Skip to content

dstansby/napari-ome-zarr

This branch is 1 commit ahead of, 28 commits behind ome/napari-ome-zarr:main.

Folders and files

NameName
Last commit message
Last commit date

Latest commit

92a37ad · Jul 16, 2024
Nov 20, 2023
Dec 15, 2021
Apr 14, 2022
Jul 16, 2024
May 27, 2021
Apr 14, 2022
Aug 22, 2023
Jan 6, 2022
May 27, 2021
May 27, 2021
Nov 3, 2022
Apr 14, 2022
Nov 20, 2023
Apr 14, 2022
Nov 20, 2023

Repository files navigation

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

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.

About

A napari plugin for zarr backed OME-NGFF images

Resources

License

Citation

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages

  • Python 100.0%