I was hoping for some help measuring % Area fraction on a set of histological images. Essentially, I am trying to evaluate the OD of my stained tissue.
I am working on a composite image which is the result of multiplying an original RGB microscopy images with a second image, an ROI mask of a sub-region of interest created from the original image. This multiplied image contains a large black area surrounding the tissue of interest.
My ultimate goal is to threshold this composite image in order to quantify the % Area of pixels specifically in the tissue of interest within the ROI mask. Because the area outside of ROI mask is black, I am unable to get an accurate measurement of % Area within the ROI.
Is there a way to set all black (0 value) pixels in my original multiplied image to “transparent” so that after thresholding only pixels within the ROI are measured?
I have tried using the paste control>transparent-white and transparent-zero, however when I paste the image the black background is still present. I’ve also tried setting the background to transparent in Photoshop, however, this is not preserved when I open the image up again in ImageJ.
Any help on this matter would be appreciated. I may not have made myself clear and will gladly clarify any points.