The Worm Project

Revision as of 15:23, 17 April 2009

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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 containing the five semicolon-delimited fields:

• ID
• x coordinates of spine
• y coordinates of spine
• Distance from head to middle
• Distance from tail to middle

Each line of the file corresponds to a single worm. The text files has the same filename as the Raw images but with a ".txt" insted of an ".tif"

Notes

• In labeled images the background pixels must be assigned a value of 0.
• Tracker can accept binary images if labeled images are not available.
• 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 Input

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

Example Output

Here is an example output file for two worms. The second worm has an ID of 2 and a spine located at (157.459,369.683), (159.604,369.997), (161.898,370.368) and so on. Its distance from head to middle is 19.2118 and its distance from tail to middle is 16.0946.

1;[369.82,371.349,372.789,374.39,376.439,378.419,380.234,381.82,383.194,384.059,384.818,386.148,387.559,389.189,391.3,393.475,395.241,396.649,397.159,396.831,395.746,];[370.92,372.608,374.19,375.698,376.535,377.454,378.579,380.147,381.75,383.823,385.814,387.542,389.238,390.555,391.14,391.763,393.033,394.74,396.684,398.732,400.708];21.137;18.4725 2;[157.459,159.604,161.898,163.988,166.354,168.441,170.68,172.77,174.311,175.499,176.057,177.13,178.31,179.708,181.498,183.774,185.704,187.342,188.815,189.888,192.148,];[369.683,369.997,370.368,370.455,370.641,371.14,371.109,370.141,368.846,366.973,364.864,362.968,361.064,359.34,358.18,358.378,359.298,360.749,362.438,364.465,365.231];19.2118;16.0946

Papers

• 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.