napari-ome-zarr

A napari plugin for zarr backed OME-NGFF images

https://github.com/ome/napari-ome-zarr

Science Score: 54.0%

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
○
Academic publication links
✓
Committers with academic emails
5 of 12 committers (41.7%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (16.8%) to scientific vocabulary

Keywords

napari-plugin ngff python zarr

Keywords from Contributors

napari imaging python-template software-carpentry training transcriptomics neuroscience mesh particles qt

Last synced: 6 months ago · JSON representation ·

Repository

A napari plugin for zarr backed OME-NGFF images

Basic Info

Host: GitHub
Owner: ome
License: bsd-3-clause
Language: Python
Default Branch: main
Homepage: https://www.napari-hub.org/plugins/napari-ome-zarr
Size: 143 KB

Statistics

Stars: 33
Watchers: 10
Forks: 24
Open Issues: 32
Releases: 9

Topics

napari-plugin ngff python zarr

Created over 4 years ago · Last pushed 6 months ago

Metadata Files

Readme License Citation

napari-ome-zarr

A reader for zarr backed OME-NGFF images.

This napari plugin was generated with Cookiecutter using with @napari's cookiecutter-napari-plugin template.

Installation

Install napari if not already installed.

You can install napari-ome-zarr via pip. Activate the same environment as you installed napari into, then:

pip install napari-ome-zarr

Usage

Napari will use napari-ome-zarr plugin 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://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.3/9836842.zarr/"

If a dialog in napari pops up, encouraging you to choose a reader, choose napari-ome-zarr and click OK. You can stop it happening with addition of --plugin napari-ome-zarr as in the example below.

To open a local file::

napari --plugin napari-ome-zarr 13457227.zarr

OR in python::

import napari

viewer = napari.Viewer()
viewer.open("https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0101A/13457537.zarr", plugin="napari-ome-zarr")

napari.run()

Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the BSD-3 license, "napari-ome-zarr" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.

Owner

Name: Open Microscopy Environment
Login: ome
Kind: organization
Email: ome-users@lists.openmicroscopy.org.uk

Website: https://www.openmicroscopy.org/
Twitter: openmicroscopy
Repositories: 337
Profile: https://github.com/ome

Software and data format standards for management of microscopy image data. Joint project between international private and public research

Citation (CITATION.cff)

# YAML 1.2
# Metadata for citation of this software according to the CFF format (https://citation-file-format.github.io/)
cff-version: 1.2.0
message: If you use this software, please cite it using these metadata.
title: napari-ome-zarr
doi: 10.5281/zenodo.5620851
authors:
- given-names: Josh
  family-names: Moore
  affiliation: '@openmicroscopy'
- given-names: Will
  family-names: Moore
  affiliation: '@openmicroscopy'
- given-names: Sébastien
  family-names: Besson
  affiliation: University of Dundee
- given-names: Draga
  family-names: Doncila Pop
repository-code: https://github.com/ome/napari-ome-zarr
references:
  - type: article
    title: "OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies "
    journal: Nature Methods
    volume: 18
    number: 12
    pages: 1496–1498
    doi: 10.1038/s41592-021-01326-w
    year: 2021
    date-published: 2021-11-29
    authors:
      - family-names: Moore
        given-names: Josh
        orcid: "https://orcid.org/0000-0003-4028-811X"
      - family-names: Allan
        given-names: Chris
      - family-names: Besson
        given-names: Sébastien
        orcid: "https://orcid.org/0000-0001-8783-1429"
      - family-names: Burel
        given-names: Jean-Marie
      - family-names: Diel
        given-names: Erin
        orcid: "https://orcid.org/0000-0003-2526-3512"
      - family-names: Gault
        given-names: David
      - family-names: Kozlowski
        given-names: Kevin
      - family-names: Lindner
        given-names: Dominik
      - family-names: Linkert
        given-names: Melissa
      - family-names: Manz
        given-names: Trevor
        orcid: "https://orcid.org/0000-0001-7694-5164"
      - family-names: Moore
        given-names: Will
        orcid: "https://orcid.org/0000-0002-7264-8338"
      - family-names: Pape
        given-names: Constantin
        orcid: "https://orcid.org/0000-0001-6562-7187"
      - family-names: Tischer
        given-names: Christian
      - family-names: Swedlow
        given-names: Jason
        orcid: "https://orcid.org/0000-0002-2198-1958"

