I’m having some trouble with creating masks for automating the counts of chromosomes in mouse cells. Here is the image I start with (it’s a jpg unfortunately):
I start out processing it with a gaussian blur (3 sigma), and a kuwahara filter (5 sampling window width), and then an auto local threshold (phansalkar, radius of 15, white objects on black background), and wind up with a mask that looks like this:
Apologies for using a jpg for this image as well, but the tif won’t upload for some reason.
I’m trying to get ROIs around the V-shaped objects in the middle of this image, but I’m having trouble with watershedding them correctly and avoiding the large, non-mitotic nuclei in the image. I’ve tried playing with the irregular watershedding without much success.