ImageJ Automatic Nuclei Counter

Hi everyone,

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.

Thank you!


Ideally, we would need the original image to help you but for 3D segmentation in Fiji, you should use the 3D suite developed by @ThomasBoudier

This plugin takes into account data from different slices for segmentation. There is a Neubias presentation about it here.



Hi @cwatkins,

or you give the APEER platform a try and use the 3D Segmentation and Analysis Module (which is entirely based on Fiji and MorphoLibJ) to segment and count your cells in a 3D stack.