Discussion: handling pull/push of annotations

[psobolewskiPhD]

One thing I noticed is that annotations will be duplicated if you do a pull to get the annotations, edit them, and do a push.
The QuPath OMERO extension implements the option to delete existing annotations (for the specific user), both on pull and on push.
It does not do/use a diff or anything like that.

[jo-mueller]

Another aspect to this:

Currently, the OMERO browser allows to open multiple images from OMERO in parallel. I.e., opening one image from the remote does not remove the current one, which I think is not too bad, tbh (but this can be questioned). The ROI upload, however, will browse all shapes/points/labels and add the data as ROIs to the image currently selected in the ROI widget.

I think there are multiple ways to solve this:

• Revert to opening one image at a time. This way, we can be (relatively) certain that all open ROI layers (shapes/points/labels) relate to a single image.
• Add the image_id to the metadata of the shapes/image/labels layer when uploading ROIs. THis way, we could filter out annotations from layers that are not linked to the image selected in the ROI widget. This has follow-up implications: How does one "link" a segmentation layer to an OMERO image?
  • New widget? Select multiple layers, hit "Link" and write

    metadata = {
        "omero": {"@id": number}
    }

    into each selected layer's metadata.
  • Write @id into the layer's metadata: Probably a good idea to begin with but doesn't solve the problem for segmentation layers not created by the ROI widget.
  • Is it possible to add an entry in the context menu of the layer selection widget? I.e., select multiple layers, rightclick, and select link to OMERO image?