Is there a way to calculate the average of the areas highlighted with the wand tool


I’m trying to find a way to objectively assess disruption of the reticulin network in tumors. Is there a way to calculate the average area enclosed by the reticulin fibers. I’ve attached an image of a reticulin stain, I was able to highlight the areas I’m interested in, however I’m not sure how to find the average of those areas. Thanks for your help.


If you export the Annotations Measurements, see exporting measurements here, it is probably easiest to create your summary measurements (and standard deviations etc) in other software like Excel. If you script it (bottom of the help page) you could potentially create a CSV per image. There are also other forum posts on exporting measurements in various ways.

If you really want to dig into the coding, there are ways to create summary measurements, but they also would involve creating another annotation to store that measurement in. I have not looked into how to store measurements as part of the image, but it might be possible (for Export type, Image).
Make sure to check if any scripts you want to adjust are based on the same version of QuPath you are using.

I have a related question - is there a way to measure the average intensity of the annotations?

Analyze-> Calculate features->Add intensity features -

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Thanks! Just curious - what’s a circular tile (one of the options for the Region field)?

Not sure there is much information other than what was already stated.

Circular is probably the most useful there, though I have only used it for classifiers and to determine background levels when manually calculating features.

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