I have a problem regarding the subcellular detection in Qupath. Basically I have some fluorescence images with in-situ dots in 2 channels. My tissue samples are Lung with quite alot of auto-fluorescence, in combination with some weak signal I get several false positives with my subcellular detections.
The good news is that I have scanned an empty channel where auto-fluorescence is strongly detected. I can use “add intensity features” in my auto-fluorescence channel to add intensities to all my detections. Now I want to remove all subcellular detections with auto-fluorescence intensities above a certain threshhold and then update my cell-detections to the correct number of spots/cell.
Is this possible through a script? I saw Petes warning about adding/deleting spots but that is exactly what I want do do. I previewed my auto-fluorescence measurements and believe removing false positive detections based on the auto-fluorescence intensity should work fairly well.
True Spot Intensities:
False Spot Intensities: