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python-bioformats

Read and write life sciences file formats

https://github.com/cellprofiler/python-bioformats

Science Score: 23.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    8 of 28 committers (28.6%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.9%) to scientific vocabulary

Keywords from Contributors

qt microscopy profiling gtk tk wx docs
Last synced: 10 months ago · JSON representation

Repository

Read and write life sciences file formats

Basic Info
  • Host: GitHub
  • Owner: CellProfiler
  • License: other
  • Language: Python
  • Default Branch: master
  • Size: 219 MB
Statistics
  • Stars: 140
  • Watchers: 15
  • Forks: 48
  • Open Issues: 77
  • Releases: 13
Created over 12 years ago · Last pushed about 1 year ago
Metadata Files
Readme License

README.rst 

NOTE: We have not archived this repository to allow us to make rare, mandatory updates for our own internal use, however it is not actively maintained and should be considered archived.

-----------------------------------------------------------------------------------------------------

Python-bioformats is a Python wrapper for Bio-Formats, a standalone
Java library for reading and writing life sciences image file
formats. Bio-Formats is capable of parsing both pixels and metadata
for a large number of formats, as well as writing to several
formats. Python-bioformats uses the python-javabridge to start a Java
virtual machine from Python and interact with it. Python-bioformats
was developed for and is used by the cell image analysis software
CellProfiler (cellprofiler.org).  While we are gratified that others
outside the CellProfiler team find it useful, we maintain python-bioformats
essentially for the CellProfiler project and **cannot guarantee support 
for other users.** Please consider visiting our forum at forum.image.sc 
for additional support help.

PyPI record: https://pypi.python.org/pypi/python-bioformats

Documentation: http://pythonhosted.org/python-bioformats/

GitHub repository: https://github.com/CellProfiler/python-bioformats

Report bugs here: https://github.com/CellProfiler/python-bioformats/issues

python-bioformats is licensed under the GNU General Public License
(GPL).  Many files are licensed under the more permissive BSD license.
See the accompanying files COPYING and LICENSE for details.

Copyright (c) 2009-2021 Broad Institute. All rights reserved.


.. |Travis CI Status| image:: https://travis-ci.org/CellProfiler/python-bioformats.svg?branch=master
   :target: https://travis-ci.org/CellProfiler/python-bioformats

Owner

  • Name: CellProfiler
  • Login: CellProfiler
  • Kind: organization
  • Location: Cambridge, MA

Software for quantitative analysis of biological images

GitHub Events

Total
  • Issues event: 5
  • Watch event: 9
  • Issue comment event: 5
  • Pull request event: 2
  • Fork event: 3
Last Year
  • Issues event: 5
  • Watch event: 9
  • Issue comment event: 5
  • Pull request event: 2
  • Fork event: 3

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 146
  • Total Committers: 28
  • Avg Commits per committer: 5.214
  • Development Distribution Score (DDS): 0.856
Past Year
  • Commits: 2
  • Committers: 2
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.5
Top Committers
Name Email Commits
mcquin m****n@b****g 21
Vebjorn Ljosa v****n@l****m 17
Lee Kamentsky l****k@b****g 16
John Kirkham k****j@j****g 12
Allen Goodman a****n@i****m 11
Alistair Muldal a****l@g****m 10
ZhengXu x****1@g****m 6
Beth Cimini b****7 5
Niko Ehrenfeuchter n****r@u****h 5
Thomas Fish t****h@d****k 5
bethac07 b****i@b****g 5
Matthew Bowden b****m@s****u 5
David Stirling d****g@b****g 4
rky95813 r****3@p****k 4
Beth Cimini b****i@g****m 3
Kesavan p****n@t****n 2
Emil Rozbicki e****z@g****m 2
mcquin m****l@g****m 2
caspervdw c****w@g****m 2
Joseph Botros j****s@g****m 1
Alessio Buccino a****7@g****m 1
HACKERMD m****n@g****m 1
Claire McQuin m****n 1
Nate Johnson j****0@g****m 1
Thomas Fish 5****h 1
cclauss c****s@b****h 1
Josh Moore j****h@g****m 1
Genevieve Buckley 3****y 1
Committer Domains (Top 20 + Academic)
broadinstitute.org: 4 glencoesoftware.com: 1 bluewin.ch: 1 tifrh.res.in: 1 pw079.diamond.ac.uk: 1 spu.edu: 1 diamond.ac.uk: 1 unibas.ch: 1 janelia.hhmi.org: 1 ljosa.com: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 83
  • Total pull requests: 35
  • Average time to close issues: 10 months
  • Average time to close pull requests: 8 months
  • Total issue authors: 64
  • Total pull request authors: 16
  • Average comments per issue: 1.36
  • Average comments per pull request: 0.91
  • Merged pull requests: 24
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 6
  • Pull requests: 1
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 39 minutes
  • Issue authors: 5
  • Pull request authors: 1
  • Average comments per issue: 0.67
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • sebi06 (7)
  • ehrenfeu (4)
  • markemus (3)
  • bethac07 (3)
  • Nicholas-Schaub (2)
  • chengdonglin (2)
  • zacsimile (2)
  • vbmade2000 (2)
  • mcquin (2)
  • Yuvi-416 (2)
  • everyones (1)
  • kraftlj (1)
  • omsai (1)
  • morganrcu (1)
  • CDPDisk (1)
Pull Request Authors
  • mcquin (9)
  • ehrenfeu (9)
  • 0x00b1 (3)
  • rgluskin (2)
  • gnodar01 (2)
  • DavidStirling (2)
  • LeeKamentsky (1)
  • alejoe91 (1)
  • jnj16180340 (1)
  • riccardomurri (1)
  • cclauss (1)
  • thomasmfish (1)
  • bethac07 (1)
  • alimuldal (1)
  • GenevieveBuckley (1)
Top Labels
Issue Labels
Bug (2) Enhancement (2) Needs verification (1) Documentation (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 3,542 last-month
  • Total docker downloads: 5,772
  • Total dependent packages: 10
  • Total dependent repositories: 56
  • Total versions: 33
  • Total maintainers: 8
pypi.org: python-bioformats

Read and write life sciences file formats

  • Versions: 33
  • Dependent Packages: 10
  • Dependent Repositories: 56
  • Downloads: 3,542 Last month
  • Docker Downloads: 5,772
Rankings
Dependent packages count: 1.0%
Dependent repos count: 2.0%
Downloads: 3.8%
Average: 3.9%
Docker downloads count: 4.1%
Forks count: 6.1%
Stargazers count: 6.6%
Maintainers (8)
bcimini mcquin ljosa 0x00B1 gnodar01 aether anne-broadinstitute Lee.Kamentsky
Last synced: 11 months ago

Dependencies

setup.py pypi
  • boto3 >=1.14.23
  • future >=0.18.2
  • python-javabridge ==4.0.3