I’m a beginner in ImageJ. I have a question about analyzing particles with masking specific areas.
I attached 2 example images which are acquired from different layers (‘superficial’ and ‘deep’) at the same tissue location.
Using ‘deep’ layer image, I want to analyze the multiple ROIs of rectangular shape(yellow ROIs). As you can see, there are dark shadow lines(large superficial blood vessels) projected from the superficial layer. So I want to exclude the shadow areas from analyzing.
How to apply binary mask from ‘superficial’ image to ‘deep’ layer and analyze the ROIs in deep layer with excluding the masked areas from analyzing?