ome-zarr 0.0.4

Implementation of images in Zarr files.

Experimental support for images stored in Zarr filesets.

Features

• Use as a image reader plugin for napari. The napari plugin was generated with Cookiecutter along with @napari’s cookiecutter-napari-plugin template.

• Simple command-line to read and download conforming Zarr filesets.

• Helper methods for parsing related metadata.

Installation

Install the latest release of ome-zarr from PyPI:

pip install ome-zarr

Install developer mode to run from your current branch:

git clone [e-mail]:ome/ome-zarr-py.git
cd ome-zarr-py
pip install -e .

Usage

Open Zarr filesets containing images with associated OME metadata.

Use the ome_zarr command to interrogate and download Zarr datasets:

$ ome_zarr info https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/ $ ome_zarr download https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/ $ ome_zarr info 6001240.zarr/

For example, to load select images by their ID in the Image Data Resource such as http://idr.openmicroscopy.org/webclient/?show=image-6001240:

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

OR in python:

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

Alternatively, download one of these datasets with all associated metadata and open locally:

$ napari '/tmp/6001240.zarr/'

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.

License

Distributed under the terms of the GNU GPL v3.0 license, “ome-zarr-py” is free and open source software