I’ve noticed that sometimes (~50% in this one application), when I use the Subtract Annotations command in QuPath it confuses which is the parent object and which is the child, leading to it deleting everything.
Simple Tissue Detection (there’s only 1 piece of tissue, so it’s only 1 simple region)
Expand Annotations by -1000 to create an inner circle
If I select the annotations by clicking on the image or on them on the Annotations tab, it works half the time. In the annotation list, the order that it puts the objects seems to matter, and seems to change randomly. If I select the annotations by clicking on them in the Hierarchy tab, it works (almost?) 100% of the time.