I am posting here for the first time. I work with cellular autofluorescence images. I find these images quite difficult to be separated at a single cell level (using thresholding and other tools). Currently, I use a combination of ImageJ wand tool, selection tool, and threshold-analysis to generate ROIs for each cell. Is there a better tool or method that I can use to separate these cells out without extreme user-level mediation?
I have put more example images in this GitHub link below. If I get to solve this, I would add a solution in this repo. https://github.com/JenuC/segmentation_autofluorescence/tree/master/test_files