Histology Tissue Area Quantification?


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!


Hi Emma,

I think this can be done in CellProfiler, but first, your BLUE and RED images appear to be the same. Did you mistakenly upload one of them twice?


Hi Emma,

I went ahead and created a pipeline for you. I focused on measuring the area of the red & blue, and not on the intensity, as I was unclear what you wanted when you said “amount” which can refer to intensity or area. I also incorporated your Blank illumination image for illumination correction.

See how that works for you, and though you will no doubt have to optimize it, at least it will be automated at that point! Please see the comments in the Module Notes section of each module.

Hope that helps,
DL_histol.cppipe (17.8 KB)