QuPath Pixel classifier export intensity values

Hello all
Thank you for you continuous support with QuPath, it is a great software, thank you Pete for creating it.

We have optimised multiplex detection on mouse colorectal tissue and one of the markers we use is Mucine expressed in the mucosal goblet cells. As it is very difficult to find the nucleus that belongs to the goblet cell and create object classifier (see first image below) I decided to create a pixel classifier which works really well (second image below) and detects the area of tissue expressing Mucine.


From the images we have we can see that the positive Mucine area shrinks over time of the experiment however we would like to have a look at the intensity of the expression. I was wondering is there a way how I could export the Mucine pixel intensity values in the Mucine positive area?

Looking forward for your answer
Iveta

1 Like

Intensities can be added to objects using Add intensity features:
https://qupath.readthedocs.io/en/latest/docs/tutorials/superpixels.html?highlight=add%20intensity%20features#adding-features
Additional info here, though some may be out of date at this point:

If you want to dig into scripting, there are options to sum the areas and mean intensities of all objects within an annotation, and apply the global mean for positive areas to that annotation. However, it is generally bad practice to use the same fluorescent channel to both outline and measure a single channel as that inherently biases against faint areas.