Novice Qupath user with limited experience in histological analysis programs requesting some feedback on my analysis methodology.
I have done a H&E as well as ORO staining on Apoe-/- murine liver sections, and while I could manage the ORO sections quite well the HE stain seems more tricky.
For ORO a “Simple Tissue Detection” followed by a pixel classifier and export annotations script did the trick, although scripting the pixel classifier would be lovely (future version?).
But for an HE image I would like to quantify structures rather than color (in a sense), and since I am not a pathologist I am not qualified to train a classifier to the point of scoring steatosis, so I thought of a simpler solution.
I would like to classify white spaces smaller than a certain size. This is a very rudimentary method, but would suffice to at least quantify microsteatosis.
Any ideas on how to do this? I tried playing with the create objects function in the pixel classifier but it quickly ate up all my RAM when applied on whole slide images. The dream would be to only classify “white spaces” smaller than a given size, so as to exclude vessels and bile ducts.
Also, I’m having trouble applying a pixel classifier to only the annotation, it spreads across the whole slide even when annotation only is specified, and when using a lower pixel size this eats up quite a bit of processing power.
Any feedback is greatly appreciated.