I have several fluorescence microscopy images with 10+ channels (each representing a different marker) which I would like to analyze in ImageJ.
I have imported the images as a virtual stack and converted to a normal stack via Image > Duplicate. I would like to define ROIs for the entire stack based on thresholding a single marker (one slice in the stack, this is a membrane protein which should define my cells of interest). It appears that Image > Adjust > Threshold applies the same threshold across all slices in the stack. Ideally, I would like to use background subtraction to define ROIs as best as possible.
I would then like to export/save each ROI as a separate image. Is this possible?
Thank-you very much for your guidance!