Intro to Super Resolution: When and why you need it - PKU · 2016-11-28 · Tubulin and...
Transcript of Intro to Super Resolution: When and why you need it - PKU · 2016-11-28 · Tubulin and...
Imagination at work
Intro to Super Resolution: When and why you need itStructured Illumination Microscopy
Leanna Ferrand, Product Support LeaderCellular Imaging & Analysis, GE Healthcare15 November 2016
Back to Basics
Functions of a microscope
Magnification
Increase the size of an
object
Resolution
Distinguish one object
from another
Contrast
Define the boundaries of
an object
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Resolution limit of a light microscope
d = λ / 2NA
λ = wavelength of light
NA = numerical aperture of
objective
We can’t change wavelength and there is a practical limit to
how high we can push NA
This is the diffraction limit!Molecules closer than
~200nm apart will appear to be the same structure
Distance (D)
Inte
nsi
ty
Distance (D)
Inte
nsi
ty
Distance (D)
Inte
nsi
ty
411/15/2016200𝑛𝑚 =
568
2 ∗ 1.42
What is Super Resolution?
Conventional microscope
250 x 250 x 600 nm
Vs
3D-SIM
100 x 100 x 300
=
8 fold volume resolution improvement!!
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What is Super Resolution?
The diffraction limit exists because we can’t change
wavelength and there is a physical limit to how far we
can push NA. Why not?
PHYSICS! We can’t break the laws of physics, so what
can we do?
• Super Resolution technologies use physics to enable imaging below the diffraction limit
• Diffraction limit in commercially available methods:
– Confocal or Widefield: 250nm in x, y and 550nm in z
– Structured Illumination: 120 nm in x, y and 320nm in z (488nm wavelength)
– Localization Microscopy ~30-50nm in x, y
– Stimulated Emission Depletion (STED): ~50-70nm in x,y and ~300nm in z
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Super Resolution TechnologiesLocalization
How it works
• Collect series of many images, activating a few molecules at a time
• Use Gaussian model to fit and localize
• Plot all found points; create an image
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What does it get you?
• 30-50nm resolution
Advantages
• 30-50nm resolution
• Complimentary to immuno-EM
• Simple hardware design
Disadvantages
• No live cell capability for Fluors
• Limited to biology at the coverslip
• Challenging sample preparation
• Requires time-sensitive buffers
Super Resolution TechnologiesStimulated Emission Depletion - STED
How it works
• Two excitation sources, 1 traditional laser spot + 1 doughnut shaped beam
• Fluorescence w/in doughnut is quenched, leaves smaller PSF sample
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What does it get you?
• 60-70nm in lateral resolution
• 560-700nm resolution axially
Advantages
• Tunable lateral resolution; Resolution depends on power of STED beam
• Only direct visualization super resolution imaging technique; No math required
Disadvantages
• Special probes
• Multi color is limited
• Photobleaching due to laser power
• Lack of increased z resolution
Super Resolution TechnologiesStructured Illumination
How it works
• Illuminate sample with known pattern
• Measure Optical Transform Function
• Utilize maths to extract higher resolution information (frequencies)
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What does it get you?
• Two-fold increase in resolution in x, y, and z
• Significant increase in contrast
Advantages
• Multiple imaging modes
• 3D SIM mode provides two fold increase in resolution in x, y, and z
• Live cell time-lapse imaging!!
Disadvantages
• Only two-fold increase in resolution in x, y, and z
• Artifacts
• Limited z range due to widefield mode
Super Resolution Technologies
SIM Scientific Questions
When do you need SIM?
Structural and diffraction limited
• Where does a protein localize within a centrosome (or synaptonemalcomplex or structure of interest)?
• Desmosome structure
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Colocalization
• Two proteins which appear to colocalize by high resolution microscopy
Temporal and diffraction limited
• Resolving localization of two proteins through the cell cycle
• Bacterial cell dynamics
ImmunoEM fails or suggests additional information
• Does EM suggest additional information is to be gained?
• Do you need 3D data?
SIM Scientific QuestionsWhen do you need SIM?
