprincipal-investigatorsprincipal-investigators-a-hgriffiths Hari Shroff NIBIB NIH httpswwwnibibnihgovlabs-at-nibibsection-high-resolution-optical-imaging-hroi HHMI Janelia Farm Research Campus (JFRC) - Advanced Imaging Center Open Science httpswwwjaneliaorgopen-scienceadvanced-imaging-center-aic httpswwwjaneliaorgopen-science Jeanne Lawrence University of Massachussetts Medical School httpwwwumassmededucellbiolabslawrencepersonnelprincipal-investigator Jennifer Lippincott-Schwartz ndash HHMI Janelia Farm httpswwwjaneliaorgpeoplejennifer-lippincott-schwartz Jin Zhang ndash UCSD httpprofilesucsdedujinzhang Joe DeRisi - UCSF - 3D printable lab stuff httpderisilabucsfeduindexphppage=3D John Russ Chris Russ Fovea Pro plugins for Adobe Photoshop httpwwwdrjohnrusscomindexhtml httpwwwdrjohnrusscombookshtml httpwwwreindeergraphicscomfoveaprotutorialhtml Julie Theriot httpcmgmstanfordedutheriot Karl Deisseroth ndash Stanford University ndash CLARITY optical tissue clearing Optogenetics httpclarityresourcecenterorg httpwebstanfordedugroupdlaboptogeneticsindexhtml Karsten Koumlnig (Koenig) - Saarland University and JenLab GmbH - biophotonics httpwwwbltuni-saarlanddeindex_ehtm httpwwwjenlabde httpwwwthelastescape-filmcom Karsten Rodenacker ndash image measurements httpkaro03bplacednetkaroMeMisc_WWWpdfMicrosoftWord-EQUAPATpdf Kevin Eliceiri ndash UW-Madison Open Source Photonics and Software Laboratory for Optical and Computational Instrumentation (LOCI) wwwlociwiscedu Klaus Kemp ndash Microlife Services ndash diatoms and other prepared microscope slides httpwwwdiatomscouk Kurt Thorn UCSF httpthornlabucsfedu httpsnicucsfedublog httpnicucsfeduFPvisualization httpgigapancomgigapans163370 Lihong Wang - WUSTL - Optical Imaging Laboratory photoacoustic tomography

httpoilabseaswustledu httpoilabseaswustleduresearch_0html Loren Looger - HHMI JFRC - iGluSnFr fluorescent protein biosensor httpswwwjaneliaorglablooger-lab Mary-Lou Pardue ndash MIT (first ever in situ hybridization with J Gall) httpsbiologymitedupeoplemary_lou_pardue httpsenwikipediaorgwikiMary-Lou_Pardue Nancy Allbritton - UNC - Chemical cytometry microraft arrays organ-on-a-chip httpswwwbmencsueduindexphpcomponentcomprofileruserprofilenlallbri httpwwwbmeuncedulabsallbritton Navin Varadarajan - UH - single-cell Lab httpwwwcheeuhedufacultyvaradarajan httpsinglecellcheeuheducontacthtml Nicholas Shaner - Scintillon Institute - mNeonGreen httpwwwscintillonorgshaner_lab Rebecca Richards-Kortum httpbioengineeringriceedufacultyrebecca_richards-kortumaspx Robert Campbell - Fluorescent proteins optogenetic proteins httpcampbellwebchemualbertaca httpcampbellwebchemualbertacaprojects-2 Robert Murphy ndash Cell measurements web services httpmurphylabwebcmueduservices Sabine Mai - University of Manitoba - Genomic Centre for Cancer Research and Diagnosis (GCCRD) - httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBPlatformsGCCRDhtml httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBScientistsMaiAwardshtml Sally Ward and Raimund Ober - Texas AampM University - httpwwwwardoberlabcom Simon Watkins - U Pittsburgh Center for Biologic Imaging httpwwwcbppittedufacultywatkinshtml httpwwwcbppittedufacultylabwatkinshtml httpwwwcbipittedu Stefan Hell ndash Deparment Hell NanoBiopohotonics httpwwwmpibpcmpgdehell httpsenwikipediaorgwikiStefan_Hell httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014hell-factshtml Sunney Xie Harvard httpsbernsteinharvardedu Susan Cox ndash 3B microscopy httpwwwcoxphysicscomindexhtml httpwwwcoxphysicscom3b Radim Chmeliacutek - Center for innovative microscopy Experimental biophotonics group httpswwwceiteceuceitec-butexperimental-biophotonicsrg3 httpwwwbiophotczhome Taekjip Ha ndash Johns Hopkins University ndash single molecules httphamedjhmiedu

Thomas Ried ndash NCI NIH SKYM-FISH and CGH Database httpsccrcancergovGenetics-Branchthomas-ried httpsccrcancergovGenetics-Branchthomas-riedqt-staff_profile_tabs=9qt-staff_profile_tabs ftpftpncbinlmnihgovsky-cghDATA httpswwwncbinlmnihgovdbvar Viviana Gradinaru ndash CalTech ndash CLARITYPACT Optogenetics httpwwwbbecaltecheducontentviviana-gradinaru httpglabcaltechedu Vladislav Verkhusha - near infrared fluorescent proteins httpwwweinsteinyuedulabsvlad-verkhushadefaultaspx httpwwweinsteinyueduresearchfacilitiesfluorescent WE Moerner ndash Stanford University httpwebstanfordedugroupmoerner Willard Wiggans ndash micro gallery httpwwwwillard-wigancomgallery Wolf Frommer ndash Molecular sensors httpbiosensordpbcarnegiescienceedu (fluorescent protein biosensors table) Xiaowei Zhuang = Harvard httpzhuangharvardedu Yuval Garini - Bar-Ilan University - Nano-Bio-Photonics laboratory httpgarinilabbiuacil Microscopy Magazines Imaging amp Microscopy httpwwwimaging-gitcommagazine Laser Focus World httpwwwlaserfocusworldcomindexhtml Microscopy amp Analysis httpwwwmicroscopy-analysiscom Microscopy Today httpwwwmicroscopy-todaycom Microscopy-UK httpwwwmicroscopy-ukorguk Photonics Spectra Biophotonics httpwwwphotonicscomPublicationsaspx The Microscope Journal httpmcriorgv72the-microscope-journal RMS Infocus Magazine httpwwwrmsorgukstudy-readinfocus-magazinehtml Nobel Prizes in Light Microscopy and Related Fields Chemistry 1925 colloids (light sheet) Zsigmondy (Siedentopf Zsigmondy 1902) httpswwwnobelprizeorgnobel_prizeschemistrylaureates1925

Chemistry 2000 conductive polymers Heeger MacDiarmid Shirakawa (Brilliant Violets Ultraviolets Blues) httpwwwnobelprizeorgnobel_prizeschemistrylaureates2000 Chemistry 2008 green fluorescent protein GFP Shimomura Chalfie Tsien httpwwwnobelprizeorgnobel_prizeschemistrylaureates2008 Chemistry 2014 super-resolved fluorescence microscopy Betzig Hell Moerner httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014 Physics 1953 Phase Contrast Zernike httpswwwnobelprizeorgnobel_prizesphysicslaureates1953 Physics 2009 invention of an imaging semiconductor circuit ndash the CCD sensor Kao Boyle Smith httpwwwnobelprizeorgnobel_prizesphysicslaureates2009 Physics 2014 efficient blue light emitting diodes Akasaki Amano Nakamura httpwwwnobelprizeorgnobel_prizesphysicslaureates2014 Physiology or Medicine 2006 Fire and Mello RNA interference ndash gene silencing by double stranded RNA httpwwwnobelprizeorgnobel_prizesmedicinelaureates2006 Physiology or Medicine 2006 Capecchi Evans Smithies specific gene modifications in mice by the use of embryonic stem cells httpwwwnobelprizeorgnobel_prizesmedicinelaureates2007 Physiology or Medicine 2009 Blackburn Greider Szostak how chromosomes are protected by telomeres and telomerase httpwwwnobelprizeorgnobel_prizesmedicinelaureates2009 Physiology or Medicine 2012 Gurdon Yamamanka matured cells can be reprogrammed to become pluripotent httpwwwnobelprizeorgnobel_prizesmedicinelaureates2012

Table 442 Fluorophores Photophysics Data

Fluorophore Abs or Ex max (nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Acridine orange 271 520 27000 020 5

Alexa Fluor 430 431 541 16000 055 9

Alexa Fluor 488 495 519 71000 094 67

Alexa Fluor 532 532 553 81000 080 65

Alexa Fluor 546 556 573 104000 096 100

Alexa Fluor 568 578 603 91300 075 69

Alexa Fluor 594 590 617 73000 064 47

Allophycocyanin (APC) 650 660 700000 068 476

Atto 390 390 479 24000 090 22

Atto 425 436 484 45000 065 29

Atto 430LS 433 547 32000 065 21

Atto 465 453 508 75000 075 56

Atto 490LS 496 661 40000 030 12

Atto 520 525 547 105000 095 100

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 22: McNamara 20161006 revised draft tables for CPHG Light ...

