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Implementation of images in Zarr files.

Project description

Experimental support for multi-resolution images stored in Zarr filesets, according to the OME zarr spec.



Install the latest release of ome-zarr from PyPI:

pip install ome-zarr

Install developer mode to run from your current branch:

git clone
cd ome-zarr-py
pip install -e .


Open Zarr filesets containing images with associated OME metadata. The examples below use the image at

All examples can be made more or less verbose by passing -v or -q one or more times:

# ome_zarr -vvv ...


Use the ome_zarr command to interrogate Zarr datasets:

# Remote data
$ ome_zarr info

# Local data (after downloading as below)
$ ome_zarr info 6001240.zarr/


To download all the resolutions and metadata for an image:

# creates local 6001240.zarr/
$ ome_zarr download

# Specify output directory
$ ome_zarr download --output image_dir

napari plugin

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 ''

# Also works with local files
$ napari 6001240.zarr

OR in python:

import napari
with napari.gui_qt():
    viewer = napari.Viewer()'')

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

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

Release process

This repository uses bump2version to manage version numbers. To tag a release run:

$ bumpversion release

This will remove the .dev0 suffix from the current version, commit, and tag the release.

To switch back to a development version run:

$ bumpversion --no-tag [major|minor|patch]

specifying major, minor or patch depending on whether the development branch will be a major, minor or patch release. This will also add the .dev0 suffix.

Remember to git push all commits and tags.


Distributed under the terms of the BSD license, “ome-zarr-py” is free and open source software

Project details

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