ROI by exclusion to create a mask for co-localization

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ROI by exclusion to create a mask for co-localization

barenboim
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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Re: ROI by exclusion to create a mask for co-localization

Straatman, Kees (Dr.)
Not sure I totally understand what you want. Maybe an image would be helpful.

However, if you can make an ROI of all the signal in one channel you can use Edit > Selection > Make Inverse to make an ROI of the excluded area.

Best wishes

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
www.le.ac.uk/advanced-imaging-facility


-----Original Message-----
From: Linda [mailto:[hidden email]]
Sent: 11 January 2018 16:53
To: [hidden email]
Subject: ROI by exclusion to create a mask for co-localization

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.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html