I’m a newbie here and use ImageJ just for basic stuff. I found this forum because I have a small but irritating problem that I cannot resolve myself. I’m trying to analyze the amount of collagen from the trichrome stained heart cross-sections with ImageJ. Collagen stains blue and is easily distinguishable from red muscle tissue, which makes it easy to select with “color threshold”. But then: I want to measure the amount of collagen only from the left ventricle wall, not from the right ventricle or the areas without cardiac tissue (there might some fatty tissue etc.). I threshold the image, draw a ROI with “freehand selection” and then select either “measure” or “analyze particles”. The program measures the thresholded areas but ignores my ROI and I get results from the whole image. I have tried to use “ROI manager” and selected “Limit to threshold” from “Set measurements”, but still get the same results. What am I doing wrong? I noticed that ROI measurement functions correctly with 8-bit images, but there I cannot really make a difference between e.g. light purple and light blue.
Any help is appreciated