sebsacuna / napari-ome-zarr

A napari plugin for zarr backed OME-NGFF images

napari-ome-zarr

A reader for zarr backed OME-NGFF images.

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

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.