QuPath - class prediction view is missing some classes

Hi @petebankhead,

I’m trying to visualize my classes (3 colors), on the first image it worked fine. Once I tried to predict a second image, I only see 2 classes (below).

Also, Maybe it should be on another post, how do I create paren-offspring relationships in objects?

Thanks in advance,
Daniel

Hi @Daniel_Waiger,

You chose Probability as output. Which means that the resulting colour for each pixel is a weighted average of each class. Since C-tissue is grey-ish it might just be too blended in to be visible. Try to change the output to Classification and see where the grey areas are. Alternatively, change the colour of the C-tissue class to a more visible one.

Note that switching to Classification will, for each pixel, simply display the class with the highest probability (instead of a weighted average of all class probabilities).

how do I create paren-offspring relationships in objects?

I’m not sure what you mean by this. Anyway, the hierarchy tab should display the current image hierarchy. You might need to run a resolveHierarchy() command in case it isn’t updated.

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Hi @melvingelbard,

In parent-offspring I mean that if I’d like to detect objects within bigger objects and link between them.
Something like the image below:


I want to define the big object as a parent object to the smaller object in it.

Thanks for your fast response!

My previous post describes the hierarchy, which should do exactly this!
In the screenshot that you provided, the smaller annotation should appear ‘under’ its parent annotation in the hierarchy tab (you might need to run a resolveHierarchy() if it doesn’t).

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Additional information in the docs: Object hierarchy — QuPath 0.2.3 documentation

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