The Worm Project
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Tracker has the following syntax. | Tracker has the following syntax. | ||
| − | Tracker | + | 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. | 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. | ||
Revision as of 14:44, 17 April 2009
Warning! This page is under construction
Contents |
Executables
Segmentation
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.
