Metadata-Version: 2.4
Name: napari-ome-zarr
Version: 0.8.0
Summary: A reader for zarr backed OME-Zarr images.
Author: OME Team
License-Expression: BSD-3-Clause
Project-URL: Bug Tracker, https://github.com/ome/napari-ome-zarr/issues
Project-URL: Documentation, https://github.com/ome/napari-ome-zarr#README.md
Project-URL: Source Code, https://github.com/ome/napari-ome-zarr
Project-URL: User Support, https://github.com/ome/napari-ome-zarr/issues
Project-URL: bsky, https://bsky.app/profile/openmicroscopy.org
Classifier: Development Status :: 4 - Beta
Classifier: Framework :: napari
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.11
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: ome-zarr>=0.13.0
Requires-Dist: napari>=0.4.0
Dynamic: license-file

# napari-ome-zarr

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[![tests](https://github.com/ome/napari-ome-zarr/workflows/tests/badge.svg)](https://github.com/ome/napari-ome-zarr/actions)
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A reader for zarr backed [OME-NGFF](https://ngff.openmicroscopy.org/) images.

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This [napari] plugin was generated with [Cookiecutter] using with [@napari]'s [cookiecutter-napari-plugin] template.

<!--
Don't miss the full getting started guide to set up your new package:
https://github.com/napari/cookiecutter-napari-plugin#getting-started

and review the napari docs for plugin developers:
https://napari.org/docs/plugins/index.html
-->

## Installation

[Install napari] if not already installed.

You can install `napari-ome-zarr` via [pip]. Activate the same environment as you installed napari into, then:

    pip install napari-ome-zarr

## Usage

Napari will use `napari-ome-zarr` plugin to open images that the plugin recognises as ome-zarr.
The image metadata from OMERO will be used to set channel names and rendering settings
in napari::

    napari "https://livingobjects.ebi.ac.uk/idr/zarr/v0.3/9836842.zarr/"


If a dialog in napari pops up, encouraging you to choose a reader, choose ``napari-ome-zarr`` and click OK. You can stop it happening with addition of ``--plugin napari-ome-zarr`` as in the example below.

To open a local file::

    napari --plugin napari-ome-zarr 13457227.zarr

OR in python::

    import napari

    viewer = napari.Viewer()
    viewer.open("https://livingobjects.ebi.ac.uk/idr/zarr/v0.4/idr0101A/13457537.zarr", plugin="napari-ome-zarr")

    napari.run()


## Contributing

Contributions are very welcome. Tests can be run with [tox], please ensure
the coverage at least stays the same before you submit a pull request.

## License

Distributed under the terms of the [BSD-3] license,
"napari-ome-zarr" is free and open source software

## Issues

If you encounter any problems, please [file an issue] along with a detailed description.

[Install napari]: https://napari.org/stable/tutorials/fundamentals/installation.html
[napari]: https://github.com/napari/napari
[Cookiecutter]: https://github.com/audreyr/cookiecutter
[@napari]: https://github.com/napari
[MIT]: http://opensource.org/licenses/MIT
[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
[file an issue]: https://github.com/ome/napari-ome-zarr/issues
[napari]: https://github.com/napari/napari
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/
