I’m new to QuPath. I’ve been trying to import .czi files of multiple IF created on Zeiss Axioscan (compressed JPEG XR), however I keep having the same problem: I can open the files and see all the channels, but the signal intensity in every channel is much higher than what it should be. It doesn’t seem to be only a visualization problem because most of the positive signal is saturated and the pixel values are much higher than those observed on Zen at the actual scanner.
Has anyone ever experienced this problem before with czi or other file formats? Is there a way to fix this?