GitHub Events

Total

Issues event: 6
Watch event: 7
Issue comment event: 42
Push event: 37
Pull request event: 12
Pull request review event: 20
Pull request review comment event: 18
Fork event: 4

Last Year

Issues event: 6
Watch event: 7
Issue comment event: 42
Push event: 37
Pull request event: 12
Pull request review event: 20
Pull request review comment event: 18
Fork event: 4

Committers

Last synced: 8 months ago

All Time

Total Commits: 135
Total Committers: 12
Avg Commits per committer: 11.25
Development Distribution Score (DDS): 0.696

Past Year

Commits: 20
Committers: 5
Avg Commits per committer: 4.0
Development Distribution Score (DDS): 0.55

Top Committers

Name	Email	Commits
jmoore	j**h@g**m	41
William Moore	w**e@d**k	23
pre-commit-ci[bot]	6****]	20
Sebastien Besson	s**n@g**m	15
Jean-Marie Burel	j**l@d**k	12
David Stansby	d**y@g**m	11
Petr Walczysko	p**o@d**k	4
Draga Doncila Pop	d**1@s**u	4
Justin Kiggins	j**s@g**m	2
Peter Sobolewski	p**d@g**m	1
Juan Nunez-Iglesias	j**s@m**u	1
Draga Doncila Pop	d**a@g**m	1

Committer Domains (Top 20 + Academic)

dundee.ac.uk: 3 monash.edu: 1 student.monash.edu: 1 glencoesoftware.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 59
Total pull requests: 81
Average time to close issues: 3 months
Average time to close pull requests: 28 days
Total issue authors: 34
Total pull request authors: 12
Average comments per issue: 3.69
Average comments per pull request: 2.48
Merged pull requests: 58
Bot issues: 0
Bot pull requests: 20

Past Year

Issues: 6
Pull requests: 13
Average time to close issues: about 1 hour
Average time to close pull requests: about 11 hours
Issue authors: 6
Pull request authors: 3
Average comments per issue: 0.17
Average comments per pull request: 1.23
Merged pull requests: 5
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

constantinpape (8)
will-moore (6)
joshmoore (6)
maweigert (3)
psobolewskiPhD (2)
dstansby (2)
FIrgolitsch (2)
mfranzon (2)
tibuch (2)
jkh1 (2)
d33bs (1)
romainGuiet (1)
andy-sweet (1)
mathieuboudreau (1)
aloboa (1)

Pull Request Authors

pre-commit-ci[bot] (20)
will-moore (17)
dstansby (13)
jburel (12)
joshmoore (7)
psobolewskiPhD (3)
pwalczysko (2)
sbesson (2)
DragaDoncila (2)
neuromusic (1)
constantinpape (1)
jni (1)

Top Labels

Issue Labels

bug (1)

Pull Request Labels

Packages

Total packages: 2
Total downloads:
- pypi 2,713 last-month

Total dependent packages: 7
(may contain duplicates)
Total dependent repositories: 6
(may contain duplicates)
Total versions: 18
Total maintainers: 1

pypi.org: napari-ome-zarr

A reader for zarr backed OME-NGFF images.

Homepage: https://github.com/ome/napari-ome-zarr
Documentation: https://github.com/ome/napari-ome-zarr#README.md
License: BSD-3
Latest release: 0.6.1
published over 1 year ago

Versions: 13
Dependent Packages: 5
Dependent Repositories: 5
Downloads: 2,713 Last month

Rankings

Dependent packages count: 1.6%

Dependent repos count: 6.6%

Average: 7.8%

Forks count: 8.4%

Downloads: 9.7%

Stargazers count: 12.6%

Maintainers (1)

ome

Last synced: 6 months ago

conda-forge.org: napari-ome-zarr

Homepage: https://github.com/ome/napari-ome-zarr
License: BSD-3-Clause
Latest release: 0.5.2
published over 3 years ago

Versions: 5
Dependent Packages: 2
Dependent Repositories: 1

Rankings

Dependent packages count: 19.6%

Dependent repos count: 24.4%

Average: 34.1%

Forks count: 39.5%

Stargazers count: 52.9%

Last synced: 6 months ago

Dependencies

.github/workflows/test_and_deploy.yml actions

actions/checkout v2 composite
actions/setup-python v2 composite
codecov/codecov-action v1 composite

napari-ome-zarr

Science Score: 54.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

napari-ome-zarr

Installation

Usage

Contributing

License

Issues

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: napari-ome-zarr

Rankings

Maintainers (1)

conda-forge.org: napari-ome-zarr

Rankings

Dependencies