Explorable Microscopy OSCon Talk 7/28/11
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Explorable Microscopy Bringing gigapixel imagery to the micro scale Thursday, July 28, 2011
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Transcript of Explorable Microscopy OSCon Talk 7/28/11
Explorable Microscopy
Bringing gigapixel imagery to the micro scale
Thursday, July 28, 2011
Changing the wayyou see
Thursday, July 28, 2011
GigaPans are from mars
(Venus is too cloudy for pictures)
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Scanning ElectronMicroscope
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Context and detail
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An eye lash next to a dried blood sample (intern blood - Molly has turned out to be useful)
Red blood cells
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Eutetramorium mocquerysi
http://www.gigapan.org/gigapans/28734/
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Snow Algae
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Assorted Pollen
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137045 ViewsMentioned onNew Scientist Blog
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400 Images, 280 Megapixels, 287,000 Views!
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Text
Over 500,000 views of ants!
When people can explore GigaPans
they (sometimes) start to care.
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Sweeter than Ants
Text
From left to right the sweeteners are Equal (dextrose, maltodextrin, and aspartame), Splenda (dextrose, maltodextrin, and sucralose), Sugar in the raw, and regular table sugar.
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Adapt Microscopes
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•CCD from a Canon Powershot at 1000x.
•170 individual photographs
•380 megapixels
Imaging the Imager
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Pixels!
Test/Calibration Area
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Flea by Jay Longson
5,640 images
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Gene Cooper http://GigaMacro.com
Large Mosaic + Focus Stalking =
Huge numbers of images!
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Passion Butterfly 1,790 individual photographs 1.37 gigapixels
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Passion Butterfly 1,790 individual photographs 1.37 gigapixels
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Bees
Bee Frame test http://gigapan.org/gigapans/fullscreen/80976/
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Bees
Bee Frame test http://gigapan.org/gigapans/fullscreen/80976/
Thursday, July 28, 2011
Bees
Bee Frame test http://gigapan.org/gigapans/fullscreen/80976/
Thursday, July 28, 2011
Bees
Bee Frame test http://gigapan.org/gigapans/fullscreen/80976/
Thursday, July 28, 2011
Bees
Bee Frame test http://gigapan.org/gigapans/fullscreen/80976/
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Time Lapse Bees - Bleeding Edge http://timemachine.gigapan.org/wiki/Bees
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MakerBot as Imager
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MakerBot as Imager
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MakerBot as Imager
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MakerBot as Imager
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MakerBot as Imager
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Crab Shell - 200 megapixels, focus stacked, 1,560 images
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one thing.
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You. Now.
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Overview What we are doing Devices Tools and process Presentation, interaction Gigapixel imagery as Platform Exploring Time Series
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Scale Independent, Explorable Images
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Different Scales
Textile full image by Surangi - 110 megapixels http://gigapan.org/gigapans/64710/
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Focus Stacking ImageJ http://rsbweb.nih.gov/ij/
- “Like weaponized photoshop” Dan Kaminsky Extended Depth of Field Plugin for ImageJ
- http://bigwww.epfl.ch/demo/edf/ Zerene Stacker (commercial, but good) http://www.zerenesystems.com/ http://en.wikipedia.org/wiki/Focus_stacking
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Focus Stacking
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Focus Stacking
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Focus Stacking
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12 Bits
Fitz:
Do you want your board back now?
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Focus Stacking - Calibration
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Focus Stacking - HD Video Resolve 0.5 microns with a 40x objective. 1080 HD Video = 29.97two megapixel images per second. Split the frames
- qt tools by david van brink- http://omino.com/sw/qt_tools/
Normal Focus stacking
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Microscope Adapter Kit
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Poor Orphans
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Low cost Macro
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Devices
NanoGigapan MacroBot Jay’s scope at NASA Microscope Adapter Kit Low Cost Macro MakerBot
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Presentation/Interaction Large images, raw mode, tif
GigaPan site PS2 controller, demo Modest Maps viewer TMS tiles, open layers
Share, explore, work with the images
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Platform for Gigapixel Applications Macro invertebrates http://www.mcaulifferegional.org/Expedition/bioticindex.html GigaPan feature annotation tool
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Best practices in using Gigapixel Imagery for Science
Provide Full ContextDisclosure- Time of acquisition- True color, color calibration- Scale: tools for measuring scale- Number of images, resolutionRaw images: focus stacking and stitching can introduce
artifacts. For computational photography the raw images are the data.
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Best practices in using Gigapixel Imagery for Science
Provide unprocessed images
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Best practices in using Gigapixel Imagery for Science
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When is the next Where. Explore and see what you find timelapse gigapans Time series and tiles Snacking Particulates
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