Removing Annotations on Folded Tissue

Hello,

I am having trouble removing annotations from folded tissues. I have tried to use the polygon tool to encapsulate the folded tissue and then hit the “delete” button but it only deletes the object and not the annotations. Is there a way to select the annotations from a core (TMA) and remove their detection/annotation?

Thank you

Have you tried unlocking and editing the annotations directly with the brush tool to adjust the annotations themselves?

Unlock is in the context menu when an annotation is selected, under Annotations.

Hello,

The cells being detected within the folded tissue are unlocked. Thank you for your response but the brush and wand tool doesn’t seem to work :frowning: I am able to delete the individual cell detection but I was wondering if I can use a more pan tool to select a big chunk of the detected cells to remove?

Thank you

If you do not have a tissue annotation, the next best option is the Selection tool.

It is the S in the top center of the screen, and works with most of the drawing tools.
Some other description here about the interface:

If the tissue fold is dark enough, you may be able to use the background radius and threshold during Cell Segmentation to prevent them from being created in the first place.

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Added note: It may be worth looking into how QuPath works in terms of objects, since your initial question indicated “annotations.” Within QuPath, annotations means something specific (a type of object), while the cells are “detections.”

https://qupath.readthedocs.io/en/latest/docs/concepts/objects.html

Hi, Thank you for the clarification. I realized I was mixing the two up. I have tried a few methods and the one that I ended up using is ctrl + alt + left click to select the cell detections for deletion until I figured out how to use the polygon tool haha. Great software but I still have lots to learn! Thanks for all your help.

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