i am a new user of qupath i tried to analyze my fluorescence maximum projection image obtained by slide scanner.
where Af555 channel is intended for thiazine red stained plaques and AF488 is for specific cell marker. my main question is to determine the plaques area which is outside cells and how much plaque has been engulfed by cells
i can not use dapi channel for the positive cell detection because it is ex-vivo assay where i added culture cells to my slices
the problem after several trials to adjust the sitting still the watershed detection is detecting plaque inside the positive cell detections.
i do not know how i can optimize this sitting and whether qupath works for this kind of images.
another issue when i open the original image which has 2 scenes i only see one and can not find a way to see the other scene.