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ome / omero-iviewer

An OMERO.web app allowing to view images
https://www.openmicroscopy.org/omero/iviewer/
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Display annotations on ROIs #319

Open pwalczysko opened 4 years ago

pwalczysko commented 4 years ago

Motivated by the QuPath workflow and the usage of https://github.com/glencoesoftware/ome-omero-roitool . This tool imports MapAnnotations on ROIs (via an export script in QuPath and then import as OME-XML into OMERO). The MapAnnotations capture important info such as whether this ROI is an Annotation in QuPath sense (big region demarking an area of interest) or a Detection in QuPath sense (a smaller ROI encompassing a detected cell inside an Annotation). Further, things added manually in QuPath on Annotation-ROI, such as classifications (Tumor etc.).

These MapAnnotations are correctly saved on the ROIs in OMERO, but atm invisible in iviewer.

Although https://trello.com/c/gzGqioJm/222-scoping-rois-and-annotations-ui-display seems to deal with similar topics, the approach taken on that trello card is still very image-centric. I cannot see a use case such as here scoped or thought about there.

Arguably, an interesting use case for IDR too ?

cc @joshmoore @sbesson @jburel @will-moore

pwalczysko commented 4 years ago

This is how QuPath 0.2.0-m11 is doing that - note that the "Immune cells" is a value of KVP (if exported as OME-XML) and it is pertaining to the yellow ellipse

Screen Shot 2020-05-01 at 14 06 23

sbesson commented 3 years ago

In the case of an upcoming submission, we have a concrete use case of localized target represented as single Point ROIs associated with a tagged protein as well as other metadata including sequence, sequence unicity.

For the moment, the tagged protein is associated with the point as the text value as this is the primary information that can be displayed in the UI. I am considering storing the rest of the information (and probably the protein as well) as key/value pairs linked to the ROI and/or Point. It would be useful to know about the best way

NOte that in the case of a single ROI/Shape, this might raise the same concerns as the ones discussed in https://github.com/ome/omero-iviewer/issues/326 i.e. at which level should the metadata be attached and how will the UI expose it.