httpswwwnhlbinihgovresearchintramuralresearcherspiwaterman-clare Dana Peer - Columbia University - Computational Systems Biology viSNE and more software httpwwwc2b2columbiaedudanapeerlabhtml httpwwwc2b2columbiaedudanapeerlabhtmlcythtml David Mayerich - UH - STIM Laboratory Scalable Tissue Imaging and Modeling httpwwweeuhedufacultymayerich httpstimeeuhedu David Piston WUSTL httpwwwcellbiologywustledufacultytenureddavid-w-piston-phd Diane Lidke and Keith Lidke - University of New Mexico httppathologyunmeduresearchfaculty-laboratoriesthe-lidke-laboratoryindexhtml httppanda3physunmedu~klidke Donna Arndt-Jovin and Thomas Jovin - Max Planck Institute for Biophysical Chemistry Laboratory of Cellular Dynamics httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsDonnaArdndt-JovinResearchAreasAndProjects httpwww3mpibpcmpgdegroupsjovinindexphpResearchGroupsChairmanThomasJovinResearchAreasAndProjects Ed Boyden ndash MIT Media Lab ndash expansion microscopy (ExM) optogenetics httpsyntheticneurobiologyorg httpsyntheticneurobiologyorgprotocols httpsyntheticneurobiologyorgpublications httpwwwtedcomtalksed_boyden_baby_diapers_inspired_this_new_way_to_study_the_brain httpwwwextbiocombuycell Elizabeth Blackburn ndash Salk Institute - Telomeres httpswwwsalkeduscientistelizabeth-blackburn httpsenwikipediaorgwikiElizabeth_Blackburn httpswwwnobelprizeorgnobel_prizesmedicinelaureates2009blackburn-factshtml Elizabeth Hillman - Columbia university - SCAPE (Swept Confocally-Aligned Planar Excitation) high speed 3D microscopy DyCE (dynamic contrast enhancement to image and segment small animal organs live) Neuroimaging amp Neurovascular Coupling httporionbmecolumbiaedu~hillmanInstrumentationhtml httporionbmecolumbiaedu~hillmanSCAPEhtml httporionbmecolumbiaedu~hillmanMolecularhtml httporionbmecolumbiaedu~hillmanBrain_Imaginghtml Eric Betzig ndash UCSF (moving from HHMI Janelia Farm in 2016) httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014betzig-factshtml Eva Sevick-Muraca ndash UT Health Science Center at Houston molecular imaging clinical NIR fluoresceince imaging httpswwwutheduimmprofilehtmid=1005459 httpswwwutheduimmcentersmolecular-imaginghtm Evelin Schrock - Technische Universitaumlt Dresden spectral karyotyping cytogenetics httpswwwresearchgatenetprofileEvelin_Schrock Garry Nolan Stanford University ndash Mass cytometry MIBI-ToF high throughput imaging mass cytometry (42plex) httpwebstanfordedugroupnolanresourceshtml httpwebstanfordedugroupnolantechnologieshtml George McNamara ndash Cell Morphometry (41) Figure 1 right top two panels (55) The Chase (2016 temporal area maps lsquodynamic morphologyrsquo) (76) newsletter series on ldquoThe Chaserdquo (73) direct Vimeo movie of ldquoThe Chaserdquo Tiki_Goddess linkedin 10+plex blog httpsworksbepresscomgmcnamara41 httpsworksbepresscomgmcnamara55 httpsworksbepresscomgmcnamara76

httpsworksbepresscomgmcnamara73 httpsvimeocom175151196 httphomeearthlinknet~tiki_goddess httpswwwlinkedincomingeorgemcnamara httpswwwlinkedincompulsebd-biosciences-listed-tandems-horizon-brilliant-violets-mcnamara Gillian Griffiths - University of Cambridge - T-cell immunological synapse httpwwwcimrcamacukresearchprincipal-investigatorsprincipal-investigators-a-hgriffiths Hari Shroff NIBIB NIH httpswwwnibibnihgovlabs-at-nibibsection-high-resolution-optical-imaging-hroi HHMI Janelia Farm Research Campus (JFRC) - Advanced Imaging Center Open Science httpswwwjaneliaorgopen-scienceadvanced-imaging-center-aic httpswwwjaneliaorgopen-science Jeanne Lawrence University of Massachussetts Medical School httpwwwumassmededucellbiolabslawrencepersonnelprincipal-investigator Jennifer Lippincott-Schwartz ndash HHMI Janelia Farm httpswwwjaneliaorgpeoplejennifer-lippincott-schwartz Jin Zhang ndash UCSD httpprofilesucsdedujinzhang Joe DeRisi - UCSF - 3D printable lab stuff httpderisilabucsfeduindexphppage=3D John Russ Chris Russ Fovea Pro plugins for Adobe Photoshop httpwwwdrjohnrusscomindexhtml httpwwwdrjohnrusscombookshtml httpwwwreindeergraphicscomfoveaprotutorialhtml Julie Theriot httpcmgmstanfordedutheriot Karl Deisseroth ndash Stanford University ndash CLARITY optical tissue clearing Optogenetics httpclarityresourcecenterorg httpwebstanfordedugroupdlaboptogeneticsindexhtml Karsten Koumlnig (Koenig) - Saarland University and JenLab GmbH - biophotonics httpwwwbltuni-saarlanddeindex_ehtm httpwwwjenlabde httpwwwthelastescape-filmcom Karsten Rodenacker ndash image measurements httpkaro03bplacednetkaroMeMisc_WWWpdfMicrosoftWord-EQUAPATpdf Kevin Eliceiri ndash UW-Madison Open Source Photonics and Software Laboratory for Optical and Computational Instrumentation (LOCI) wwwlociwiscedu Klaus Kemp ndash Microlife Services ndash diatoms and other prepared microscope slides httpwwwdiatomscouk Kurt Thorn UCSF httpthornlabucsfedu httpsnicucsfedublog httpnicucsfeduFPvisualization httpgigapancomgigapans163370 Lihong Wang - WUSTL - Optical Imaging Laboratory photoacoustic tomography

httpoilabseaswustledu httpoilabseaswustleduresearch_0html Loren Looger - HHMI JFRC - iGluSnFr fluorescent protein biosensor httpswwwjaneliaorglablooger-lab Mary-Lou Pardue ndash MIT (first ever in situ hybridization with J Gall) httpsbiologymitedupeoplemary_lou_pardue httpsenwikipediaorgwikiMary-Lou_Pardue Nancy Allbritton - UNC - Chemical cytometry microraft arrays organ-on-a-chip httpswwwbmencsueduindexphpcomponentcomprofileruserprofilenlallbri httpwwwbmeuncedulabsallbritton Navin Varadarajan - UH - single-cell Lab httpwwwcheeuhedufacultyvaradarajan httpsinglecellcheeuheducontacthtml Nicholas Shaner - Scintillon Institute - mNeonGreen httpwwwscintillonorgshaner_lab Rebecca Richards-Kortum httpbioengineeringriceedufacultyrebecca_richards-kortumaspx Robert Campbell - Fluorescent proteins optogenetic proteins httpcampbellwebchemualbertaca httpcampbellwebchemualbertacaprojects-2 Robert Murphy ndash Cell measurements web services httpmurphylabwebcmueduservices Sabine Mai - University of Manitoba - Genomic Centre for Cancer Research and Diagnosis (GCCRD) - httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBPlatformsGCCRDhtml httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBScientistsMaiAwardshtml Sally Ward and Raimund Ober - Texas AampM University - httpwwwwardoberlabcom Simon Watkins - U Pittsburgh Center for Biologic Imaging httpwwwcbppittedufacultywatkinshtml httpwwwcbppittedufacultylabwatkinshtml httpwwwcbipittedu Stefan Hell ndash Deparment Hell NanoBiopohotonics httpwwwmpibpcmpgdehell httpsenwikipediaorgwikiStefan_Hell httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014hell-factshtml Sunney Xie Harvard httpsbernsteinharvardedu Susan Cox ndash 3B microscopy httpwwwcoxphysicscomindexhtml httpwwwcoxphysicscom3b Radim Chmeliacutek - Center for innovative microscopy Experimental biophotonics group httpswwwceiteceuceitec-butexperimental-biophotonicsrg3 httpwwwbiophotczhome Taekjip Ha ndash Johns Hopkins University ndash single molecules httphamedjhmiedu