Structural and diffraction limited: Imaging centrosomes
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A-M. Gabryjonczyk, A. Ferrand – University of Basel
Sonnen et al., JCS, 2013
Distal Proximal Walls Merged
Wide-field Deconvolved 3D-SIM
SIM Scientific QuestionsWhen do you need SIM? Temporal and diffraction limited-FtsZ dynamics in E. coli
OMX 3D-SIM – Max ProjectionWidefield – Max Projection
FtsZ-mNeonGreen
Z
X
Resolve
ring
structure in
living cells
Desmond Moore, Erickson Lab Duke
Max projections
SIM applicationsFixed samples
Wid
efi
eld
3D
-SIM
Lothar Schermelleh, Juergen Neumann, LMI Munich
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OMX 3D-Structured Illumination MicroscopyNuclear Pore Complexes
OMX 3D-Structured Illumination MicroscopyResolve ring structure at base of cilia
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Wid
efi
eld
OM
X 3
D-S
IM
1 µm
Green OverlayRed
1 µm Max projections
Shah Lab, Harvard
DeLuca Lab, Colorado State University 18
OMX 3D-Structured Illumination MicroscopyTubulin and kinetochores in PTK1 cells
Structured Illumination How does it work?
Courtesy Stephen Cody Ph.D, Monash Micro Imaging
Structured Illumination Microscopy (SIM)
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Structured Illumination Microscopy (SIM)
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Structured Illumination Microscopy (SIM)
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Fiber optic
cable
Widefield light path
ObjectiveOptics
Structured Illumination Microscopy (SIM)How is interference created?
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Fiber optic
cable
Diffraction
grating
Structured Illumination Microscopy (SIM)How is interference created?
+1
0
-1
-2
+2
Collimating
lens
Objective
Structured Illumination Microscopy (3D-SIM)Imaging Sequence
Phase 1 Phase 2 Phase 3 Phase 4 Phase 5A
ng
le 1
An
gle
2A
ng
le 3
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Structured Illumination Microscopy (SIM)
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3D-SIM 2D-SIM TIRF-SIM
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Fiber optic
cable
+1
0
-1
-2
+2
Collimating
lensDiffraction
grating
Structured Illumination Microscopy (SIM)How is interference created?
Objective
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Line spacing for each wavelength
fixed. Resolution compromised!
Back aperture
0
+1
-1
0
+1
-1
Line spacing for each wavelength
adjustable. Resolution optimized!
0
+1
-1
0
+1
-1
0
+1
-1
DeltaVision™ OMX Blaze ModuleAchieve the best resolution for each wavelength
Does it really work in live samples?
All microscopy requires compromise…
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SpatialResolution
Phototoxicity Speed
Multi-D
Z-depth, l, t
Fixed cell imaging Photon Budget
SpatialResolution
Phototoxicity Speed
Multi-D
Z-depth, l, t
Live cell imaging Photon Budget
OMX Live Cell 3D-SIM ImagingResolve details of ER structure in living yeast
Snapp Lab, Albert Einstein
ER marker
OMX 3D-SIM Widefield
OMX Live Cell 3D-SIM Imaging2-color imaging for 200 time points at 96 fps
Widefield Image OMX 3D-SIM Image
OMX Seminar | January 2015
Mito-GFPER-mCherry
Vaughan Lab, UW32
DeltaVision™ OMX Live Cell 3D-SIM ImagingLLC-PK1 cells going through mitosis
Widefield Image OMX 3D-SIM Image
Heidi Hehnly, Scott Lab UW & HHMI
EB3-GFPMax Projections
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2D SIM TIRF Applications
mCherry-LifeAct-Actin in HeLa cells; Michael Porter, AQLM 201561 time points @ 1 2D SI TIRF frame every 5 seconds for 5 minutes!
TIRF Image 2D TIRF SIM Image
DeltaVision™ OMX SR Live Cell 2D TIRF SIMActin dynamics and “Nest” formation
mCherry-LifeAct-Actin in HeLa; Michael Porter, AQLM 2015241 time points @ 1 2D-SIM TIRF frame every 15 secs for 60 mins!
