Problem with Subcellular Detection

Hello, I am trying to use Qupath v.0.2.3 to quantify positive dots on fluorescence images.
merge_notch1pyloric caeca.tif (3.5 MB)
nuclei detection.tif (605.3 KB)

I successfully detected nuclei as you can see above, but unfortunately, I cannot detect the subcellular components. I selected analyze-> Cell detection-> subcellular detection. A subcellular spot detection window appeared and I could adjust the threshold of the channel but nothing happened when I ran the analysis

Thank you in advance for your help and advice.


I have not looked at the images, but my first guess is that you do not have pixel size metadata set. Subcellular detections currently requires that there be a pixel size. You could either set that when creating the merged image, by using original file types from the microscope, or setting it in QuPath as indicated in the script below (if you know what the correct pixel size is).

Thank you very much for your precious tips. Adjusting the pixel size works! :slight_smile:

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