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A reader for zarr backed OME-NGFF images.

Project description

napari-ome-zarr

License PyPI Python Version tests codecov pre-commit.ci status

A reader for zarr backed OME-NGFF images.


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

Installation

You can install napari-ome-zarr via pip:

pip install napari-ome-zarr

Usage

Napari will use ome-zarr 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/"


# Also works with local files
$ napari 6001240.zarr

OR in python::

import napari

viewer = napari.Viewer()
viewer.open('https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.3/9836842.zarr/')

napari.run()

If single zarray is passed to the plugin, it will be opened without the use of the metadata::

$ napari '/tmp/6001240.zarr/0'

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.

Project details


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