Thomas Ried ndash NCI NIH SKYM-FISH and CGH Database httpsccrcancergovGenetics-Branchthomas-ried httpsccrcancergovGenetics-Branchthomas-riedqt-staff_profile_tabs=9qt-staff_profile_tabs ftpftpncbinlmnihgovsky-cghDATA httpswwwncbinlmnihgovdbvar Viviana Gradinaru ndash CalTech ndash CLARITYPACT Optogenetics httpwwwbbecaltecheducontentviviana-gradinaru httpglabcaltechedu Vladislav Verkhusha - near infrared fluorescent proteins httpwwweinsteinyuedulabsvlad-verkhushadefaultaspx httpwwweinsteinyueduresearchfacilitiesfluorescent WE Moerner ndash Stanford University httpwebstanfordedugroupmoerner Willard Wiggans ndash micro gallery httpwwwwillard-wigancomgallery Wolf Frommer ndash Molecular sensors httpbiosensordpbcarnegiescienceedu (fluorescent protein biosensors table) Xiaowei Zhuang = Harvard httpzhuangharvardedu Yuval Garini - Bar-Ilan University - Nano-Bio-Photonics laboratory httpgarinilabbiuacil Microscopy Magazines Imaging amp Microscopy httpwwwimaging-gitcommagazine Laser Focus World httpwwwlaserfocusworldcomindexhtml Microscopy amp Analysis httpwwwmicroscopy-analysiscom Microscopy Today httpwwwmicroscopy-todaycom Microscopy-UK httpwwwmicroscopy-ukorguk Photonics Spectra Biophotonics httpwwwphotonicscomPublicationsaspx The Microscope Journal httpmcriorgv72the-microscope-journal RMS Infocus Magazine httpwwwrmsorgukstudy-readinfocus-magazinehtml Nobel Prizes in Light Microscopy and Related Fields Chemistry 1925 colloids (light sheet) Zsigmondy (Siedentopf Zsigmondy 1902) httpswwwnobelprizeorgnobel_prizeschemistrylaureates1925

Chemistry 2000 conductive polymers Heeger MacDiarmid Shirakawa (Brilliant Violets Ultraviolets Blues) httpwwwnobelprizeorgnobel_prizeschemistrylaureates2000 Chemistry 2008 green fluorescent protein GFP Shimomura Chalfie Tsien httpwwwnobelprizeorgnobel_prizeschemistrylaureates2008 Chemistry 2014 super-resolved fluorescence microscopy Betzig Hell Moerner httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014 Physics 1953 Phase Contrast Zernike httpswwwnobelprizeorgnobel_prizesphysicslaureates1953 Physics 2009 invention of an imaging semiconductor circuit ndash the CCD sensor Kao Boyle Smith httpwwwnobelprizeorgnobel_prizesphysicslaureates2009 Physics 2014 efficient blue light emitting diodes Akasaki Amano Nakamura httpwwwnobelprizeorgnobel_prizesphysicslaureates2014 Physiology or Medicine 2006 Fire and Mello RNA interference ndash gene silencing by double stranded RNA httpwwwnobelprizeorgnobel_prizesmedicinelaureates2006 Physiology or Medicine 2006 Capecchi Evans Smithies specific gene modifications in mice by the use of embryonic stem cells httpwwwnobelprizeorgnobel_prizesmedicinelaureates2007 Physiology or Medicine 2009 Blackburn Greider Szostak how chromosomes are protected by telomeres and telomerase httpwwwnobelprizeorgnobel_prizesmedicinelaureates2009 Physiology or Medicine 2012 Gurdon Yamamanka matured cells can be reprogrammed to become pluripotent httpwwwnobelprizeorgnobel_prizesmedicinelaureates2012

Table 442 Fluorophores Photophysics Data

Fluorophore Abs or Ex max (nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Acridine orange 271 520 27000 020 5

Alexa Fluor 430 431 541 16000 055 9

Alexa Fluor 488 495 519 71000 094 67

Alexa Fluor 532 532 553 81000 080 65

Alexa Fluor 546 556 573 104000 096 100

Alexa Fluor 568 578 603 91300 075 69

Alexa Fluor 594 590 617 73000 064 47

Allophycocyanin (APC) 650 660 700000 068 476

Atto 390 390 479 24000 090 22

Atto 425 436 484 45000 065 29

Atto 430LS 433 547 32000 065 21

Atto 465 453 508 75000 075 56

Atto 490LS 496 661 40000 030 12

Atto 520 525 547 105000 095 100

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 23: McNamara 20161006 revised draft tables for CPHG Light ...

httpsworksbepresscomgmcnamara73 httpsvimeocom175151196 httphomeearthlinknet~tiki_goddess httpswwwlinkedincomingeorgemcnamara httpswwwlinkedincompulsebd-biosciences-listed-tandems-horizon-brilliant-violets-mcnamara Gillian Griffiths - University of Cambridge - T-cell immunological synapse httpwwwcimrcamacukresearchprincipal-investigatorsprincipal-investigators-a-hgriffiths Hari Shroff NIBIB NIH httpswwwnibibnihgovlabs-at-nibibsection-high-resolution-optical-imaging-hroi HHMI Janelia Farm Research Campus (JFRC) - Advanced Imaging Center Open Science httpswwwjaneliaorgopen-scienceadvanced-imaging-center-aic httpswwwjaneliaorgopen-science Jeanne Lawrence University of Massachussetts Medical School httpwwwumassmededucellbiolabslawrencepersonnelprincipal-investigator Jennifer Lippincott-Schwartz ndash HHMI Janelia Farm httpswwwjaneliaorgpeoplejennifer-lippincott-schwartz Jin Zhang ndash UCSD httpprofilesucsdedujinzhang Joe DeRisi - UCSF - 3D printable lab stuff httpderisilabucsfeduindexphppage=3D John Russ Chris Russ Fovea Pro plugins for Adobe Photoshop httpwwwdrjohnrusscomindexhtml httpwwwdrjohnrusscombookshtml httpwwwreindeergraphicscomfoveaprotutorialhtml Julie Theriot httpcmgmstanfordedutheriot Karl Deisseroth ndash Stanford University ndash CLARITY optical tissue clearing Optogenetics httpclarityresourcecenterorg httpwebstanfordedugroupdlaboptogeneticsindexhtml Karsten Koumlnig (Koenig) - Saarland University and JenLab GmbH - biophotonics httpwwwbltuni-saarlanddeindex_ehtm httpwwwjenlabde httpwwwthelastescape-filmcom Karsten Rodenacker ndash image measurements httpkaro03bplacednetkaroMeMisc_WWWpdfMicrosoftWord-EQUAPATpdf Kevin Eliceiri ndash UW-Madison Open Source Photonics and Software Laboratory for Optical and Computational Instrumentation (LOCI) wwwlociwiscedu Klaus Kemp ndash Microlife Services ndash diatoms and other prepared microscope slides httpwwwdiatomscouk Kurt Thorn UCSF httpthornlabucsfedu httpsnicucsfedublog httpnicucsfeduFPvisualization httpgigapancomgigapans163370 Lihong Wang - WUSTL - Optical Imaging Laboratory photoacoustic tomography

httpoilabseaswustledu httpoilabseaswustleduresearch_0html Loren Looger - HHMI JFRC - iGluSnFr fluorescent protein biosensor httpswwwjaneliaorglablooger-lab Mary-Lou Pardue ndash MIT (first ever in situ hybridization with J Gall) httpsbiologymitedupeoplemary_lou_pardue httpsenwikipediaorgwikiMary-Lou_Pardue Nancy Allbritton - UNC - Chemical cytometry microraft arrays organ-on-a-chip httpswwwbmencsueduindexphpcomponentcomprofileruserprofilenlallbri httpwwwbmeuncedulabsallbritton Navin Varadarajan - UH - single-cell Lab httpwwwcheeuhedufacultyvaradarajan httpsinglecellcheeuheducontacthtml Nicholas Shaner - Scintillon Institute - mNeonGreen httpwwwscintillonorgshaner_lab Rebecca Richards-Kortum httpbioengineeringriceedufacultyrebecca_richards-kortumaspx Robert Campbell - Fluorescent proteins optogenetic proteins httpcampbellwebchemualbertaca httpcampbellwebchemualbertacaprojects-2 Robert Murphy ndash Cell measurements web services httpmurphylabwebcmueduservices Sabine Mai - University of Manitoba - Genomic Centre for Cancer Research and Diagnosis (GCCRD) - httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBPlatformsGCCRDhtml httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBScientistsMaiAwardshtml Sally Ward and Raimund Ober - Texas AampM University - httpwwwwardoberlabcom Simon Watkins - U Pittsburgh Center for Biologic Imaging httpwwwcbppittedufacultywatkinshtml httpwwwcbppittedufacultylabwatkinshtml httpwwwcbipittedu Stefan Hell ndash Deparment Hell NanoBiopohotonics httpwwwmpibpcmpgdehell httpsenwikipediaorgwikiStefan_Hell httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014hell-factshtml Sunney Xie Harvard httpsbernsteinharvardedu Susan Cox ndash 3B microscopy httpwwwcoxphysicscomindexhtml httpwwwcoxphysicscom3b Radim Chmeliacutek - Center for innovative microscopy Experimental biophotonics group httpswwwceiteceuceitec-butexperimental-biophotonicsrg3 httpwwwbiophotczhome Taekjip Ha ndash Johns Hopkins University ndash single molecules httphamedjhmiedu

