The Worm Project

Warning! This page is under construction

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 has the following syntax.

Tracker "StringBeforeLabeledImageFilename" "StringBeforeRawImageFilename" StartFrame EndFrame

For each frame tracker returns a text file file containing the five semicolon-delimited fields: ID, x coordinate, y coordinate, distance from head to middle and distance from tail to middle. Each line of the file corresponds to a single worm.

Notes

• The input images should be single-slice 8-bit TIFs. Other image formats have not been tested.
• The frame number must have 4 digits.
• The frame number must be at to the end of the image name.

Example

To track worms with the following image sequence...

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

...with their associated labeled image sequence...

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

...the following command should be used.

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.