My current project is to quantify the %area of tissue stained with Luxol Fast Blue, a histochemical stain for myelin (sample image below). It is also stained with hemotoxylin. My overall strategy, which works in ImageJ on smaller images, is to do color deconvolution (I created custom stain vectors and clumsily updated the native Colour Deconvolution with them), draw an ROI on the hemotoxylin channel to avoid bias, then threshold and count number of stained pixels on the LFB channel. However, I would like to upscale this to larger images, and am therefore getting QuPath involved. I can recreate the color deconvolution in QuPath fairly easily, but I had trouble finding a simple thresholding function based on only one stain vector, especially since cell detection is not involved in this analysis at all. So then I tried sending it to ImageJ, but I can’t get my updated Colour Deconvolution plugin to work in the QuPath form of ImageJ (I have it in a .java file…I think my trouble is I can’t get it to compile).
In summary, I think the two best options are to achieve the thresholding/quantification in QuPath or get my Colour Deconvolution file to compile in QuPath’s version of ImageJ. I greatly appreciate any advice you can share!