<https://lh3.googleusercontent.com/-ALNkfB8SfsI/VRaHXMyexWI/AAAAAAAABN4/7Tass...> In order to separate nuclei from H&E or H&DAB stained images I have tried color deconvolution (a slightly modified variant from skimage.color) to get the hematoxylin part. It should be possible to extract the eosin (red colored) part to remove nuclei and particles of thrombocytes prior to watershed segmentation. However, it seems to be necessary for color deconvolution to have a neutral and not saturated background. Can you provide test images not saturated (see histogram attached) and blank field images? Kai Am Donnerstag, 26. März 2015 21:42:14 UTC+1 schrieb Claiborne Morton:

Hey thanks for all the help, here is the original image. Also I am removing the smallest particles later on in the process using a function that does the removal based on the average size of healthy (highly circular) cells, which is why I had not removed them in the images I have already posted.

On Thursday, March 19, 2015 at 6:07:58 PM UTC-4, Claiborne Morton wrote:

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Hey guys, Im still having trouble finding ways to separate touching particles if the are not both circular. Further when dealing with elliptical shapes, a single particle tends to incorrectly get cut in half. Any ideas how I could change parameters in the water-shedding function to correct for this? Attached are a few problem cases so you can see examples.

Thanks, Clay [image: Inline image 1]