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:
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
Inline image 1