WormBinarization

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