I stumbled over an issue using QuPath:
- Have a parent annotation (“tissue”)
- tissue contains child annotations (“gland” “stroma”)
- ran the Analyze → Cell detection → Cell detection built-in plugin (via menu and also tried via script) to detect cells in the “tissue” annotation
- all existing child annotations got deleted - no warning / no questions asked - prior cell detection
- cell detection worked nicely but “gland” and “stroma” annotations were gone (have backups)
Now I am wondering if I am not seeing the option to NOT delete existing child annotations or if this is a bug?
Can I protect the annotations? Do I have to move them “a lvl up” (not really what I want)? Any tips or suggestions welcome (want to automate/work with scripts as much as possible)