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If you check upload ROIs, all ROIs are uploaded as new ROIs. If you check update ROIs, ROIs which are already in OMERO get updated and new ROIs get uploaded.
you are correct. I must have clicked Upload instead of Update.
The option should be either one of the other. The UI selection allows to have both
Also when the update option is selected, the ones created in OMERO are updated with an ImageJ comment even if they have not been modified in ImageJ.
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