The Worm Project
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===Tracking=== | ===Tracking=== | ||
| + | Tracker has the following syntax. | ||
| + | |||
Tracker "StringBeforeLabeledImageFilename" "StringBeforeRawImageFilename" StartFrame EndFrame | 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\Im0000.tif | ||
C:\data\Im0001.tif | C:\data\Im0001.tif | ||
| Line 20: | Line 28: | ||
C:\data\Im0004.tif | C:\data\Im0004.tif | ||
| − | ... | + | ...with their associated labeled image sequence... |
C:\data\LabeledIm0000.tif | C:\data\LabeledIm0000.tif | ||
C:\data\LabeledIm0001.tif | C:\data\LabeledIm0001.tif | ||
| Line 27: | Line 35: | ||
C:\data\LabeledIm0004.tif | C:\data\LabeledIm0004.tif | ||
| + | ...the following command should be used. | ||
Tracker "C:\data\Im" "C:\data\LabeledIm" 0 4 | Tracker "C:\data\Im" "C:\data\LabeledIm" 0 4 | ||
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.
