WormBinarization
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(New page: The '''Worm Binarization Module''' has the following syntax. WormBinarization [StringBeforeFilename] [MaskFilename] [StartFrame] [EndFrame][Levell] '''Notes''' WormBinarization accepts ...) |
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| − | The '''Worm Binarization Module''' has the following syntax | + | The '''Worm Binarization Module''' has the following syntax: |
| − | WormBinarization [StringBeforeFilename] [MaskFilename] [StartFrame] [EndFrame][Levell] | + | WormBinarization [StringBeforeFilename] [MaskFilename] [StartFrame] [EndFrame][Levell] |
'''Notes''' | '''Notes''' | ||
| − | WormBinarization accepts a series of grayscale images and returns a series of corresponding binary images | + | *WormBinarization accepts a series of grayscale images and returns a series of corresponding binary images |
| − | * The mask file used as an input is generated by performing a maximum intensity projection of the | + | * The mask file used as an input is generated by performing a maximum intensity projection of the entire image sequence. |
| − | + | ||
* 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 | + | * The frame number must have n digits. We have tested this data with n == 4. |
* 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. | ||
Latest revision as of 14:53, 24 April 2009
The Worm Binarization Module has the following syntax:
WormBinarization [StringBeforeFilename] [MaskFilename] [StartFrame] [EndFrame][Levell]
Notes
- WormBinarization accepts a series of grayscale images and returns a series of corresponding binary images
- The mask file used as an input is generated by performing a maximum intensity projection of the entire image sequence.
- The input images should be single-slice 8-bit TIFs. Other image formats have not been tested.
- The frame number must have n digits. We have tested this data with n == 4.
- 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\bw0000.tif C:\data\bw0001.tif C:\data\bw0002.tif C:\data\bw0003.tif C:\data\bw0004.tif
...the following command should be used.
WormBinarization "C:\data\Im" "C:\data\bwIm" 0 4 0.145
Example Output
