I’m trying to estimate cortical porosity from a H&E slide. I’ve subtracted background and made binary, then inverted to make the pores black and the bone white. Was it correct to invert the binary? I’ve tried running particle analyser in BoneJ, but it is measuring the osteocytes as well as the pores. I’ve set a scale using measurements from a micrometer. When I set a minimum volume, even if its ridiculously low, I get no results. If I do volume fraction it takes into account the osteocyte lacunae.
I’ve tried playing around with a few of the suggestions in this forum but haven’t yet found a solution. I’d love some thoughts on the best way I can get this to work. I couldn’t find the ROI interpolator .