Explorable Microscopy OSCon Talk 7/28/11

Explorable
Microscopy

Bringing gigapixel imagery to the micro scale

Thursday, July 28, 2011

Changing the way
you see


GigaPans are from mars

 (Venus is too cloudy for pictures)


Scanning Electron
Microscope


Context and detail


An eye lash next to a dried blood sample
(intern blood - Molly has turned out to
be useful)

Red blood cells


Eutetramorium
mocquerysi

http://www.gigapan.org/gigapans/28734/


Snow Algae


Assorted Pollen


137045 Views
Mentioned on
New Scientist Blog


400 Images, 280 Megapixels, 287,000 Views!


Over 500,000 views of ants!

When people can explore GigaPans
Text

they (sometimes) start to care.


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.


Adapt Microscopes


Imaging the Imager

•CCD from a Canon
Powershot at 1000x.

•170 individual
photographs

•380 megapixels


Test/Calibration Area

Pixels!


Flea by
Jay Longson

5,640 images


Gene Cooper
http://GigaMacro.com
Large Mosaic + Focus Stalking =

Huge numbers of images!


 Passion Butterfly
 1,790 individual photographs
 1.37 gigapixels


Bees


Bee Frame test http://gigapan.org/gigapans/fullscreen/80976/


Bees

Bee Frame test http://gigapan.org/gigapans/fullscreen/80976/


Time Lapse Bees - Bleeding Edge
 http://timemachine.gigapan.org/wiki/Bees


MakerBot as Imager


Crab Shell - 200 megapixels, focus stacked, 1,560 images


one thing.


You. Now.


Overview
 What we are doing
 Devices
 Tools and process
 Presentation, interaction
 Gigapixel imagery as Platform
 Exploring Time Series


Scale Independent, Explorable Images


Different Scales

Textile full image by Surangi - 110 megapixels http://gigapan.org/gigapans/64710/


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


Focus Stacking


12 Bits

Fitz:

Do you want your
board back now?


Focus Stacking - Calibration


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


Microscope Adapter Kit


Poor Orphans


Low cost Macro


Devices

 NanoGigapan
 MacroBot
 Jay’s scope at NASA
 Microscope Adapter Kit
 Low Cost Macro
 MakerBot


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


Platform for Gigapixel Applications
 Macro invertebrates http://www.mcaulifferegional.org/Expedition/bioticindex.html
 GigaPan feature annotation tool



Best practices
in using Gigapixel Imagery for Science
 Provide Full Context
 Disclosure
- Time of acquisition
- True color, color calibration
- Scale: tools for measuring scale
- Number of images, resolution
 Raw images: focus stacking and stitching can introduce
artifacts. For computational photography the raw images are
the data.


Best practices

Provide unprocessed images


Best practices


When is the next Where.
 Explore and see what you find
 timelapse gigapans
 Time series and tiles
 Snacking
 Particulates


Explorable Microscopy OSCon Talk 7/28/11

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