Skip to content

Add labels support for import#181

Open
will-moore wants to merge 1 commit intoome:masterfrom
will-moore:labels_import
Open

Add labels support for import#181
will-moore wants to merge 1 commit intoome:masterfrom
will-moore:labels_import

Conversation

@will-moore
Copy link
Copy Markdown
Member

@will-moore will-moore commented Sep 18, 2025

This reverts commit 9fea245.

To test:

  • with a bioformats2raw image (2 out of 3 images have labels):
$ omero zarr import https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0079A/idr0079_images.zarr --labels --target 23619
  • regular image
$ omero zarr import https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr --labels --target 23619

This PR converts labels into masks. This is not a similar "import" than the one we have for images
The current tooling in OMERO will need to be reviewed in order to support a true "import" of labels
i.e. only reference to it

@snoopycrimecop
Copy link
Copy Markdown
Member

snoopycrimecop commented Sep 27, 2025

Conflicting PR. Removed from build OMERO-plugins-push#543. See the console output for more details.
Possible conflicts:

--conflicts Conflict resolved in build OMERO-plugins-push#576. See the console output for more details.

@snoopycrimecop
Copy link
Copy Markdown
Member

snoopycrimecop commented Jan 24, 2026

Conflicting PR. Removed from build OMERO-plugins-push#31. See the console output for more details.
Possible conflicts:

--conflicts Conflict resolved in build OMERO-plugins-push#41. See the console output for more details.

@jburel
Copy link
Copy Markdown
Member

jburel commented Feb 5, 2026

--exclude

@imagesc-bot
Copy link
Copy Markdown

This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/supporting-ome-zarr-labels-in-omero/119816/5

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

4 participants