The Worm Project

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Contents 1 Executables 1.1 Segmentation 1.2 Detection 1.3 Tracking 1.4 Behaviors

Executables

Segmentation

See FARSIGHT Features

Detection

Detect [LabeledImageFilename] [OutputFilename]

Tracking

Tracker "StringBeforeLabeledImageFilename" "StringBeforeRawImageFilename" StartFrame EndFrame

Example

To track worms with the following raw 8-bit images...

C:\data\Im0000.tif
C:\data\Im0001.tif
C:\data\Im0002.tif
C:\data\Im0003.tif
C:\data\Im0004.tif

...and associated labeled or binary images...

C:\data\LabeledIm0000.tif
C:\data\LabeledIm0001.tif
C:\data\LabeledIm0002.tif
C:\data\LabeledIm0003.tif
C:\data\LabeledIm0004.tif

Tracker "C:\data\Im" "C:\data\LabeledIm" 0 4

• Roussel R, Morton CA, Finger FP, Roysam B, “A Computational Model for C. elegans Locomotory Behavior: Application to Multi-Worm Tracking,” IEEE Transactions on Biomedical Engineering. 2007 Oct; 54(10):1786-97.
• Reid DB, "An algorithm for tracking multiple targets," IEEE Transactions on Automatic Control. 1979 Dec; 24(6):843-854.

Behaviors

• Pierce-Shimomura JT, Morse TM, Lockery SR, "The Fundamental Role of Pirouettes in Caenorhabditis elegans Chemotaxis," The Journal of Neuroscience. 1999 Nov; 19(21):9557–9569.