Thomas Ried ndash NCI NIH SKYM-FISH and CGH Database httpsccrcancergovGenetics-Branchthomas-ried httpsccrcancergovGenetics-Branchthomas-riedqt-staff_profile_tabs=9qt-staff_profile_tabs ftpftpncbinlmnihgovsky-cghDATA httpswwwncbinlmnihgovdbvar Viviana Gradinaru ndash CalTech ndash CLARITYPACT Optogenetics httpwwwbbecaltecheducontentviviana-gradinaru httpglabcaltechedu Vladislav Verkhusha - near infrared fluorescent proteins httpwwweinsteinyuedulabsvlad-verkhushadefaultaspx httpwwweinsteinyueduresearchfacilitiesfluorescent WE Moerner ndash Stanford University httpwebstanfordedugroupmoerner Willard Wiggans ndash micro gallery httpwwwwillard-wigancomgallery Wolf Frommer ndash Molecular sensors httpbiosensordpbcarnegiescienceedu (fluorescent protein biosensors table) Xiaowei Zhuang = Harvard httpzhuangharvardedu Yuval Garini - Bar-Ilan University - Nano-Bio-Photonics laboratory httpgarinilabbiuacil Microscopy Magazines Imaging amp Microscopy httpwwwimaging-gitcommagazine Laser Focus World httpwwwlaserfocusworldcomindexhtml Microscopy amp Analysis httpwwwmicroscopy-analysiscom Microscopy Today httpwwwmicroscopy-todaycom Microscopy-UK httpwwwmicroscopy-ukorguk Photonics Spectra Biophotonics httpwwwphotonicscomPublicationsaspx The Microscope Journal httpmcriorgv72the-microscope-journal RMS Infocus Magazine httpwwwrmsorgukstudy-readinfocus-magazinehtml Nobel Prizes in Light Microscopy and Related Fields Chemistry 1925 colloids (light sheet) Zsigmondy (Siedentopf Zsigmondy 1902) httpswwwnobelprizeorgnobel_prizeschemistrylaureates1925

Chemistry 2000 conductive polymers Heeger MacDiarmid Shirakawa (Brilliant Violets Ultraviolets Blues) httpwwwnobelprizeorgnobel_prizeschemistrylaureates2000 Chemistry 2008 green fluorescent protein GFP Shimomura Chalfie Tsien httpwwwnobelprizeorgnobel_prizeschemistrylaureates2008 Chemistry 2014 super-resolved fluorescence microscopy Betzig Hell Moerner httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014 Physics 1953 Phase Contrast Zernike httpswwwnobelprizeorgnobel_prizesphysicslaureates1953 Physics 2009 invention of an imaging semiconductor circuit ndash the CCD sensor Kao Boyle Smith httpwwwnobelprizeorgnobel_prizesphysicslaureates2009 Physics 2014 efficient blue light emitting diodes Akasaki Amano Nakamura httpwwwnobelprizeorgnobel_prizesphysicslaureates2014 Physiology or Medicine 2006 Fire and Mello RNA interference ndash gene silencing by double stranded RNA httpwwwnobelprizeorgnobel_prizesmedicinelaureates2006 Physiology or Medicine 2006 Capecchi Evans Smithies specific gene modifications in mice by the use of embryonic stem cells httpwwwnobelprizeorgnobel_prizesmedicinelaureates2007 Physiology or Medicine 2009 Blackburn Greider Szostak how chromosomes are protected by telomeres and telomerase httpwwwnobelprizeorgnobel_prizesmedicinelaureates2009 Physiology or Medicine 2012 Gurdon Yamamanka matured cells can be reprogrammed to become pluripotent httpwwwnobelprizeorgnobel_prizesmedicinelaureates2012

Table 442 Fluorophores Photophysics Data

Fluorophore Abs or Ex max (nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Acridine orange 271 520 27000 020 5

Alexa Fluor 430 431 541 16000 055 9

Alexa Fluor 488 495 519 71000 094 67

Alexa Fluor 532 532 553 81000 080 65

Alexa Fluor 546 556 573 104000 096 100

Alexa Fluor 568 578 603 91300 075 69

Alexa Fluor 594 590 617 73000 064 47

Allophycocyanin (APC) 650 660 700000 068 476

Atto 390 390 479 24000 090 22

Atto 425 436 484 45000 065 29

Atto 430LS 433 547 32000 065 21

Atto 465 453 508 75000 075 56

Atto 490LS 496 661 40000 030 12

Atto 520 525 547 105000 095 100

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 24: McNamara 20161006 revised draft tables for CPHG Light ...

httpoilabseaswustledu httpoilabseaswustleduresearch_0html Loren Looger - HHMI JFRC - iGluSnFr fluorescent protein biosensor httpswwwjaneliaorglablooger-lab Mary-Lou Pardue ndash MIT (first ever in situ hybridization with J Gall) httpsbiologymitedupeoplemary_lou_pardue httpsenwikipediaorgwikiMary-Lou_Pardue Nancy Allbritton - UNC - Chemical cytometry microraft arrays organ-on-a-chip httpswwwbmencsueduindexphpcomponentcomprofileruserprofilenlallbri httpwwwbmeuncedulabsallbritton Navin Varadarajan - UH - single-cell Lab httpwwwcheeuhedufacultyvaradarajan httpsinglecellcheeuheducontacthtml Nicholas Shaner - Scintillon Institute - mNeonGreen httpwwwscintillonorgshaner_lab Rebecca Richards-Kortum httpbioengineeringriceedufacultyrebecca_richards-kortumaspx Robert Campbell - Fluorescent proteins optogenetic proteins httpcampbellwebchemualbertaca httpcampbellwebchemualbertacaprojects-2 Robert Murphy ndash Cell measurements web services httpmurphylabwebcmueduservices Sabine Mai - University of Manitoba - Genomic Centre for Cancer Research and Diagnosis (GCCRD) - httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBPlatformsGCCRDhtml httpswwwumanitobacainstitutesmanitoba_institute_cell_biologyMICBScientistsMaiAwardshtml Sally Ward and Raimund Ober - Texas AampM University - httpwwwwardoberlabcom Simon Watkins - U Pittsburgh Center for Biologic Imaging httpwwwcbppittedufacultywatkinshtml httpwwwcbppittedufacultylabwatkinshtml httpwwwcbipittedu Stefan Hell ndash Deparment Hell NanoBiopohotonics httpwwwmpibpcmpgdehell httpsenwikipediaorgwikiStefan_Hell httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014hell-factshtml Sunney Xie Harvard httpsbernsteinharvardedu Susan Cox ndash 3B microscopy httpwwwcoxphysicscomindexhtml httpwwwcoxphysicscom3b Radim Chmeliacutek - Center for innovative microscopy Experimental biophotonics group httpswwwceiteceuceitec-butexperimental-biophotonicsrg3 httpwwwbiophotczhome Taekjip Ha ndash Johns Hopkins University ndash single molecules httphamedjhmiedu

Thomas Ried ndash NCI NIH SKYM-FISH and CGH Database httpsccrcancergovGenetics-Branchthomas-ried httpsccrcancergovGenetics-Branchthomas-riedqt-staff_profile_tabs=9qt-staff_profile_tabs ftpftpncbinlmnihgovsky-cghDATA httpswwwncbinlmnihgovdbvar Viviana Gradinaru ndash CalTech ndash CLARITYPACT Optogenetics httpwwwbbecaltecheducontentviviana-gradinaru httpglabcaltechedu Vladislav Verkhusha - near infrared fluorescent proteins httpwwweinsteinyuedulabsvlad-verkhushadefaultaspx httpwwweinsteinyueduresearchfacilitiesfluorescent WE Moerner ndash Stanford University httpwebstanfordedugroupmoerner Willard Wiggans ndash micro gallery httpwwwwillard-wigancomgallery Wolf Frommer ndash Molecular sensors httpbiosensordpbcarnegiescienceedu (fluorescent protein biosensors table) Xiaowei Zhuang = Harvard httpzhuangharvardedu Yuval Garini - Bar-Ilan University - Nano-Bio-Photonics laboratory httpgarinilabbiuacil Microscopy Magazines Imaging amp Microscopy httpwwwimaging-gitcommagazine Laser Focus World httpwwwlaserfocusworldcomindexhtml Microscopy amp Analysis httpwwwmicroscopy-analysiscom Microscopy Today httpwwwmicroscopy-todaycom Microscopy-UK httpwwwmicroscopy-ukorguk Photonics Spectra Biophotonics httpwwwphotonicscomPublicationsaspx The Microscope Journal httpmcriorgv72the-microscope-journal RMS Infocus Magazine httpwwwrmsorgukstudy-readinfocus-magazinehtml Nobel Prizes in Light Microscopy and Related Fields Chemistry 1925 colloids (light sheet) Zsigmondy (Siedentopf Zsigmondy 1902) httpswwwnobelprizeorgnobel_prizeschemistrylaureates1925