TIRF Image 2D TIRF SIM Image
DeltaVision™ OMX SR Live Cell 2D TIRF SIMActin dynamics & Cell Viability over 60 minutes!
GFP-tagged caveolin movement
visualized with 2D-SIM TIRF
DeltaVision™ OMX SR Live Cell 2D TIRF SIMVisualize individual Caveolin to enable tracking
TIRF Image 2D TIRF SIM Image
GFP-Caveolin in HeLa; Michael Porter, AQLM 2015151 time points @ 1 2D-SIM TIRF frame every 2 seconds for 5 minutes!
mCherry-Tubulin, GFP-Clathrin; Michael Porter, AQLM 2015360 time points @ 1 2D-SIM TIRF frame every 30 seconds for 3 hours!
DeltaVision™ OMX SR Live Cell 2D TIRF SIMClathrin plaques and microtubule dynamics
TIRF Image 2D TIRF SIM Image
Solutions from GEHCStructured Illumination Microscopy
DeltaVision OMX SR
• Compact single enclosure system
• SIM only or Ring-TIRF only configurations available
• 2D/3D SIM light pattern generator (New Blaze module)
• 48 x 24 mm stage travel stage
• Multi-camera mounting and alignment system
• Compact Laser illumination system
• Multifunction environmental control system
Traditional SIM Light Paths: Rotary Stage or Cube Rotation Compromises
• Need to control 3 parameters within one device:
– Beam positioning for SIM
– Phase stepping
– Angular rotation
• Only one wavelength can get optimal resolution in any experiment
• Slow!
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OMX BLAZE Structured Illumination Light Path
How did we get fast enough for live cell imaging?
Separate out the parameters!
Diffraction Grating splits the laser light into orders or beams
Phase Control Module positions the orders/beams to: Create the desired SI interference pattern Optimize resolution for each wavelength Create the phase shifts during experiments
Angle Control Module rotates the orders/beams to the 3 angles
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What are the features of a great live cell super resolution system?
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Optimal resolution
for all wavelengths
Localization
microscopy
Ring TIRF
Environmental
control3D SIM
Ultra-fast
widefield imaging
2D SIM
2D TIRF SIM
Acquisition speed
DeltaVision OMX SR: Improve your science, don’t reinvent it!
Super Resolution Technologies
“The more resolution you ask for the more pain you can expect . You want to use the method that gives you the poorest resolution but still gets you the biological answer you are looking for.”
– Eric Betzig, Science webinar July 2015
• OMX users published 115 peer-reviewed papers in 2015 alone!
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Sample Prep Recommendations for SIM and for conventional microscopy
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SIM Sample Prep RecommendationsMount sample on #1.5 coverslips
Objective
#1.5 Coverslips are 170 µm thick
Microscopes are optimized for #1.5 cover glass!
High precision #1.5 coverslips
require less optimization!
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SIM Sample Prep RecommendationsDo NOT mount sample on glass slide
Objective
Glass Slide
#1.5 Coverslipx
Mounting on the slide introduces an
uncontrollable variable!
The working range of a high NA objective is very small <200µm!
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SIM Sample Prep RecommendationsMount sample on #1.5 coverslips
Objective
Glass Slide
#1.5 Coverslip
Mounting on the coverslip helps keep the sample in the working range of the
objective!
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SIM Sample Prep RecommendationsDo NOT mount tissue sections on glass slide
Glass Slide
#1.5 CoverslipxTissue Section
• Tissue sections are not flat• Uneven surface can add additional distance from objective• Makes matching RI difficult
Mounting on slide introduces additional
uncontrollable distances
Objective
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SIM Sample Prep RecommendationsMount tissue section on #1.5 coverslip
Glass Slide
#1.5 CoverslipTissue Section
Objective
Keeps sample within working range of objective & can help with imaging deeper structures
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SIM Sample Prep RecommendationsDo not use DAPI in the mounting media
Objective
Glass Slide
Coverslip
DAPI can cause high levels of background! To
image with DAPI, perform a separate labeling step &
wash well!
Use glycerol based mounting media with an anti-fade agent
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Fixed Sample Preparation
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Mounting and Antifades.
