I’m very new to CellProfiler and hoping to find some help with my project. I have tissue slides (liver, kidney, brain, spleen, and tumour) stained with Prussian Blue for iron quantification. I need to quantify the amount of iron (blue) relative to the amount of tissue (red). I was able to figure it out on software called Fiji (See the Red/Blue quantification images attached). Those are what I want, plus a calculation of area. The final figure I want is ((Area Blue)/(Area Red+Blue)) but I’ve been using excel for the actual calculation.
Unfortunately the method I used still needed some things done manually (I outlined the tissue section with the polygon tool to crop outside, and needed to select the colour threshold manually each time). I fiddled around a while trying to get the same results, but I’m stumped. I have 13,000 images so doing it manually is not going to work! I downloaded the pipeline from here: cellprofiler.org/forum/viewtopic … area#p4031 but it isn’t giving me the right results, and I’m not sure how to correct it.
Any help or tips on how to proceed would be appreciated!