ROI by exclusion to create a mask for co-localization

Posted by barenboim on Jan 11, 2018; 4:52pm
URL: http://imagej.273.s1.nabble.com/ROI-by-exclusion-to-create-a-mask-for-co-localization-tp5019871.html

Hi There,

I have taken images of fluorescently labeled neurons (via IHC) that are tagged to show a specific brain sub-structure.  I want to then evaluate the expression of another protein that is tagged with a different fluor ONLY within that brain structure.  Initially I tried using the ROI function to outline the sub-structure in one fluor and then threshold and count particles in the other fluor.  The problem is that the initial ROI selection is not specific enough (done manually) and I end up evaluating positive signals of cells that are not in the sub-structure of interest.

I am interested in creating a ROI by exclusion (rather than inclusion), perhaps a mask that will exclude all signals that are not in my cells of interest and then use this mask to evaluate expression in the other fluor.
If anyone has an idea how to accomplish this I would very much appreciate your help.

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