The Worm Project
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m (→Tracking: adding example file) |
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Tracker [StringBeforeLabeledImageFilename] [StringBeforeRawImageFilename] [StartFrame] [EndFrame] | Tracker [StringBeforeLabeledImageFilename] [StringBeforeRawImageFilename] [StartFrame] [EndFrame] | ||
| − | For each frame tracker returns a text | + | 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''' | '''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 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 have 4 digits. | ||
* The frame number must be at to the end of the image name. | * The frame number must be at to the end of the image name. | ||
| − | '''Example''' | + | '''Example Input''' |
To track worms with the following image sequence... | To track worms with the following image sequence... | ||
| Line 38: | Line 47: | ||
Tracker "C:\data\Im" "C:\data\LabeledIm" 0 4 | Tracker "C:\data\Im" "C:\data\LabeledIm" 0 4 | ||
| + | '''Example Output''' | ||
| + | |||
| + | Here is an example output file for two worms... | ||
| + | |||
| + | ---- | ||
| + | |||
| + | <code> | ||
| + | 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 | ||
| + | </code> | ||
| + | |||
| + | ---- | ||
| + | |||
| + | |||
| + | The second worm has an ID of 1 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. | ||
| + | |||
| + | '''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. | * 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. | * Reid DB, '''"An algorithm for tracking multiple targets,"''' IEEE Transactions on Automatic Control. 1979 Dec; 24(6):843-854. | ||
Revision as of 15:22, 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 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...
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
The second worm has an ID of 1 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.
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.
