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Explorable
                          Microscopy

                          Bringing gigapixel imagery to the micro scale




Thursday, July 28, 2011
Changing the way
                              you see



Thursday, July 28, 2011
GigaPans are from mars




                           (Venus is too cloudy for pictures)


Thursday, July 28, 2011
Thursday, July 28, 2011
Thursday, July 28, 2011
Thursday, July 28, 2011
Scanning Electron
    Microscope




Thursday, July 28, 2011
Thursday, July 28, 2011
Thursday, July 28, 2011
Context and detail




Thursday, July 28, 2011
Thursday, July 28, 2011
An eye lash next to a dried blood sample
                          (intern blood - Molly has turned out to
                          be useful)




                                 Red blood cells

Thursday, July 28, 2011
Thursday, July 28, 2011
Thursday, July 28, 2011
Eutetramorium
                                                            mocquerysi




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




Thursday, July 28, 2011
Thursday, July 28, 2011
Snow Algae


Thursday, July 28, 2011
Thursday, July 28, 2011
Thursday, July 28, 2011
Thursday, July 28, 2011
Assorted Pollen




Thursday, July 28, 2011
137045 Views
                          Mentioned on
                          New Scientist Blog




Thursday, July 28, 2011
400 Images, 280 Megapixels, 287,000 Views!

Thursday, July 28, 2011
Over 500,000 views of ants!

                          When people can explore GigaPans
                                                     Text




                          they (sometimes) start to care.




Thursday, July 28, 2011
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.


Thursday, July 28, 2011
Adapt Microscopes




Thursday, July 28, 2011
Imaging the Imager

                                               •CCD from a Canon
                                                Powershot at 1000x.

                                               •170 individual
                                                photographs

                                               •380 megapixels



Thursday, July 28, 2011
Test/Calibration Area




                            Pixels!



Thursday, July 28, 2011
Flea by
  Jay Longson

  5,640 images




Thursday, July 28, 2011
Thursday, July 28, 2011
Thursday, July 28, 2011
Thursday, July 28, 2011
Gene Cooper
                          http://GigaMacro.com
                          Large Mosaic + Focus Stalking =

                          Huge numbers of images!




Thursday, July 28, 2011
Thursday, July 28, 2011
Thursday, July 28, 2011
 Passion Butterfly
                           1,790 individual photographs
                           1.37 gigapixels




Thursday, July 28, 2011
 Passion Butterfly
                           1,790 individual photographs
                           1.37 gigapixels




Thursday, July 28, 2011
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/


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




Thursday, July 28, 2011
MakerBot as Imager




Thursday, July 28, 2011
MakerBot as Imager




Thursday, July 28, 2011
MakerBot as Imager




Thursday, July 28, 2011
MakerBot as Imager




Thursday, July 28, 2011
MakerBot as Imager




Thursday, July 28, 2011
Crab Shell - 200 megapixels, focus stacked, 1,560 images




Thursday, July 28, 2011
Thursday, July 28, 2011
Thursday, July 28, 2011
Thursday, July 28, 2011
Thursday, July 28, 2011
Thursday, July 28, 2011
one thing.




Thursday, July 28, 2011
You. Now.




Thursday, July 28, 2011
Overview
           What we are doing
           Devices
           Tools and process
           Presentation, interaction
           Gigapixel imagery as Platform
           Exploring Time Series




Thursday, July 28, 2011
Scale Independent, Explorable Images




Thursday, July 28, 2011
Different Scales




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


Thursday, July 28, 2011
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




Thursday, July 28, 2011
Focus Stacking




Thursday, July 28, 2011
Focus Stacking




Thursday, July 28, 2011
Focus Stacking




Thursday, July 28, 2011
12 Bits



                          Fitz:

                          Do you want your
                          board back now?




Thursday, July 28, 2011
Focus Stacking - Calibration




Thursday, July 28, 2011
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




Thursday, July 28, 2011
Thursday, July 28, 2011
Thursday, July 28, 2011
Thursday, July 28, 2011
Thursday, July 28, 2011
Thursday, July 28, 2011
Thursday, July 28, 2011
Thursday, July 28, 2011
Microscope Adapter Kit




Thursday, July 28, 2011
Poor Orphans




Thursday, July 28, 2011
Thursday, July 28, 2011
Thursday, July 28, 2011
Thursday, July 28, 2011
Thursday, July 28, 2011
Low cost Macro




Thursday, July 28, 2011
Thursday, July 28, 2011
Thursday, July 28, 2011
Thursday, July 28, 2011
Devices

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




Thursday, July 28, 2011
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




Thursday, July 28, 2011
Platform for Gigapixel Applications
      Macro invertebrates http://www.mcaulifferegional.org/Expedition/bioticindex.html
      GigaPan feature annotation tool
     




Thursday, July 28, 2011
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.

Thursday, July 28, 2011
Best practices
     in using Gigapixel Imagery for Science




        Provide unprocessed images




Thursday, July 28, 2011
Best practices
     in using Gigapixel Imagery for Science




Thursday, July 28, 2011
When is the next Where.
           Explore and see what you find
           timelapse gigapans
           Time series and tiles
           Snacking
           Particulates




Thursday, July 28, 2011
Thursday, July 28, 2011

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Explorable Microscopy OSCon Talk 7/28/11