Chemistry 2000 conductive polymers Heeger MacDiarmid Shirakawa (Brilliant Violets Ultraviolets Blues) httpwwwnobelprizeorgnobel_prizeschemistrylaureates2000 Chemistry 2008 green fluorescent protein GFP Shimomura Chalfie Tsien httpwwwnobelprizeorgnobel_prizeschemistrylaureates2008 Chemistry 2014 super-resolved fluorescence microscopy Betzig Hell Moerner httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014 Physics 1953 Phase Contrast Zernike httpswwwnobelprizeorgnobel_prizesphysicslaureates1953 Physics 2009 invention of an imaging semiconductor circuit ndash the CCD sensor Kao Boyle Smith httpwwwnobelprizeorgnobel_prizesphysicslaureates2009 Physics 2014 efficient blue light emitting diodes Akasaki Amano Nakamura httpwwwnobelprizeorgnobel_prizesphysicslaureates2014 Physiology or Medicine 2006 Fire and Mello RNA interference ndash gene silencing by double stranded RNA httpwwwnobelprizeorgnobel_prizesmedicinelaureates2006 Physiology or Medicine 2006 Capecchi Evans Smithies specific gene modifications in mice by the use of embryonic stem cells httpwwwnobelprizeorgnobel_prizesmedicinelaureates2007 Physiology or Medicine 2009 Blackburn Greider Szostak how chromosomes are protected by telomeres and telomerase httpwwwnobelprizeorgnobel_prizesmedicinelaureates2009 Physiology or Medicine 2012 Gurdon Yamamanka matured cells can be reprogrammed to become pluripotent httpwwwnobelprizeorgnobel_prizesmedicinelaureates2012

Table 442 Fluorophores Photophysics Data

Fluorophore Abs or Ex max (nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Acridine orange 271 520 27000 020 5

Alexa Fluor 430 431 541 16000 055 9

Alexa Fluor 488 495 519 71000 094 67

Alexa Fluor 532 532 553 81000 080 65

Alexa Fluor 546 556 573 104000 096 100

Alexa Fluor 568 578 603 91300 075 69

Alexa Fluor 594 590 617 73000 064 47

Allophycocyanin (APC) 650 660 700000 068 476

Atto 390 390 479 24000 090 22

Atto 425 436 484 45000 065 29

Atto 430LS 433 547 32000 065 21

Atto 465 453 508 75000 075 56

Atto 490LS 496 661 40000 030 12

Atto 520 525 547 105000 095 100

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 25: McNamara 20161006 revised draft tables for CPHG Light ...

Thomas Ried ndash NCI NIH SKYM-FISH and CGH Database httpsccrcancergovGenetics-Branchthomas-ried httpsccrcancergovGenetics-Branchthomas-riedqt-staff_profile_tabs=9qt-staff_profile_tabs ftpftpncbinlmnihgovsky-cghDATA httpswwwncbinlmnihgovdbvar Viviana Gradinaru ndash CalTech ndash CLARITYPACT Optogenetics httpwwwbbecaltecheducontentviviana-gradinaru httpglabcaltechedu Vladislav Verkhusha - near infrared fluorescent proteins httpwwweinsteinyuedulabsvlad-verkhushadefaultaspx httpwwweinsteinyueduresearchfacilitiesfluorescent WE Moerner ndash Stanford University httpwebstanfordedugroupmoerner Willard Wiggans ndash micro gallery httpwwwwillard-wigancomgallery Wolf Frommer ndash Molecular sensors httpbiosensordpbcarnegiescienceedu (fluorescent protein biosensors table) Xiaowei Zhuang = Harvard httpzhuangharvardedu Yuval Garini - Bar-Ilan University - Nano-Bio-Photonics laboratory httpgarinilabbiuacil Microscopy Magazines Imaging amp Microscopy httpwwwimaging-gitcommagazine Laser Focus World httpwwwlaserfocusworldcomindexhtml Microscopy amp Analysis httpwwwmicroscopy-analysiscom Microscopy Today httpwwwmicroscopy-todaycom Microscopy-UK httpwwwmicroscopy-ukorguk Photonics Spectra Biophotonics httpwwwphotonicscomPublicationsaspx The Microscope Journal httpmcriorgv72the-microscope-journal RMS Infocus Magazine httpwwwrmsorgukstudy-readinfocus-magazinehtml Nobel Prizes in Light Microscopy and Related Fields Chemistry 1925 colloids (light sheet) Zsigmondy (Siedentopf Zsigmondy 1902) httpswwwnobelprizeorgnobel_prizeschemistrylaureates1925

Chemistry 2000 conductive polymers Heeger MacDiarmid Shirakawa (Brilliant Violets Ultraviolets Blues) httpwwwnobelprizeorgnobel_prizeschemistrylaureates2000 Chemistry 2008 green fluorescent protein GFP Shimomura Chalfie Tsien httpwwwnobelprizeorgnobel_prizeschemistrylaureates2008 Chemistry 2014 super-resolved fluorescence microscopy Betzig Hell Moerner httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014 Physics 1953 Phase Contrast Zernike httpswwwnobelprizeorgnobel_prizesphysicslaureates1953 Physics 2009 invention of an imaging semiconductor circuit ndash the CCD sensor Kao Boyle Smith httpwwwnobelprizeorgnobel_prizesphysicslaureates2009 Physics 2014 efficient blue light emitting diodes Akasaki Amano Nakamura httpwwwnobelprizeorgnobel_prizesphysicslaureates2014 Physiology or Medicine 2006 Fire and Mello RNA interference ndash gene silencing by double stranded RNA httpwwwnobelprizeorgnobel_prizesmedicinelaureates2006 Physiology or Medicine 2006 Capecchi Evans Smithies specific gene modifications in mice by the use of embryonic stem cells httpwwwnobelprizeorgnobel_prizesmedicinelaureates2007 Physiology or Medicine 2009 Blackburn Greider Szostak how chromosomes are protected by telomeres and telomerase httpwwwnobelprizeorgnobel_prizesmedicinelaureates2009 Physiology or Medicine 2012 Gurdon Yamamanka matured cells can be reprogrammed to become pluripotent httpwwwnobelprizeorgnobel_prizesmedicinelaureates2012

Table 442 Fluorophores Photophysics Data

Fluorophore Abs or Ex max (nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Acridine orange 271 520 27000 020 5

Alexa Fluor 430 431 541 16000 055 9

Alexa Fluor 488 495 519 71000 094 67

Alexa Fluor 532 532 553 81000 080 65

Alexa Fluor 546 556 573 104000 096 100

Alexa Fluor 568 578 603 91300 075 69

Alexa Fluor 594 590 617 73000 064 47

Allophycocyanin (APC) 650 660 700000 068 476

Atto 390 390 479 24000 090 22

Atto 425 436 484 45000 065 29

Atto 430LS 433 547 32000 065 21

Atto 465 453 508 75000 075 56

Atto 490LS 496 661 40000 030 12

Atto 520 525 547 105000 095 100

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 26: McNamara 20161006 revised draft tables for CPHG Light ...

Chemistry 2000 conductive polymers Heeger MacDiarmid Shirakawa (Brilliant Violets Ultraviolets Blues) httpwwwnobelprizeorgnobel_prizeschemistrylaureates2000 Chemistry 2008 green fluorescent protein GFP Shimomura Chalfie Tsien httpwwwnobelprizeorgnobel_prizeschemistrylaureates2008 Chemistry 2014 super-resolved fluorescence microscopy Betzig Hell Moerner httpswwwnobelprizeorgnobel_prizeschemistrylaureates2014 Physics 1953 Phase Contrast Zernike httpswwwnobelprizeorgnobel_prizesphysicslaureates1953 Physics 2009 invention of an imaging semiconductor circuit ndash the CCD sensor Kao Boyle Smith httpwwwnobelprizeorgnobel_prizesphysicslaureates2009 Physics 2014 efficient blue light emitting diodes Akasaki Amano Nakamura httpwwwnobelprizeorgnobel_prizesphysicslaureates2014 Physiology or Medicine 2006 Fire and Mello RNA interference ndash gene silencing by double stranded RNA httpwwwnobelprizeorgnobel_prizesmedicinelaureates2006 Physiology or Medicine 2006 Capecchi Evans Smithies specific gene modifications in mice by the use of embryonic stem cells httpwwwnobelprizeorgnobel_prizesmedicinelaureates2007 Physiology or Medicine 2009 Blackburn Greider Szostak how chromosomes are protected by telomeres and telomerase httpwwwnobelprizeorgnobel_prizesmedicinelaureates2009 Physiology or Medicine 2012 Gurdon Yamamanka matured cells can be reprogrammed to become pluripotent httpwwwnobelprizeorgnobel_prizesmedicinelaureates2012

Table 442 Fluorophores Photophysics Data

Fluorophore Abs or Ex max (nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Acridine orange 271 520 27000 020 5

Alexa Fluor 430 431 541 16000 055 9

Alexa Fluor 488 495 519 71000 094 67

Alexa Fluor 532 532 553 81000 080 65

Alexa Fluor 546 556 573 104000 096 100

Alexa Fluor 568 578 603 91300 075 69

Alexa Fluor 594 590 617 73000 064 47

Allophycocyanin (APC) 650 660 700000 068 476

Atto 390 390 479 24000 090 22

Atto 425 436 484 45000 065 29

Atto 430LS 433 547 32000 065 21

Atto 465 453 508 75000 075 56

Atto 490LS 496 661 40000 030 12

Atto 520 525 547 105000 095 100

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 27: McNamara 20161006 revised draft tables for CPHG Light ...

