Implementation of images in Zarr files.
Project description
Experimental support for multi-resolution images stored in Zarr filesets, according to the OME zarr spec.
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. The examples below use the image at http://idr.openmicroscopy.org/webclient/?show=image-6001240.
All examples can be made more or less verbose by passing -v or -q one or more times:
# ome_zarr -vvv ...
info
Use the ome_zarr command to interrogate Zarr datasets:
# Remote data $ ome_zarr info https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/ # Local data (after downloading as below) $ ome_zarr info 6001240.zarr/
download
To download all the resolutions and metadata for an image:
# creates local 6001240.zarr/ $ ome_zarr download https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/ # Specify output directory $ ome_zarr download https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/ --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 '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
with napari.gui_qt():
viewer = napari.Viewer()
viewer.open('https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.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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