Pixel Classifier

Hi Pete,

we are so happy with QuPath and even more with the new version! Very useful!
We tested the Pixel classification in Masson Trichrome staining’s to segment the image in 4 different classes.
We managed to do it so well but when we are adding more scans to the project in order to obtain the segmentation in all of them using the same trained classifier we didn’t succeed.

We saved the classifier but when opening in a new image it does not load…
Can that be done? We have 100 different scans to analyze and would be great to do it in a batch mode…

Many thanks for all you effort in QuPath!


Not yet with the pixel classifier. It is one of the features I am most looking forward to as well! For the moment you could do a similar analysis with SLICs in batch. Though it would not be as precise or fast, it could be run for all images in the project.

Thanks for your quick response!
How can I do that? It will differentiate 4 different classes?

SLICs are just like cells, only you have to add measurements to them via Analyze->Calculate features->Add Intensity Features.
You can then classify them using a trained classifier, scripts, or if you want something crazy, this. Though you would need the variant altered to work off of tiles instead of cell objects :slight_smile:

Some links on the old forum may help, here, here andhere.

Most of that will be far less useful once the pixel classifier is scriptable, but it might help for now.

I’ll try it!

Many thanks!!

@monia106 Thanks for your kind words - glad you like it!

As @Research_Associate already mentioned, the pixel classifier is a work in progress… I need to find more time to work on which features/options should be available, and making it scriptable. Don’t know yet how long it will take, but it’s a very high priority (not least because I also need this functionality for multiple projects).

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Hopping so!:slightly_smiling_face: