This document discusses using gigapixel imagery to view objects under microscopes. It shows examples of gigapixel images taken of various biological and microscopic subjects, such as blood cells, pollen, insects, and snow algae. It also describes the tools and techniques used to create gigapixel microscope images, including focus stacking, different microscope devices, and adapting non-microscope cameras to capture gigapixel images. The goal is to provide explorable, high-resolution images that increase understanding of microscopic subjects.

1. Explorable
Microscopy
Bringing gigapixel imagery to the micro scale
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2. Changing the way
you see
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3. GigaPans are from mars
 (Venus is too cloudy for pictures)
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7. Scanning Electron
Microscope
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10. Context and detail
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12. 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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15. Eutetramorium
mocquerysi
http://www.gigapan.org/gigapans/28734/
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17. Snow Algae
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21. Assorted Pollen
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22. 137045 Views
Mentioned on
New Scientist Blog
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23. 400 Images, 280 Megapixels, 287,000 Views!
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24. Over 500,000 views of ants!
When people can explore GigaPans
Text
they (sometimes) start to care.
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25. 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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26. Adapt Microscopes
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27. Imaging the Imager
•CCD from a Canon
Powershot at 1000x.
•170 individual
photographs
•380 megapixels
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28. Test/Calibration Area
Pixels!
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29. Flea by
Jay Longson
5,640 images
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33. Gene Cooper
http://GigaMacro.com
Large Mosaic + Focus Stalking =
Huge numbers of images!
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36.  Passion Butterfly
 1,790 individual photographs
 1.37 gigapixels
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37.  Passion Butterfly
 1,790 individual photographs
 1.37 gigapixels
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39. Bees

Bee Frame test http://gigapan.org/gigapans/fullscreen/80976/
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40. Bees
Bee Frame test http://gigapan.org/gigapans/fullscreen/80976/
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41. Bees
Bee Frame test http://gigapan.org/gigapans/fullscreen/80976/
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42. Bees
Bee Frame test http://gigapan.org/gigapans/fullscreen/80976/
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43. Bees
Bee Frame test http://gigapan.org/gigapans/fullscreen/80976/
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44. Time Lapse Bees - Bleeding Edge
 http://timemachine.gigapan.org/wiki/Bees
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45. MakerBot as Imager
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46. MakerBot as Imager
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47. MakerBot as Imager
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48. MakerBot as Imager
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49. MakerBot as Imager
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50. Crab Shell - 200 megapixels, focus stacked, 1,560 images
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56. one thing.
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57. You. Now.
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58. Overview
 What we are doing
 Devices
 Tools and process
 Presentation, interaction
 Gigapixel imagery as Platform
 Exploring Time Series
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59. Scale Independent, Explorable Images
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60. Different Scales
Textile full image by Surangi - 110 megapixels http://gigapan.org/gigapans/64710/
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61. 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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62. Focus Stacking
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63. Focus Stacking
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64. Focus Stacking
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65. 12 Bits
Fitz:
Do you want your
board back now?
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66. Focus Stacking - Calibration
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67. 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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75. Microscope Adapter Kit
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76. Poor Orphans
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81. Low cost Macro
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85. Devices
 NanoGigapan
 MacroBot
 Jay’s scope at NASA
 Microscope Adapter Kit
 Low Cost Macro
 MakerBot
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86. 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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87. Platform for Gigapixel Applications
 Macro invertebrates http://www.mcaulifferegional.org/Expedition/bioticindex.html
 GigaPan feature annotation tool

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88. 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.
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89. Best practices
in using Gigapixel Imagery for Science
Provide unprocessed images
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90. Best practices
in using Gigapixel Imagery for Science
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91. When is the next Where.
 Explore and see what you find
 timelapse gigapans
 Time series and tiles
 Snacking
 Particulates
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