Atto 532 534 560 115000 090 104

Atto 565 566 590 120000 097 116

Atto 590 598 634 120000 090 108

Atto 610 616 646 150000 070 105

Atto 620 620 641 120000 050 60

Atto 635 637 660 120000 045 54

Atto 655 655 680 125000 050 63

Atto 680 675 699 125000 040 50

ATTO-Dino 1 (dsDNA) 490 531 179000 070 125

ATTO-Dino 2 (dsDNA) 506 535 162000 070 113

Bacteriochlorin (ldquoBCrdquo) 713 717 120000 011 13

Bacteriochlorin BC-T2-T12 737 744 120000 014 17

Bacteriochlorin BC-Ph3-Ph13 736 742 120000 012 14

Bacteriochlorin BC-T2-OMe5-T12 732 739 120000 018 22

Bacteriochlorin BC-V3-V13 750 756 120000 010 12

Bacteriochlorin BC-PE3-PE13 763 768 120000 015 18

Bacteriochlorin BC-A3-A13 768 774 120000 009 11

Bacteriochlorin BC-F3-F13 771 777 120000 007 8

BODIPY 507545 513 549 82800 073 60

BODIPY FL 504 510 70000 090 63

BODIPY TR 588 616 68000 084 57

B-phycoerythrin (B-PE) 545 575 2410000 098 2362

Calcein 494 516 81000 078 63

Cascade Blue 378 423 26000 054 14

Coumarin 6 456 500 54000 078 42

Cresyl violet perchlorate 603 622 83000 054 45

Cy3 552 570 150000 015 23

Cy3B 552 570 130000 067 87

Cy5 649 670 250000 028 70

Cy55 675 694 250000 023 58

Cy7 755 778 250000 028 70

DAPI (in DMSO) 353 465 27000 058 16

DAPI (in H2O) 344 487 27000 004 1

DsRed 558 583 75000 070 52

Eosin Y 525 543 112000 067 75

EYFP 514 527 84000 061 51

Fluorescein 490 514 90000 092 83

FM 1-43 479 598 40000 030 12

Fura-2 Ca++ free 363 512 28000 023 6

Fura-2 Ca++ saturated 335 505 34000 049 17

Fura-2 Mn++ saturated 335 - - 0 0

Fura-2 Zn++ saturated 345 505 34000 069 24

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 28: McNamara 20161006 revised draft tables for CPHG Light ...

Hoechst 33258 (in DMF) 354 486 46000 035 16

Hoechst 33258 (in H2O) 345 507 46000 003 2

Indo-1 Ca++ free 346 475 33000 038 13

Indo-1 Ca++ saturated 330 401 33000 056 18

IRDye38 778 806 179000 035 62

IRDye40 768 788 140000 038 53

IRDye700 681 712 170000 048 81

IRDye78 768 796 220000 031 68

IRDye80 767 791 250000 021 53

IRDye800 787 812 275000 015 41

JOE 520 548 73000 060 44

Lucifer Yellow CH 230 542 24200 021 5

merocyanine 540 559 579 138000 039 54

neo-Cy5 (DMSO) 656 675 195000 025 49

NIR1 761 796 268000 023 62

NIR2 662 684 250000 034 85

NIR3 750 777 275000 028 77

NIR4 650 671 260000 043 1112

Oregon Green 488 496 516 76000 090 68

Oregon Green 514 506 526 88000 096 85

Oysterreg - 645 (ethanol) 651 669 250000 040 100

Oysterreg - 656 (ethanol) 665 684 220000 050 11

Pacific Blue 400 447 29500 055 16

Perylene 253 435 38500 094 36

Phenylalanine 222 279 195 002 lt01

POPOP 256 407 47000 093 44

Quinine sulfate (in 05M H2SO4) 256 451 5700 055 3

Rhodamine 110 496 520 80000 089 71

Rhodamine 6G 530 552 116000 095 110

Rhodamine B 543 565 106000 070 74

Rose bengal 559 571 90400 011 10

R-Phycoerythrin (R-PE) 480 578 1960000 068 1333

SNIR1 666 695 218000 024 52

SNIR3 667 697 245000 024 59

Star 440 SXP 436 515 22700 068 15

Star 470 SXP 472 624 29000 012 4

Star 488 503 524 64500 089 57

Star 512 511 530 84000 082 69

Star 520SXP 515 612 60000 005 3

Star 580 587 607 72000 090 65

Star 600 604 627 43500 073 32

Star 635 639 654 63000 051 32

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 29: McNamara 20161006 revised draft tables for CPHG Light ...

Star 635P 635 651 125000 092 115

Star Red 638 655 212000 090 191

Sulforhodamine 101 576 591 139000 090 125

Texas Red 586 605 108000 077 83

Texas Red-X 583 603 116000 090 104

TMR 540 565 95000 068 65

Trp 287 348 6000 031 2

Tyr 275 303 1500 021 03

Brilliant Violets Brilliant Ultraviolets Brilliant Blue

Brilliant Violet BV421 405 421 2500000 065 1625

Brilliant Violet BV510 405 510 577000 044 254

Brilliant Violet BV570 405 570 2300000 008 184

Brilliant Violet BV605 405 603 2400000 029 696

Brilliant Violet BV650 405 645 2500000 017 425

Brilliant Violet BV711 405 711 2800000 015 420

Brilliant Violet BV785 405 785 2500000 004 100

Brilliant Ultraviolet BUV395 348 395

Brilliant Ultraviolet BUV496 348 496

Brilliant Ultraviolet BUV563 348 563

Brilliant Ultraviolet BUV661 348 661

Brilliant Ultraviolet BUV737 348 737

Brilliant Ultraviolet BUV805 348 805

Brilliant Blue BB515 490 515

Fluorescent nanocrystal quantum dots

Product

Em Peak Em FWHM

Extinction

Coefficient

Quantum

Yield

Brightness

Index

QD525 525 le32 320000 060 192

QD565 565 le34 1100000 040 440

QD585 585 le34 2200000 040 880

QD605 605 le27 2400000 040 960

QD625 625 gt2300

QD655 655 le34 5700000 040 2280

QD705 705 wide

eVolve 605 605

eVolve 655 655

Brightness Index = Extinction coefficient Quantum Yield 1000 Table features fluorophores for which all four major

photophysical parameters absorption (excitation) maximum fluorescence emission maximum extinction coefficient (M-1

cm-1) and fluorescence quantum yield are available QD625 values details have not been published but is brighter than

QD605 or QD655

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 30: McNamara 20161006 revised draft tables for CPHG Light ...

