QuPath threshold cell-intensity

How is the threshold value calculated in the Single Measurement Classifier in QuPath? After selecting a channel, the classifier suggests this threshold value.
image

For me it usually shows up as the mean value among detections for that value.

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The default is the mean. It isn’t really intended to be used, but just to give a sensible starting point.

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Thanks for the clarification.
I would like to draw your attention to the Supplementary section of this paper. They have compared several clustering techniques to determine the threshold of the intensity-distribution automatically. Wondering if the technique they recommend (i.e. Silhouette scanning) would be a better approximation for the threshold?!

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Looks interesting, I’ll check it out – thanks :slight_smile:

Reminds me of this as well, though it was more for image segmentation. Nice short video on how it works, though the implementation uses numpy.

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