.. image:: https://github.com/ome/omero-web-zarr/workflows/OMERO/badge.svg
:target: https://github.com/ome/omero-web-zarr/actions
.. image:: https://badge.fury.io/py/omero-web-zarr.svg
:target: https://badge.fury.io/py/omero-web-zarr
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
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