Selecting multiple TMA cores in QuPath

How does one select multiple TMA cores in QuPath?
The reason I’m asking is since sometimes cell detection stops in the middle of the run and I’m forced to detect the cells in each core individually.


You should be able to select them by clicking/double-clicking with the Alt key pressed.

If it stops then I’d guess it’s a memory issue. This may help:
Specifically, decreasing the number of parallel threads might help it get a bit further without the need for manual effort.

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If you want a more programmatic way of selecting a few at a time, I’d take a look at these scripts, and one of the TMA ones. Depending on your needs, you might be able to do something like core.getName().contains(“A”) to do all of row A, and cycle through the rows like that.

Or you might go almost purely with the TMA core script and select “it” (in “each” statements, the object you are cycling through is referred to by default as it) as you cycle through each TMA core anyway, and run one cell detection on one annotation at a time. Potentially by doing something like:
getCurrentHierarchy().getSelectionModel().setSelectedObjects(list, null)
after it.setMissing. That would run the cell detection on the annotation created inside the core. I think. Too tired to test at the moment.

Thank you, both suggestions solved my issue :sunglasses: