Importing annotations from caseviewer

Hello, I am switching from caseviewer to qupath. Needless to say I am a newbie on qupath :smiley: Can I import the annotations from caseviewer to qupath? And after I import them, is it possible to move the annotations (because they are text annotations on the side of the actual structure it wants to point and I want to put them in the middle)? Thanks!

Hi @RichelleDB, welcome to QuPath :slight_smile:
Alas, I’ve never used CaseViewer myself and I’ve no idea how it stores its annotations - or if they are in any kind of open format that QuPath could support.

I know some other people have written import scripts to get annotations into QuPath from other places (e.g. here), but I don’t think I’ve seen any for CaseViewer.

I took a quick look, and I’m not sure CaseViewer has a way to even export the annotations themselves (just the data from the annotations, area, perimeter, etc). 3DHistech has historically been rather bad about integrating with open source or making their files accessible.
If you can provide a sample file of exported annotations, someone else (not me!) on the forum might be able to figure out a way to convert them into something QuPath friendly.

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Hi @petebankhead :slight_smile: The annotations were added using PanoramicViewer but since that is not available anymore, it can still be opened using the caseviewer. I am not sure if this helps but the annotations are stored as .dat in a folder with the same file name as the image.

@RichelleDB ah, I’m afraid that sounds like a proprietary format that can’t be supported in QuPath.

When annotated are created in QuPath, they are open and can be exported various ways (e.g. see here) so you aren’t restricted in what you can do with them, but sadly this is not the case for other software in this field…

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