Hello everyone, I need to count cells in Nissl staining of frontal cortex using QuPath. The cell detection command was the best tool to do it but the crowded cells cannot be resolved, for instance, five crowded cells are counted as a big single cell (I changed the parameters many times). The best solution would be to keep those “wrong” detections and modify them by hand, but i don’t know how to edit detections, since those are different from anotations. Can I do that in QuPath? Thanks.
Detections can’t be edited manually, that is one of the features of detections that make QuPath able to handle millions of them. You might be able to manually draw annotations and convert those into cells/detections. You will need extra steps if you want to expand cytoplasms around them, though, and it gets into quite a bit of scripting.
Thanks! I will try it that way