omero-web-zarr


Nameomero-web-zarr JSON
Version 0.1.1 PyPI version JSON
download
home_pagehttps://github.com/ome/omero-web-zarr
SummaryOMERO.web plugin for OME-Zarr
upload_time2023-06-15 13:45:49
maintainer
docs_urlNone
authorThe Open Microscopy Team
requires_python
licenseAGPL-3.0
keywords omero zarr ome web
VCS
bugtrack_url
requirements No requirements were recorded.
Travis-CI No Travis.
coveralls test coverage No coveralls.
            .. 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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