Implementation of images in Zarr files.
Project description
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 git@github.com: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 BSD license, “ome-zarr-py” is free and open source software
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