We’re trying to automatically count the number of nuclei in a 26 Z-stack fluorescent image. So far we have isolated the individual nuclei (after thresholding, watershed, and analyzing particles). However, if a nuclei spans two stacks, ImageJ recounts it each time. I’m wondering if there’s a way to count each nuclei only once?
The attached image demonstrates the question. 17 and 22 are the same nucleus, but they are being counted separately.