Automated mask arithmetic in QuPath

[EL_Pollo_Diablo (Johannes Müller)]

Hi all,

I’m a bit new to QuPath and couldn’t really get the following to work (as a script). Here’s my case:

I have a picture of a histological section (large object) within which I manually contour an annotation. I have a well-working classifier for the background as well:

Now, is there an (automated way) to generate an annotation for the checkered area based on the annotations of Background and “Annotation”? It’s not a difficult process: The checkered area = intersection(not(Annotation), not(Background)) - I just don’t know how to do it programmatically in QuPath.

Thanks in advance!

[Research_Associate (MicroscopyRA)]

Sounds very similar to what was mentioned here:

Subdividing an existing annotation into annotations of interests

Another example plus the link to JTS stuff on the official docs page: Counting Cytoplasm + Nuclei labelled in different channels in QuPath - #3 by Research_Associate Way, way more involved, but examples of both intersect and subtraction

And here if you want to do it manually:

QuPath Subtract Annotations confused about Hierarchy

Final comment for tonight! Probably. Always make sure the interior annotation is selected first if you are using the right click context menu subtraction. Think “Subtract First from the Second” where it would be written as Second-First = result. The order of selection is important.

Subtraction is now in the context menu*->Annotations->Edit multiple->Subtract selected*.

[Research_Associate (MicroscopyRA)]

Now that I look in the scripts, there is also this: https://gist.github.com/Svidro/5829ba53f927e79bb6e370a6a6747cfd#file-object-subtraction-groovy