Antibody streptavidin tetramerspentamersdextramers and other macromolecular labeling have ldquodegree of labelingrsquo

(doL) issues As a simplistic rule of thumb one fluorophore can be conjugated to the surface of a protein for every 25000

dalton molecular weight An IgG molecule is ~155000 dalton so ~6 fluorophores can be conjugated without too much

quenching or causing the protein to crash out of solution With random labeling of lysines such as isothiocyantate

chemistry (FITC TRITC) there is a risk of the reactive dye making a covalent bond in an Fab binding site which would

occlude binding to the target antigen epitope If both Fabs were occluded this dye-IgG would not bind antigenic epitope at

all but could bind non-specifically increasing background If there are 50 reactive lysines on the surface of an IgG

molecule and degree of labeling is 6 (+- some variability) the population of antibody molecules applied to a specimen is

going to be very heterogeneous a small reaction may not have any identical antibody molecules DoL of different batches

of antibodies are unlikely to be identical Isotype controls whether a mouse IgG1 monoclonal antibody (defined specificity

different than your interest) or polyclonal affinity purified from sera are at best imperfect controls Immunoglobulins also

vary in glycosylation disulfide bonding and single nucleotide polymorphisms ndash including some that result in amino acid

substitutions that affect Fc Receptor binding affinity A recent (2015) trend has been for vendors ex Miltenyi Biotec

REAfinity to use the same ldquobackbonersquo for their entire product line antibodies

The Fluorophore dyes section of the table is abridged from a 4700+ entry data table Excel file the authors posted on the

internet

httpsworksbepresscomgmcnamara9 = PubSpectra

the website download also contains 400+ entry fluorescent proteins data table Excel file Spectra for many of these dyes

and commercial filters and light sources are available through an interactive website at

httpwwwspectraarizonaedu

QD data from Quantum Dot Corp (acquired by Molecular Probes Thermo Fisher) eVolve 605 and eVolve 655 are Cd

containing quantum dots from Affymetrix eBiosciences (acquired by Thermo Fisher) Bacteriochlorins (BCrsquos) have small

Stokes shifts (Emission maximum ndash Excitation maximum) They have almost as large extinction coefficients in the

ultraviolet 350-390 nm range so for practical use have a huge practical Stokes shifts on the order of 400 nm (they also

have an additional excitation peak in the 480-550 nm range Taniguchi et al (2008) include a graph comparing the full

width half maxima (FWHM) emission spectra of Cyanine dyes (~50 nm) near infrared quantum dots (66 nm QD705 74

nm QD800) BCrsquos (~20 nm) and lsquoexpandedrsquo porphyrins (gt120 nm) We suggest with the right excitation light sources (355

nm laser or ~360 and ~390 nm LEDs) and emission separation (filter wheel one camera cascading filters to multiple

cameras or PMTs) that four or more BCrsquos could be 700-800 nm emission range If a palette of five BCrsquos could be closely

conjugated to Brilliant Blue BB515 excitation peak 488 nm extremely efficient energy transfer in the visible absorption

peaks (~500-550 nm) could enable extreme multiplexing Additional multiplexing may be gained by 355 nm excitation of

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 31: McNamara 20161006 revised draft tables for CPHG Light ...

BUV395 to five BCrsquos Our thanks to Dr Bruce Pitner NIRvana Sciences for discussions extinction coefficient estimates

with respect to NIRvana dyes and Taniguchi et al (2008) and Taniguchi and Lindsey (2016) Additional dye data from

Sednev et al (2015 BioLegend 2016 Brilliant Violets httpwwwbiolegendcombrilliantviolet

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 32: McNamara 20161006 revised draft tables for CPHG Light ...

Table 443 Fluorescent Proteins Photophysics Data

Fluorescent Protein Abs or Ex max

(nm)

Em max (nm)

Extinction Coefficient

Quantum Yield

Brightness Index

Brightness relative to

eGFP

AcS-CFP (acid stable) 440 480 36700 035 13 038

Amarillo (GFPmut3Y203) 514 526 na

na na na

amFP486 Anemonia majano 458 486 40000 024 10 029

amilCFP 441 489 29500 09 27 079

Aqua (GFPmut3L64T65W66) 425 450 na na na na

Aquamarine 430 474 26000 089 23 069

Azure (eGFPY66H) 385 450 na na na na

Azurite 383 447 51000 048 24 073

Bronze (GFPmut3T65W66Y203)

468 507 na na na na

Celeste (eGFP66) 456 490 na na na na

Cerulean 433 475 43000 058 25 074

cgreGFP 485 500 63000 086 54 161

Chlopsid FP 1 + bilirubin 489 523 77000 047 36 108

Chlopsid FP 1-GGG + bilirubin 489 523 77000 011 8 025

Chlopsid FP 2 + bilirubin 489 523 77000 037 28 085

Clavularia sp 456 484 35300 048 17 050

Clover 505 515 111000 076 84 251

CreiLOV 450 495 12500 051 6 019

CyOFP1 497 589 40000 076 30 090

CyOFP1 497 589 40000 076 30 090

CyPet 435 477 35000 051 18 053

dLanYFP 513 524 125000 09 113 335

dsFP483 Discosoma striata 443 483 23900 046 11 033

E2-Crimson 605 646 58500 012 7 021

EBFP 377 446 30000 015 5 013

EBFP2 383 448 32000 045 14 043

EcFbFP (Flavin based) 450 495 12500 039 5 015

ECFP 433 475 33000 014 5 014

eCGP123 493 504 68000 07 48 142

eforCPRFP (chromoprotein) 589 609 111300 016 18 053

eGFP 488 507 56000 06 34 100

eqFP611 559 611 78000 045 35 104

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 33: McNamara 20161006 revised draft tables for CPHG Light ...

eqFP650 592 650 65000 024 16 046

eqFP670 605 670 70000 006 4 013

EYFP 514 526 72000 076 55 163

FF-GFP (fast folding) 490 514 71750 064 46 137

FFTS-YFP (fast folding thermostable)

510 528 95000 068 65 192

FusionRed 580 608 94500 019 18 053

gfasCP (chromoprotein) 577 - 205200 - none none

GFP Aequorea victoria (ldquowild-typerdquo)

397 509 27600 08 22 066

GFPmut3b 500 515 38520 044 17 050

HcRed-Tandem 590 637 160000 004 6 019

hmKeima415 430 612 28000 029 8 024

hmKeima85 438 612 32000 034 11 032

IFP14 684 708 92000 007 6 019

IFP20 690 711 86000 008 7 020

iLOV 450 495 12500 034 4 013

iRFP670 643 670 114000 011 13 037

iRFP670 643 670 114000 011 13 037

iRFP670 663 682 90000 011 10 029

iRFP682 663 682 90000 011 10 029

iRFP702 673 702 93000 008 7 022

iRFP713 690 713 98000 006 6 018

iRFP720 702 720 96000 006 6 017

Katushka 588 635 65000 034 22 066

Katushka2S 588 633 67000 044 29 088

Kriek (photostable mCherry) 593 618 100000 008 8 024

LanFP6-G 499 517 36800 001 2 001

LanFP10-A 492 504 59000 008 5 014

LanFP10-G 492 502 57000 003 2 005

lanRFP-ΔS83 521 592 71000 010 7 021

LanYFP 513 524 150000 095 143 424

LSS-mKate1 463 624 31200 008 2 007

LSS-mKate2 460 605 26000 017 4 013

LSSmOrange 437 572 52000 045 23 070

mAG (monomeric Azami Green)

491 504 52000 076 40 118

mAmetine 406 526 45000 058 26 078

mApple 568 592 75000 049 37 109

Mar (GFPmut3T65W66) 425 450 na na na na

mBeRFP 446 611 65000 027 18 052

mBlueberry2 402 467 51000 048 24 073

mCardinal 604 659 87000 019 17 049

mCerulean2 432 474 47000 060 28 084

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 34: McNamara 20161006 revised draft tables for CPHG Light ...

mCerulean2N 440 484 49000 048 24 070

mCerulean2N(T65S) 439 481 40000 087 35 104

mCerulean3 434 474 34000 084 29 085

mCherry 587 610 72000 022 16 047

mCherry (Cranfill 2016) 586 610 85000 030 26 076

mCherry cp196V12 587 610 49500 021 10 031

mCitrine 516 529 77000 076 59 174

mClover3 506 518 109000 078 85 253

meffRFP 560 576 99600 056 56 166

meleRFP 573 579 45600 085 39 115

mEmerald 487 509 57000 068 39 115

mGarnet 598 670 95000 009 9 025

miniSOG 447 496 16700 037 6 018

mKalama1 385 456 36000 045 16 048

mKate2 588 633 62500 04 25 074

mKeima 440 620 14400 024 3 010

mKO (Monomeric Kusabira-Orange)

548 559 51600 06 31 092

mKOκ 551 563 105000 061 64 191

mLumin 587 621 70000 046 32 096

mMiCy (monomeric Midoriishi-Cyan)

470 496 22150 07 16 046

mNeonGreen 506 517 116000 08 93 276

mNeptune 600 650 59000 02 12 035

mNeptune S28H 590 652 70000 025 18 052

mNeptune25 599 643 95000 028 27 079

modBFP 390 455 27000 033 9 027

modBFP H148K 390 455 25000 017 4 013

mOrange 548 562 71000 069 49 146

mOrange2 549 585 58000 060 35 104

Mostaza (eGFPY203) 425 450 na na na na

mPapaya (Cranfill 2016) 528 540 62000 074 46 137

mPapaya1 530 541 43000 083 36 106

mPlum 590 649 41000 01 4 012

mPlum (Cranfill 2016) 589 645 80000 033 26 079

mRaspberry 598 625 86000 015 13 038

mRFP1 (Cranfill 2016) 586 609 55000 035 19 057

mRojoA 596 633 82000 002 2 005

mRojoA-VHSV 592 622 117000 004 5 014

mRojoA-VYGV 591 616 60000 005 3 009

mRuby 558 605 112000 035 39 117

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 35: McNamara 20161006 revised draft tables for CPHG Light ...

