ez-zarr

ez-zarr: A Python package for easy access and visualisation of OME-Zarr filesets - Published in JOSS (2025)

https://github.com/fmicompbio/ez_zarr

Science Score: 98.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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Found codemeta.json file
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Found .zenodo.json file
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DOI references
Found 6 DOI reference(s) in README and JOSS metadata
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Links to: joss.theoj.org
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JOSS paper metadata
Published in Journal of Open Source Software

Keywords

ome-zarr

Last synced: 6 months ago · JSON representation ·

Repository

GIve easy, high-level access to ome-zarr fileset

Basic Info

Host: GitHub
Owner: fmicompbio
License: mit
Language: Python
Default Branch: main
Homepage: https://fmicompbio.github.io/ez_zarr/
Size: 38.3 MB

Statistics

Stars: 17
Watchers: 3
Forks: 2
Open Issues: 3
Releases: 20

Topics

ome-zarr

Created about 2 years ago · Last pushed 7 months ago

Metadata Files

Readme License Citation

ez_zarr

Goals

The aim of ez_zarr is to provide easy, high-level access to OME-Zarr filesets (high content screening microscopy data, stored according to the NGFF specifications in OME-Zarr with additional metadata fields, for example the ones generated by the Fractal platform).

The goal is that users can write simple scripts working with plates, wells and fields of view, without having to understand how these are represented within an OME-Zarr fileset.

In addition to the python package, we also provide an R package that automatically generates and wraps a python environment with ez_zarr and all dependencies, available at https://github.com/fmicompbio/ezzarr.

Example

You can use ez_zarr from the command line to get information about an OME-Zarr fileset: ez_zarr tests/example_data/plate_ones.zarr

or from within python to get access to all its functionality: ```

import module

from ezzarr import omezarr

open an Image

img = omezarr.Image('tests/exampledata/plateonesmip.zarr/B/03/0') img

Image 0

path: tests/exampledata/plateones_mip.zarr/B/03/0

n_channels: 2 (some-label-1, some-label-2)

npyramidlevels: 3

pyramidzyxscalefactor: [1. 2. 2.]

fullresolutionzyx_spacing (micrometer): [1.0, 0.1625, 0.1625]

segmentations: organoids

tables (measurements): FOVROItable

legacy objects from `hcs_wrappers`

from ezzarr import hcswrappers

plate3d = hcswrappers.FractalZarr('tests/exampledata/plateones.zarr') plate_3d

FractalZarr plate_ones.zarr

path: tests/exampledata/plateones.zarr

n_wells: 1

n_channels: 2 (some-label-1, some-label-2)

npyramidlevels: 3

pyramidzyxscalefactor: {'0': array([1. 2. 2.])}

fullresolutionzyx_spacing: [1.0, 0.1625, 0.1625]

segmentations:

