Count cells and messure the area


I am trying to count cells and messure the area of the cells and clusters with Fiji. I have a stack of pictures and they all look similar to this one:

I already solved the light gradient problem with the Bandpass Filter and now I am stucked trying thresholding. I tryed a couple different filters and thresholding methods. The best result I got was with substract Background and then using otsu threshold. Then it looked like this:

Does anyone knows a better method, where I would not loose the structure and the Area of the cells?

Thanks a lot.

You may want to try CellPose on the images that have been Bandpass filtered. There was a post here showing brightfield results.

From the paper

Note that you can run it on the website to test it before going through the trouble of setting up a Python environment for batch processing (which you still may want to do if you have hundreds of images).

If you want to put the labeled image back into FIJI, @waisman has created a plugin for that as well.


Some time ago, I used PHANTAST plugin for ImageJ to separate cells from the background: (GitHub - nicjac/PHANTAST-FIJI: Repository for the FIJI/ImageJ implementation of the phase contrast microscopy segmentation toolbox (PHANTAST)). After getting a mask with PHANTAST you can multiply it by your original image. Thus you’ll preserve the structural features of cells and cell clusters, while the background will be 0.