error during ITK Watershed Auto Seeded

[Yulia Fridman]

Hello,

I'm trying to segment arabidopsis root, and while applying ITK Watershed Auto Seeded filter I get the next error message (please see the attached file).

What am I doing wrong and how can I resolve it?

Thank you in advance, Yulia

[Pierre Barbier de Reuille]

Yes, this can happen if you have too much noise. The reason is: the watershed algorithm will label each voxel with a unique number identifying which cell it is a part of. In LithoGraphX, every voxel can store a number from 0 to 65535. So if the Watershed finds more than 65534 cells (0 is for the outside), it will run out of unique numbers and display the error you see.

Depending on the image you have a few choices:

1. Try using the new "Sieve" algorithm to filter out noise. You will find it in the Stack algorithms in the "Morphology" folder. The main parameter is minimum volume of objects that are not noise. This means anything smaller than the volume you input will be removed. A good number to put is something a bit smaller than the smallest cell you expect to see.
2. If your background noise is too high, you can increase the "Level" parameter in the Watershed algorithm.
3. At last, you can also try to either increase the radius of the Gaussian blue, or to run it another time with a similar radius.

The main advantage of the new "Sieve" algorithm (available on version 1.1.6 or later) is the conservation of the shape of larger objects, where the Gaussian blur will tend to smooth everything.

[Pierre Barbier de Reuille]

Increasing blur solved the problem.