tables (measurements): FOVROItable

```

A more extensive example is available from here, also available as an ipynb notebook.

Install

ez_zarr is available for all major platforms (macOS, Linux and Windows) and modern versions of python. It can be installed using pip or conda:

Using `pip`

PyPI - Downloads

The release version of ez_zarr can be installed using pip: pip install ez-zarr

To install also the dependencies required for running unit tests or to download the example data and run the examples given in the documentation, install ez_zarr with the dev and doc extras, respectively: pip install "ez-zarr[dev,doc]"

The current (development) ez_zarr can be installed from github.com using: pip install git+ssh://git@github.com/fmicompbio/ez_zarr.git

Using `conda`

Alternatively, you can install ez-zarr from the conda-forge channel using: conda install -c conda-forge --override-channels ez-zarr

Software status

Supported versions of `zarr`

ez-zarr currently supports OME-Zarr v0.4 and v0.5 (corresponding to version 2 and 3 of the zarr format, and thus version 2 and 3 of the zarr python package). OME-Zarr v0.5 support was introduced in ez-zarr v0.4.0.

Contributors and License

ez_zarr is released under the MIT License, and the copyright is with the Friedrich Miescher Insitute for Biomedical Research (see LICENSE).

ez_zarr is being developed at the Friedrich Miescher Institute for Biomedical Research by @silvbarb, @csoneson and @mbstadler.

Citing ez-zarr

If you are using ez-zarr in published research, please cite the paper:

Barbiero et al., (2025). ez-zarr: A Python package for easy access and visualisation of OME-Zarr filesets. Journal of Open Source Software, 10(109), 7882, https://doi.org/10.21105/joss.07882

Need help?

If you run into problems when using ez_zarr, please first check whether the answer is available in the help pages for the individual functions underneath 'Documentation' or in the 'Getting started' vignette. If not, please open an issue and explain your problem. Try to provide a reproducible example, and always include the code you used, that will make it much easier for us to help.

Contributions

If you would like to contribute to ez_zarr, you can do so by sending a pull request to this repository. If the contribution involves changes in the functionality provided by ez_zarr, we encourage you to first open an issue to discuss the intended contribution.

Owner

Login: fmicompbio
Kind: user

Repositories: 17
Profile: https://github.com/fmicompbio

JOSS Publication

ez-zarr: A Python package for easy access and visualisation of OME-Zarr filesets

Published

May 17, 2025

DOI

10.21105/joss.07882

Volume 10, Issue 109, Page 7882

Authors

Silvia Barbiero

Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland, University of Basel, Basel, Switzerland

Charlotte Soneson

Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland, SIB Swiss Institute of Bioinformatics, Basel, Switzerland

Prisca Liberali

Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland, University of Basel, Basel, Switzerland, ETH Zürich, Department for Biosystems Science and Engineering (D-BSSE), Basel, Switzerland

Michael B. Stadler

Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland, University of Basel, Basel, Switzerland, SIB Swiss Institute of Bioinformatics, Basel, Switzerland

Editor

Adam Tyson

Citation (CITATION.cff)

cff-version: "1.2.0"
authors:
- family-names: Barbiero
  given-names: Silvia
  orcid: "https://orcid.org/0000-0001-7177-6947"
- family-names: Soneson
  given-names: Charlotte
  orcid: "https://orcid.org/0000-0003-3833-2169"
- family-names: Liberali
  given-names: Prisca
  orcid: "https://orcid.org/0000-0003-0695-6081"
- family-names: Stadler
  given-names: Michael B.
  orcid: "https://orcid.org/0000-0002-2269-4934"
contact:
- family-names: Stadler
  given-names: Michael B.
  orcid: "https://orcid.org/0000-0002-2269-4934"
doi: 10.5281/zenodo.15370320
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Barbiero
    given-names: Silvia
    orcid: "https://orcid.org/0000-0001-7177-6947"
  - family-names: Soneson
    given-names: Charlotte
    orcid: "https://orcid.org/0000-0003-3833-2169"
  - family-names: Liberali
    given-names: Prisca
    orcid: "https://orcid.org/0000-0003-0695-6081"
  - family-names: Stadler
    given-names: Michael B.
    orcid: "https://orcid.org/0000-0002-2269-4934"
  date-published: 2025-05-17
  doi: 10.21105/joss.07882
  issn: 2475-9066
  issue: 109
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 7882
  title: "ez-zarr: A Python package for easy access and visualisation of
    OME-Zarr filesets"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.07882"
  volume: 10
title: "ez-zarr: A Python package for easy access and visualisation of
  OME-Zarr filesets"

GitHub Events

Total

Create event: 14
Issues event: 32
Release event: 7
Watch event: 3
Delete event: 10
Issue comment event: 51
Push event: 82
Pull request review event: 3
Pull request event: 18
Fork event: 1

Last Year

Create event: 14
Issues event: 32
Release event: 7
Watch event: 3
Delete event: 10
Issue comment event: 51
Push event: 82
Pull request review event: 3
Pull request event: 18
Fork event: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 28
Total pull requests: 18
Average time to close issues: 19 days
Average time to close pull requests: 10 days
Total issue authors: 8
Total pull request authors: 3
Average comments per issue: 1.36
Average comments per pull request: 1.39
Merged pull requests: 13
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 22
Pull requests: 9
Average time to close issues: 21 days
Average time to close pull requests: 4 days
Issue authors: 8
Pull request authors: 2
Average comments per issue: 1.27
Average comments per pull request: 0.89
Merged pull requests: 6
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

pr4deepr (8)
mbstadler (6)
silvbarb (4)
csoneson (4)
alessandrofelder (2)
imagejan (2)
ianhi (1)
dstansby (1)

Pull Request Authors

csoneson (10)
mbstadler (6)
silvbarb (2)

Top Labels

Issue Labels

enhancement (4) documentation (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- pypi 512 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 20
Total maintainers: 1

pypi.org: ez-zarr

Give easy, high-level access to ome-zarr filesets.

Homepage: https://github.com/fmicompbio/ez_zarr
Documentation: https://fmicompbio.github.io/ez_zarr/
License: mit
Latest release: 0.4.1
published 7 months ago

Versions: 20
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 512 Last month

Rankings

Dependent packages count: 9.9%

Average: 37.7%

Dependent repos count: 65.6%

Maintainers (1)

mbstadler

Last synced: 6 months ago

Dependencies

.github/workflows/documentation.yaml actions

actions/checkout v3 composite
actions/setup-python v4 composite
mhausenblas/mkdocs-deploy-gh-pages master composite
quarto-dev/quarto-actions/render v2 composite
quarto-dev/quarto-actions/setup v2 composite

.github/workflows/test_and_deploy.yaml actions

actions/checkout v3 composite
actions/setup-python v4 composite
codecov/codecov-action v3 composite

docs/doc-requirements.txt pypi

mkdocs ==1.5.2
mkdocs-autorefs ==0.5.0
mkdocs-gen-files ==0.4.0
mkdocs-include-markdown-plugin ==4.0.4
mkdocs-literate-nav ==0.5.0
mkdocs-material ==9.1.21
mkdocs-section-index ==0.3.5
mkdocstrings ==0.22.0

docs/qmd-requirements.txt pypi

jupyter ==1.0.0
matplotlib ==3.8.2
session-info ==1.0.0

pyproject.toml pypi

ez-zarr

Science Score: 98.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

ez_zarr

Goals

Example

import module

open an Image

Image 0

path: tests/exampledata/plateones_mip.zarr/B/03/0

n_channels: 2 (some-label-1, some-label-2)

npyramidlevels: 3

pyramidzyxscalefactor: [1. 2. 2.]

fullresolutionzyx_spacing (micrometer): [1.0, 0.1625, 0.1625]

segmentations: organoids

tables (measurements): FOVROItable

legacy objects from hcs_wrappers

FractalZarr plate_ones.zarr

path: tests/exampledata/plateones.zarr

n_wells: 1

n_channels: 2 (some-label-1, some-label-2)

npyramidlevels: 3

pyramidzyxscalefactor: {'0': array([1. 2. 2.])}

fullresolutionzyx_spacing: [1.0, 0.1625, 0.1625]

segmentations:

tables (measurements): FOVROItable

Install

Using pip

Using conda

Software status

Supported versions of zarr

Contributors and License

Citing ez-zarr

Need help?

Contributions

Owner

JOSS Publication

ez-zarr: A Python package for easy access and visualisation of OME-Zarr filesets

Authors

Editor

Tags

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: ez-zarr

Rankings

Maintainers (1)

Dependencies

legacy objects from `hcs_wrappers`

Using `pip`

Using `conda`

Supported versions of `zarr`