mRuby2 559 600 113000 038 43 128

mRuby3 558 592 128000 045 58 171

mStable (before activation) 603 644 13000 007 1 003

mStable (after activation) 597 633 45000 017 7 022

mStrawberry 574 596 90000 029 26 078

mTagBFP 399 456 41400 063 26 078

mTagBFP2 399 454 50600 064 32 096

mTFP1 462 492 64000 084 54 160

mTurquoise (Cranfill 2016) 434 474 31000 084 26 078

mTurquoise2 (Cranfill 2016) 434 473 31000 092 29 085

mTurquoise2 434 474 30000 093 28 083

mUKG 483 499 60000 072 43 129

mvCitrine-145(3) (Cl- low sensitivity)

516 529 66000 073 48 143

mVenus 515 528 92000 057 52 156

mWasabi 493 509 70000 08 56 167

NirFP 605 670 15700 006 1 003

NowGFP 492 502 57000 076 43 129

NTnC GECI zero Ca++ 505 518 108000 071 77 230

NTnC GECI saturated Ca++ 505 518 52000 065 34 101

NTnC-G166DG202D 505 518 108000 071 77 230

oxBFP 385 448 31000 056 17 052

oxCerulean 435 477 56000 041 23 068

oxGFP 486 510 87000 058 50 150

oxmCerulean3 (moxCerulean3) 434 474 41000 087 36 106

oxmNeonGreen (moxNeonGreen)

505 520 111000 074 82 244

oxVenus 514 526 89000 049 44 130

PhiYFP Ser161Ala 524 537 103000 076 78 233

PhiYFPv 524 537 101300 059 60 178

pmimGFP (copepod tetrameric)

491 505 79000 092 73 216

PpFbFP 450 495 12500 017 2 006

psamCFP 404 492 30800 096 30 088

RFP639 588 639 69000 018 12 037

R-GECO GECI Ca++ free 445 577 22000 006 1 002

R-GECO GECI Ca++ saturated 561 589 51000 020 10 305

Sandercyanin BLA (bilivirdin IX alpha)

375 630

675 21000 13500

002 1 1

001 01

Sapphire 399 511 29000 064 19 055

Sapphire-T (T- Sapphire) 399 511 44000 06 26 079

sarcGFP 483 500 76700 096 74 219

scubRFP 570 578 66400 06 40 119

sfGFP (superfolder) 485 510 83000 065 54 161

ShadowG (dark acceptor) 486 510 89000 lt001 none none

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 36: McNamara 20161006 revised draft tables for CPHG Light ...

sgBCP (S gigantea) 608 122500 none none

sgBCP-Q62M 608 123000 none none

sgBCP-S157T 611 85600 none none

sgBCP-S157C 604 58000 none none

shBFP (S haddoni) 401 458 15400 079 12 036

shBFP-N158KL173I 375 458 19500 078 15 045

shBFP-N158SL173I 375 458 24100 084 20 060

Sirius 355 424 15000 024 4 011

smURFP + biliverdin (BV) 642 670 180000 018 32 096

smURFP + BVMe2 642 670 65000 012 8 023

sREACh (dark acceptor) 517 531 115000 007 8 024

SCFP1 434 477 29000 024 7 021

SCFP2 434 474 29000 041 12 035

SCFP3A 433 474 30000 056 17 050

SCFP3A 434 474 30000 050 15 045

SHardonnay (eYFP-Y203F) 511 524 89000 075 67 200

SYFP2 515 527 101000 068 69 204

TagCFP 458 480 37000 057 21 063

TagGFP 482 505 58000 059 34 102

TagGFP2 483 506 56500 06 34 101

TagRFP 555 584 100000 048 48 143

TagRFP657 611 657 34000 01 3 010

TagRFP675 598 675 46000 008 4 011

TagRFP675 N143S 578 633 45000 038 17 051

TagRFP675 Q41M 595 643 46600 018 8 025

TagYFP 508 524 64000 062 40 118

TDsmURFP + biliverdin (BV) 642 670 170000 018 31 091

tdTomato 554 581 92000 055 51 151

TGP (Thermal Green Protein) 493 507 64000 066 42 126

Topaz 514 527 94500 06 57 169

UnaG 498 527 77300 051 39 117

VafLOV 450 495 12500 023 3 009

Venus2 (V2) 515 528 184000 057 105 312

Venus3 (V3) 515 528 276000 057 157 468

Venus4 (V4) 515 528 368000 057 210 624

Venus5 (V5) 515 528 460000 057 262 780

Venus6 (V6) 515 528 552000 057 315 936

Violeta (GFPmut3W66) 350 425 na na na na

vsfGFP-0 (dimer) 485 510 209000 076 159 473

vsfGFP-0 (monomer) 485 510 104500 070 73 218

WasCFP 492 505 51000 085 43 129

WiPhy (Wi-Phy) 700 722 118000 006 7 021

WiPhy2 (Wi-Phy2) 696 719 118000 009 10 031

YPet 517 530 104000 077 80 238

zFP506 Zoanthus sp 496 506 35600 063 22 067

zFP538 Zoanthus sp 528 538 20200 042 8 025

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf
Page 37: McNamara 20161006 revised draft tables for CPHG Light ...

Table ignores photostability (photoinstability) molecular weight monomer vs dimer vs tetramer oligomerization

aggregation prone-ness pKa (pH sensitivity) and more Jellyfish (EGFP) coral Amphioxus etc fluorescent proteins

require one or two oxygen molecules to manufacture the chromophore bonds (a product is H2O2) LOV proteins require

Flavin cofactor Wi-Phy iRFPs UnaG require biliverdin This table also excludes photocontrollable fluorescent proteins

photoactivatable photoconvertible photoswitchable Cranfill et al (2016) published an experimental direct comparison of

several popular fluorescent proteins with literature comparisons NTnC GECI (genetically engineered Ca++ ion indicator)

is used as an example of a small state of the art fluorescent protein biosensor also shown is Ca++ ion insensitive double

mutant control (Barykina et al 2016) NTnC is an inverse signal (No Ca++ bright Ca++ saturated ~50 brightness) FP

biosensor ndash the paper shows simultaneous use with R-GECO (red fluorescence dark to bright) FP biosensor ndash these

could be used together to enhance ratiometric response Subcellular localization ex to cytoplasmic side of plasma

membrane could be used to further improve signal-to-noise ratio and provide compartment specific data The NTnC

Ca++ insensitive double mutant and mCherry (R-GECOrsquos parent Zhao et al 2011) could be simultaneously localized and

concentrated to the nucleolus Golgi body or other lsquoout of the wayrsquo compartment PubMed

(httpswwwncbinlmnihgovpubmed) Google ScienceDirect Highwire Press and other search engines and publishers

can be used to find full text publications of all fluorophores and fluorescent proteins listed Photo-changeable fluorescent

proteins are reviewed in Turkowyd et al (2016) and summarized in Lambert T Thorn (2016) SandercyaninBLA is a

lipocalin family member non-fluorescent apo-protein is 18 kDa fluorescent tetramer is 75 kDa quantum yield in 70

D2O is 166x that of in H2O (00267 vs 0016) (Ghosh et al (2016)

  • From the SelectedWorks of George McNamara
  • Fall October 3 2016
  • McNamara 20161006 revised draft tables for CPHG Light Microscopy and Image Analysispdf
  • tmp2O7op4pdf

Apache Beam @ GCPUG.TW Flink.TW 20161006

Apache Beam @ GCPUG.TW Flink.TW 20161006

From Root to McNamara

From Root to McNamara

ALEX MCNAMARA - PUBLICITY

ALEX MCNAMARA - PUBLICITY

Presentación McNamara

Presentación McNamara

N McNamara - espace.library.uq.edu.au

N McNamara - espace.library.uq.edu.au

McNamara Airway

McNamara Airway

McNamara, A.J.

McNamara, A.J.

McNamara S32A 06

McNamara S32A 06

Diario Resumen 20161006

Diario Resumen 20161006

20161006 rsp2016 ohkawa-presen

20161006 rsp2016 ohkawa-presen

Niamh McNamara BA, PhD

Niamh McNamara BA, PhD

20161006 taiwan user_community_final

20161006 taiwan user_community_final

KATHLEEN R. MCNAMARA

KATHLEEN R. MCNAMARA

Análisis de Mcnamara

Análisis de Mcnamara

McNamara - KsuWeb

McNamara - KsuWeb

McNamara Graesser Coh-Metrix

McNamara Graesser Coh-Metrix

Sydney McNamara

Sydney McNamara

George McNamara

George McNamara

Portfolio: Laura McNamara

Portfolio: Laura McNamara

Mrs. McNamara

Mrs. McNamara