• Probably the most critical step from the imaging point of view.
• Mounting agents are designed to stabilize the sample but more importantly provide controlled(known?) refractive index to match optics.
• May protect against photobleaching if antifade agent included in formulation
• Many different formulations available.– Organic solvent based resins.
– Glycerol:Polyalcohol:Water mixes.
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Considerations for Mounting Agents
• Hardening mounting agents may give inconsistent refractive index values in sample depending on effectiveness of curing
• Non-hardening mounting agents may not preserve samples long term but typically have more stable RI
• Antifade agents generally a good idea for repeated imaging situations (3D-SIM)
• Most effective antifade reagents are not live cell compatible
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Considerations for Mounting Agents
• Hardening agents may also cause significant specimen compression if they shrink during curing, e.g. PVA/Mowiol based formulas.
• To avoid compression artifacts consider mounting sample with spacer or gasket to prevent coverslip being sucked down onto slide.
• Do not use any mounting agent that has a counterstain in it (like DAPI) as it will increase background significantly and usually gets worse over time.
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OMX Sample Prep RecommendationsMount with non-hardening mounting media
Non-hardening varieties (Vectashield) help preserve 3D structure
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Optical Considerations
• Coverslips
• Spherical Aberration – yes you have it too!
• Chromatic aberration/alignment
• Sub-resolution alignment
• Clean your lenses
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Use the right coverslips…
• Most microscope objectives are designed for #1.5 or 170 nm thick coverslips
• If you use something different you will not be able to properly correct the spherical aberration and your ability to image at depth will be compromised
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Sample Induced Spherical Aberration
X
Z
SphericalAberrationIdeal
C
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Spherical Aberration Is Real
Axial Stretching and Signal Degradation due to Spherical aberration.
100x Oil Immersion objective , 1.4 NA. 25 micron depth, 0.25 nm steps
RI 1.5 mounting media RI 1.38 mounting media
Coverslip Position
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Why do I care, I only look in 2D?
X
Y
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Axial Chromatic Aberration
UncorrectedAchromat
CorrectedApochromat
Objective
Type
Spherical
Aberration
Chromatic
Aberration
Field
Curvature
Achromat 1 Color 2 Colors No
Plan Achromat 1 Color 2 Colors Yes
Fluorite 2-3 Colors 2-3 Colors No
Plan Fluorite 3-4 Colors 2-4 Colors Yes
Plan Apochromat 3-4 Colors 4-5 Colors Yes
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SIM Sample Prep RecommendationsSummary
• Least strict requirements of all the super resolution methods
• Get sample as close as possible to #1.5 coverslip
• Use photostable dyes
• Consider using antifade agents in mounting media
• Minimize refractive index mismatch
AppendixSelected Publications in Structured Illumination Microscopy3D-SIM1. Wynne, et al. Kinetochore function is controlled by a phospho-
dependent coexpansion of inner and outer components. (http://jcb.rupress.org/content/210/6/899.long)
2. Crawley, et al. Intestinal brush border assembly driven by protocadherin-based intermicrovillar adhesion. (http://www.cell.com/cell/abstract/S0092-8674(14)00215-3)
3. Zhao, et al. The Cep63 paralogue Deup1 enables massive de novo centriole biogenesis for vertebrate multiciliogenesis. (http://www.nature.com/ncb/journal/v15/n12/full/ncb2880.html)
4. Das, et al. Apical abscission alters cell polarity and dismantles the primary cilium during neurogenesis. (https://www.sciencemag.org/content/343/6167/200.short)
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AppendixSelected Publications in Structured Illumination MicroscopyLive Cell1. Strauss, et al. 3D-SIM Super resolution microscopy reveals a bead-
like arrangement for FtsZ and the division machinery: implications for triggering cytokinesis. (http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001389)
2. Conduit, et al. A molecular mechanism of mitotic centrosome assembly in Drosophila. (http://elifesciences.org/content/early/2014/08/22/eLife.03399)
3. Liu, et al. Novel thioredoxin-like proteins are components of a protein complex coating the cortical microtubules of Toxoplasma gondii. (http://ec.asm.org/content/12/12/1588.long)
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