1. 2 Last Workshop… ImageJ basics –Image manipulation –Setting scale –Making measurements...

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Last Workshop…

• ImageJ basics– Image manipulation– Setting scale– Making measurements– Counting particles

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Today’s Plan…

• Advanced Image Analysis– Working with “stacks”

• Where to get images– Finding existing images– Creating your own images

• Online exercises– SimpleScience.org

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Stacks

• A collection of multiple images packaged together into a single computer file

• Think of a deck of cards– X & Y dimensions are spatial– Z dimension can be:

• Spatial (depth)• Temporal (time - video)• Spectral (color)

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CHANNEL

DEPTH

TIME

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Where To Get Images…

• Use somebody else’s

• Create your own

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Online Image Archives

• http://www.goes.noaa.gov/• http://www.osei.noaa.gov/• http://www.nwas.org/committees/rs/nwasat.html• http://glovis.usgs.gov/• http://images.jsc.nasa.gov/• http://serc.carleton.edu/NAGTWorkshops/visuali

zation/collections/imagearchives.html

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Creating Your Own Image Stacks

• Most any camera can be used to create scientifically useful images– Still– Video

• In most cases, Z dimension will be time

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Still Cameras

• Whenever possible, use tripod• Digital images have date/time stamps• Stacks can be built up manually in ImageJ

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Using Video In ImageJ

• QuickTime movies are opened as stacks– Must have QuickTime 7 installed

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Joe PowChester F. Carlson Center for Imaging Science

Rochester Institute of Technology

pow@cis.rit.edu