Different selection in each layer

Hi all: haven’t been able to figure this one out. The basic premise is defining cell boundaries in one color (let’s say red) by thresholding, creating a selection, and restoring that selection on, let’s say, a channel of green cells (the original red cells now being indicated with red outlines). All well and good. Now I would like to do this in all positions of a Z stack, where the red cells in a given position will fade out while moving through Z, while others fade in. Again, the goal is to create a selection on the red channel in each layer and restore it to the corresponding green layer. Does anyone know a way to do this? thanks much!

Hi @htpetrie

You are looking for a segmentation :slight_smile:

Dependent on the image quality and density of cells this task can get difficult. If you need help with a specific image it would help if you upload it here.

Cheers

Thank you for the reply. That is correct, segmentation (or thresholding) is the first step, as mentioned above. i’m just not sure how to do this in all planes. I have uploaded a relevant cropped substack below. Thanks again for your uelp.