Converting ROIs from ImageJ to Qupath

I want to convert my ROIs I made on ImageJ to Qupath. The QuPath website state that in an older version of ImageJ there is a Plugin which lets you convert the ROIs easily. However in every ImageJ version I tried, there is no QuPath pluging where I can do this.

I already tried to open ImageJ in Qupath, here I see the correct plugin. However, I cannot drop my images there…

Did I miss the correct ImageJ version?
Or how else can I tackle this problem and still convert my ImageJ ROIs to QuPath?

There are a few options for this I think.

I assume when you say you can’t drop your images it’s because you need Bio-Formats? Because you can drag and drop open images on the QuPath packaged ImageJ. However, you can set QuPath’s ImageJ to use whichever plugins via Extensions ‣ ImageJ ‣ Set ImageJ plugins directory so you could add Bio-Formats to that if that’s the issue.

Possibly easier, if you save your images as ImageJ TIFFs, the ROIs get saved with it so when you tick the “Import Objects” option in the QuPath “Add Images” dialog then I think it will find the ROIs and add them.

Alternatively, you can Save your ROIs via the command on the ROI Manager (via More > Save) and open them using the ROI Manager in QuPath ImageJ (via More > Open)


Thanks for the quick response, this works!