ezomero

A module with convenience functions for writing Python code that interacts with OMERO.

https://github.com/thejacksonlaboratory/ezomero

Science Score: 67.0%

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

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 2 DOI reference(s) in README
○
Academic publication links
✓
Committers with academic emails
4 of 13 committers (30.8%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (12.6%) to scientific vocabulary

Keywords

imaging-solutions omero omero-api omero-server python

Keywords from Contributors

napari

Last synced: 6 months ago · JSON representation ·

Repository

A module with convenience functions for writing Python code that interacts with OMERO.

Basic Info

Host: GitHub
Owner: TheJacksonLaboratory
License: gpl-2.0
Language: Python
Default Branch: main
Homepage:
Size: 1.53 MB

Statistics

Stars: 45
Watchers: 10
Forks: 18
Open Issues: 5
Releases: 23

Topics

imaging-solutions omero omero-api omero-server python

Created about 5 years ago · Last pushed 6 months ago

Metadata Files

Readme Contributing License Code of conduct Citation

WARNING: from 08/08/2025, this repository is unmaintained and read-only.

ezomero

A module with convenience functions for writing Python code that interacts with OMERO.

Installation

ezomero's dependencies are easily pip-installable from PyPI, except for zeroc-ice==3.6.5. For those, we recommend pip-installing using one of the wheels provided by Glencoe Software (use the one compatible with your OS/Python version - link provided is for Linux wheels, for more information see this Glencoe Software blog post).

In general, we strongly recommend starting from a clean virtual environment, pip installing zeroc-ice from a Glencoe wheel, and only then doing pip install ezomero.

If you want to use get_table and post_table to/from Pandas dataframes, you need to install ezomero[tables] - that install an optional pandas dependency. Installing ezomero without this will default get_table and post_table to use lists of row lists as their default.

Usage

In general, you will need to create a BlitzGateway object using ezomero.connect(), then pass the conn object to most of these helper functions along with function-specific parameters.

Documentation

Documentation is available at https://thejacksonlaboratory.github.io/ezomero/

Development

You will need Docker installed and running to run the tests.

Setup your "omero" python environment with a local ezomero and pytest: ```

conda activate omero # Activate your omero environment with conda or pip (omero) > cd /yourlocalclone/ezomero (omero) > pip install -e . (omero) > pip install pytest ```

To run the tests, startup the test OMERO server with Docker and run pytest ```

cd /yourlocalclone/ezomero docker-compose -f tests/docker-compose.yml up -d conda activate omero (omero) > python -m pytest .\tests ```

Owner

Name: The Jackson Laboratory
Login: TheJacksonLaboratory
Kind: organization
Location: Bar Harbor, ME | Farmington, CT | Sacramento, CA

Website: https://www.jax.org/
Repositories: 145
Profile: https://github.com/TheJacksonLaboratory

The Jackson Laboratory: Leading the search for tomorrow's cures.

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: ezomero
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Erick
    orcid: 'https://orcid.org/0000-0002-7545-3675'
    family-names: Martins Ratamero
    affiliation: The Jackson Laboratory
  - given-names: Kiya
    family-names: Govek
    affiliation: The Jackson Laboratory
    orcid: 'https://orcid.org/0000-0002-2105-0715'
  - given-names: Julio
    family-names: Mateos-Langerak
    affiliation: 'University of Montpellier, CNRS, INSERM'
    orcid: 'https://orcid.org/0000-0003-1579-0773'
  - given-names: Fernando
    family-names: Cervantes Sanchez
    affiliation: The Jackson Laboratory
    orcid: 'https://orcid.org/0000-0003-0652-2750'
  - given-names: David
    family-names: Mellert
    affiliation: The Jackson Laboratory
    orcid: 'https://orcid.org/0000-0001-6606-0274'
repository-code: 'https://github.com/TheJacksonLaboratory/ezomero'
abstract: >-
  Many research laboratories need to manage, process, and
  analyze the increasingly large volumes and complexity of
  data being produced by state-of-the-art bioimaging
  platforms. OMERO is a popular open-source client-server
  application that provides a unified interface for managing
  and working with bioimages and their associated
  measurements and metadata. Integrating OMERO into analysis
  pipelines, such as those developed around the scientific
  Python ecosystem, will thus be a common pattern across the
  field of bioimaging. While OMERO has a powerful Python
  API, it provides minimal abstraction from the underlying
  OMERO object model and associated methods, which represent
  more complexity than most users are interested in for the
  context of an analysis script. We introduce ezomero, which
  was designed to provide a convenience layer on top of
  existing OMERO APIs and return data types that are either
  Python primitive or commonly used in scientific Python.
  Ezomero has minimal dependencies in addition to the OMERO
  Python library itself and is installable directly from
  PyPI. Here, we provide an overview of ezomero as well as
  several vignettes to illustrate how it can be used to
  accelerate discovery.
license: GPL-2.0
preferred-citation:
  type: article
  authors:
  - given-names: Erick
    orcid: 'https://orcid.org/0000-0002-7545-3675'
    family-names: Martins Ratamero
    affiliation: The Jackson Laboratory
  - given-names: Kiya
    family-names: Govek
    affiliation: The Jackson Laboratory
    orcid: 'https://orcid.org/0000-0002-2105-0715'
  - given-names: Julio
    family-names: Mateos-Langerak
    affiliation: 'University of Montpellier, CNRS, INSERM'
    orcid: 'https://orcid.org/0000-0003-1579-0773'
  - given-names: Fernando
    family-names: Cervantes Sanchez
    affiliation: The Jackson Laboratory
    orcid: 'https://orcid.org/0000-0003-0652-2750'
  - given-names: David
    family-names: Mellert
    affiliation: The Jackson Laboratory
    orcid: 'https://orcid.org/0000-0001-6606-0274'
  title: "Easing OMERO adoption with ezomero"
  doi: 10.1101/2023.06.29.546930

