Hello, I have some immunofluorescence images of mouse epididymis sections like this one and I am trying to exclude the lumen (dark inner circle) and analyse only the epithelial region (red outer circle), Does anyone know of an efficient way to go about this on Fiji/Image J? Many thanks
You can can select the outer region by creating two ROI’s, then add them to the ROI Manager and then apply the boolean operation ‘xor’ in the ROI Manager on the two ROI’s to combine them for a ring region.
The new region again can be added to the ROI Manager and the two ROI’s can be deleted afterwards.
Finally the new ring region can be measured (see bad drawings below).
If you have created all ring regions you can also measure them in one shot with the Particle Analysis function in ImageJ.
Don’t forget to save all ROI’s with the ROI Manager.
By the way you can also threshold your image (convert a copy to 8-bit) and then use the Wand tracing tool to create rough or precise selections (see screenshot below inner selection):
Thank you very much…it worked! Although, I ended up using normal ‘measure’ function as the ‘analyse particles’ function did not work. I think that would only apply if it was the other way round and I was excluding the outer region to measure the particles in the inner region.