Version:

  • 0.3.1

Release date:

  • 01 November 2021

First released:

  • 14 June 2021

License:

  • BSD-3-Clause

GitHub activity:

  • Stars: 9
  • Forks: 9
  • Issues + PRs: 5

Python versions supported:

  • >=3.7

Operating system:

  • OS Independent

Requirements:

  • napari-plugin-engine (>=0.1.4)
  • ome-zarr (>=0.2.0)
  • numpy

napari-ome-zarr

A reader for zarr backed OME-NGFF images.

This plugin provides a reader for zarr backed OME-NGFF images in napari. The reader will inspect the .zattrs metadata provided and pass any relevant metadata, including channel, scale and colormap metadata.

Opening an ome-zarr image in napari

The example above uses the image at https://idr.openmicroscopy.org/webclient/?show=image-6001240

This plugin is designed to allow bioimaging researchers and analysts to explore their multi-resolution images stored in Zarr filesets (according to the OME zarr spec) without needing an intricate understanding of zarr, or the spec itself.

This plugin supports reading all images recognised as ome-zarr, namely, containing well-formed .zattrs and .zgroup files, as well as the appropriate directory hierarchy as described in the spec. The image metadata from OMERO will be used to set channel names, colormaps and rendering settings in napari.

You can open local or remote images using napari at the terminal and the path to your file:

$ napari 'https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/'

# also works with local files
$ napari 6001240.zarr

OR in python:

import napari

viewer = napari.Viewer()
viewer.open('https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/')
napari.run()

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

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

If an image group contains labels, they will also be opened, and added as a separate layer in napari.

When the labels group metadata additionally contains "rgba" and "properties" keys, the labels will be given appropriate colors and the properties will be displayed in the status bar.

Working with ome-zarr images can be more convenient using the command-line interface and utility functions of our associated library ome-zarr. For more information please see the package documentation for ome-zarr.

If you discover a bug with the plugin, or would like to request a new feature, please raise an issue on our repository at https://github.com/ome/napari-ome-zarr.

If you would like assistance with using the plugin, or converting images to ome-zarr format, please reach out on image.sc.

Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud. J. Moore, et al. Editors. Open Microscopy Environment Consortium, 20 November 2020. This edition of the specification is https://ngff.openmicroscopy.org/0.1/. The latest edition is available at https://ngff.openmicroscopy.org/latest/. (doi:10.5281/zenodo.4282107)

How to cite this plugin

If you use this plugin in your work, please cite it using the following citation. Don’t forget to cite napari too!

Moore J., Moore W., Besson S., Doncila Pop D. (2021). napari-ome-zarr (version 0.3.0). DOI: 10.5281/zenodo.5620852 URL: https://github.com/ome/napari-ome-zarr

Version:

  • 0.3.1

Release date:

  • 01 November 2021

First released:

  • 14 June 2021

License:

  • BSD-3-Clause

GitHub activity:

  • Stars: 9
  • Forks: 9
  • Issues + PRs: 5

Python versions supported:

  • >=3.7

Operating system:

  • OS Independent

Requirements:

  • napari-plugin-engine (>=0.1.4)
  • ome-zarr (>=0.2.0)
  • numpy

Version:

  • 0.3.1

Release date:

  • 01 November 2021

First released:

  • 14 June 2021

License:

  • BSD-3-Clause

GitHub activity:

  • Stars: 9
  • Forks: 9
  • Issues + PRs: 5

Python versions supported:

  • >=3.7

Operating system:

  • OS Independent

Requirements:

  • napari-plugin-engine (>=0.1.4)
  • ome-zarr (>=0.2.0)
  • numpy

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