GitHub Events

Total

Create event: 3
Release event: 2
Issues event: 8
Watch event: 7
Issue comment event: 34
Push event: 35
Pull request event: 27
Fork event: 8

Last Year

Create event: 3
Release event: 2
Issues event: 8
Watch event: 7
Issue comment event: 34
Push event: 35
Pull request event: 27
Fork event: 8

Committers

Last synced: 7 months ago

All Time

Total Commits: 160
Total Committers: 13
Avg Commits per committer: 12.308
Development Distribution Score (DDS): 0.225

Past Year

Commits: 41
Committers: 7
Avg Commits per committer: 5.857
Development Distribution Score (DDS): 0.195

Top Committers

Name	Email	Commits
Erick Ratamero	e****s	124
Dave Mellert	D**t@j**g	15
Tom Boissonnet	t**t@h**e	4
William Moore	w**e@d**k	3
Peter Sobolewski	7****D	3
Kiya Govek	k**k@j**g	3
jean-marie burel	j**l@d**k	2
juliomateoslangerak	j**k@i**r	1
Sherman Siu	s**u@u**a	1
Maarten Paul	m**l@g**m	1
Johannes Soltwedel	3****r	1
JensWendt	9****t	1
Fernando Cervantes Sanchez	i**r@g**m	1

Committer Domains (Top 20 + Academic)

dundee.ac.uk: 2 jax.org: 2 uwaterloo.ca: 1 igh.cnrs.fr: 1 hhu.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 53
Total pull requests: 92
Average time to close issues: 3 months
Average time to close pull requests: 14 days
Total issue authors: 17
Total pull request authors: 14
Average comments per issue: 2.75
Average comments per pull request: 1.28
Merged pull requests: 78
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 5
Pull requests: 26
Average time to close issues: 12 days
Average time to close pull requests: 11 days
Issue authors: 3
Pull request authors: 7
Average comments per issue: 1.8
Average comments per pull request: 1.58
Merged pull requests: 17
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

erickmartins (16)
mellertd (13)
juliomateoslangerak (4)
TorecLuik (3)
will-moore (3)
romainGuiet (2)
abhamacher (2)
psobolewskiPhD (1)
BlanchardMR (1)
MalloryWittwer (1)
jo-mueller (1)
SaibotMagd (1)
tymiao1220 (1)
JensWendt (1)
n-loureiro (1)

Pull Request Authors

erickmartins (65)
Tom-TBT (10)
mellertd (8)
psobolewskiPhD (5)
jburel (4)
govekk (3)
jo-mueller (2)
shermansiu (2)
tstoeter (2)
will-moore (2)
Yu-AnChen (2)
dfrkp (1)
fercer (1)
juliomateoslangerak (1)
JensWendt (1)

Top Labels

Issue Labels

enhancement (3) documentation (2) good first issue (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- pypi 905 last-month

Total dependent packages: 4
Total dependent repositories: 5
Total versions: 23
Total maintainers: 1

pypi.org: ezomero

A suite of convenience functions for working with OMERO. Written and maintained by the Research IT team at The Jackson Laboratory.

Documentation: https://ezomero.readthedocs.io/
License: gpl-2.0
Latest release: 3.2.1
published 8 months ago

Versions: 23
Dependent Packages: 4
Dependent Repositories: 5
Downloads: 905 Last month

Rankings

Dependent packages count: 1.9%

Dependent repos count: 6.6%

Average: 8.4%

Downloads: 9.9%

Forks count: 11.4%

Stargazers count: 12.1%

Maintainers (1)

erick.ratamero

Last synced: 6 months ago

Dependencies

setup.py pypi

dataclasses *
numpy *
omero-py *

.github/workflows/run_tests_pr.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/run_tests_push.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/upload_to_pypi.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

.github/workflows/upload_to_test_pypi.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite

tests/docker-compose.yml docker

openmicroscopy/omero-server latest
openmicroscopy/omero-web-standalone latest
postgres 11

ezomero

Science Score: 67.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

WARNING: from 08/08/2025, this repository is unmaintained and read-only.

ezomero

Installation

Usage

Documentation

Development

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

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: ezomero

Rankings

Maintainers (1)

Dependencies