Skip to main content
Join the official 2020 Python Developers SurveyStart the survey!

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

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

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for ome-zarr, version 0.0.15
Filename, size File type Python version Upload date Hashes
Filename, size ome_zarr-0.0.15-py3-none-any.whl (19.7 kB) File type Wheel Python version py3 Upload date Hashes View
Filename, size ome-zarr-0.0.15.tar.gz (18.2 kB) File type Source Python version None Upload date Hashes View

Supported by

Pingdom Pingdom Monitoring Google Google Object Storage and Download Analytics Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page