Awesome
napari-ome-zarr
A reader for zarr backed OME-NGFF images.
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://uk1s3.embassy.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://uk1s3.embassy.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.