omero-web-zarr

OMERO.web plugin for OME-Zarr.

Implementation of [OME-NGFF](https://ngff.openmicroscopy.org/latest/) API with an omero-web app.

This plugin supports OME-NGFF v0.1, v03, v0.4. For a given Image ID in OMERO, the following URL will refer to an OME-NGFF image:

https://[omero-server]/zarr/image/ID.zarr/

Note: This app has not been extensively tested and should not be considered "production ready".

Currently supports [OME-NGFF v0.3](https://ngff.openmicroscopy.org/0.3/index.html) and [OME-NGFF v0.4](https://ngff.openmicroscopy.org/0.4/index.html).

Development

Install with:

$ pip install -e .

Configuration

$ omero config append omero.web.apps '"omero_web_zarr"'

# Allow to open-with Vizarr

$ omero config append omero.web.open_with '["web_zarr_vizarr", "omero_web_zarr_index", {"supported_objects":["image"], "label": "Vizarr", "script_url": "omero_web_zarr/openwith.js"}]'

# Open with ome-ngff-validator

$ omero config append omero.web.open_with '["web_zarr_validator", "omero_web_zarr_index", {"supported_objects":["image"], "label": "NGFF validator", "script_url": "omero_web_zarr/openwith_validator.js"}]'

Then you will be able to access OMERO Images in OME-NGFF format v0.3 or v0.4 with a URLs like:

# base URL for Image ID
[omero-server]/zarr/v0.4/image/[ID].zarr

# URLS for .zattrs, .zgroup
[omero-server]/zarr/v0.4/image/[ID].zarr/.zattrs
[omero-server]/zarr/v0.4/image/[ID].zarr/.zgroup

# .zarray of the dataset at path '0'
[omero-server]/zarr/v0.4/image/[ID].zarr/0/.zarray

# first 3D chunk of the dataset at path '0'
[omero-server]/zarr/v0.4/image/[ID].zarr/0/0/0/0

You can see this in action using the [Vizarr](https://github.com/hms-dbmi/vizarr/) viewer.

This omero-web app self-hosts Vizarr to avoid CORS issues (delegating to https://hms-dbmi.github.io/vizarr/).

In the webclient UI you can use the context menu to Open With > Vizarr, or use your Image ID and go directly to:

[omero-server]/zarr/vizarr/?source=[omero-server]/zarr/v0.4/image/[ID].zarr

Testing

To run integration tests (in your omero-web conda environment above) with pytest. See [OMERO testing docs](https://docs.openmicroscopy.org/latest/omero/developers/testing.html) for setting ICE_CONFIG and dependencies etc., then:

$ pytest test/integration/test_ngff.py

License

The application is released under the AGPL.

Copyright

2022-2023, The Open Microscopy Environment