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cellprofiler

An open-source application for biological image analysis

https://github.com/cellprofiler/cellprofiler

Science Score: 36.0%

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
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    31 of 142 committers (21.8%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.0%) to scientific vocabulary

Keywords from Contributors

closember microscopy profiling imaging gtk qt tk wx cryptocurrencies cytomining
Last synced: 10 months ago · JSON representation

Repository

An open-source application for biological image analysis

Basic Info
  • Host: GitHub
  • Owner: CellProfiler
  • License: other
  • Language: Python
  • Default Branch: main
  • Homepage: http://cellprofiler.org
  • Size: 188 MB
Statistics
  • Stars: 1,024
  • Watchers: 44
  • Forks: 403
  • Open Issues: 345
  • Releases: 51
Created about 15 years ago · Last pushed 10 months ago
Metadata Files
Readme Contributing License Citation

README.md

CellProfiler

Version Docs Image.sc forum

CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. More information can be found in the CellProfiler Wiki.

What version of CellProfiler should I use?

We recommend the stable release of CellProfiler.

You can download a stable release for macOS and Windows from the CellProfiler website.

If youre contributing or planning to contribute to CellProfiler, you should compile CellProfiler from source. Instructions for compiling CellProfiler on Linux, macOS and Windows are available from CellProfilers GitHub wiki.

If youre the maintainer of a third-party CellProfiler module, you should use the nightly release of CellProfiler. You can download a nightly release for macOS and Windows from the CellProfiler website. Let us know if weve inadvertently broken your module by submitting a GitHub issue.

If youre an enthusiastic CellProfiler user, you should try the beta release of CellProfiler. You can download a beta release for macOS and Windows from the CellProfiler website. Let us know if you encounter a bug by submitting a GitHub issue.

Owner

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

Software for quantitative analysis of biological images

GitHub Events

Total
  • Fork event: 34
  • Create event: 30
  • Commit comment event: 4
  • Issues event: 67
  • Watch event: 110
  • Delete event: 16
  • Member event: 1
  • Issue comment event: 73
  • Push event: 214
  • Pull request review event: 44
  • Pull request review comment event: 25
  • Gollum event: 21
  • Pull request event: 40
Last Year
  • Fork event: 34
  • Create event: 30
  • Commit comment event: 4
  • Issues event: 67
  • Watch event: 110
  • Delete event: 16
  • Member event: 1
  • Issue comment event: 73
  • Push event: 214
  • Pull request review event: 44
  • Pull request review comment event: 25
  • Gollum event: 21
  • Pull request event: 40

Committers

Last synced: 12 months ago

All Time
  • Total Commits: 15,437
  • Total Committers: 142
  • Avg Commits per committer: 108.711
  • Development Distribution Score (DDS): 0.875
Past Year
  • Commits: 195
  • Committers: 8
  • Avg Commits per committer: 24.375
  • Development Distribution Score (DDS): 0.451
Top Committers
Name Email Commits
carpenter c****r@1****7 1,925
Lee Kamentsky l****k@b****g 1,848
leek l****k@1****7 1,517
mrl m****l@1****7 1,035
mbray m****y@1****7 928
Allen Goodman a****n@i****m 831
thouis t****s@1****7 726
dlogan d****n@1****7 701
David Stirling d****g@b****g 538
cellprofiler c****r@1****7 531
Beth Cimini b****7 372
mcquin m****n@b****g 353
braymp m****y@b****g 336
Nodar Gogoberidze g****1@g****m 306
klmadden k****n@1****7 216
junliu j****u@1****7 205
Thouis (Ray) Jones t****s@g****m 194
afraser a****r@1****7 169
reipince r****e@1****7 169
Matthew Bowden b****m@s****u 154
(no author) (****)@1****7 147
friman f****n@1****7 145
Claire McQuin m****n 144
Anne Carpenter a****e@b****g 139
ljosa l****a@1****7 135
anne a****e@1****7 135
David Stirling d****0@h****k 123
mvokes m****s@1****7 102
Vebjorn Ljosa v****n@l****m 94
colin c****n@1****7 85
and 112 more...
Committer Domains (Top 20 + Academic)
broadinstitute.org: 13 glencoesoftware.com: 2 vsingan-lm.dhcp.lbl.gov: 1 domestic.build: 1 iwr.uni-heidelberg.de: 1 cg-router1.broadinstitute.org: 1 emmenlauer.de: 1 emory.edu: 1 uni-konstanz.de: 1 leoank.me: 1 amsat.org: 1 wisc.edu: 1 imba.oeaw.ac.at: 1 bluewin.ch: 1 ljosa.com: 1 hotmail.co.uk: 1 vpa84-8bb.broad.mit.edu: 1 glasgow.ac.uk: 1 node1378.broadinstitute.org: 1 mayo.edu: 1 vm5a3-282.broadinstitute.org: 1 wm69b-6fa.broadinstitute.org: 1 sms.ed.ac.uk: 1 login.cluster.embl.de: 1 ens.fr: 1 cardiff.ac.uk: 1 dev-aics-mbp-002.corp.alleninstitute.org: 1 spu.edu: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 246
  • Total pull requests: 157
  • Average time to close issues: about 1 year
  • Average time to close pull requests: 2 months
  • Total issue authors: 116
  • Total pull request authors: 21
  • Average comments per issue: 1.91
  • Average comments per pull request: 1.2
  • Merged pull requests: 101
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 54
  • Pull requests: 52
  • Average time to close issues: 21 days
  • Average time to close pull requests: 14 days
  • Issue authors: 23
  • Pull request authors: 7
  • Average comments per issue: 0.8
  • Average comments per pull request: 0.48
  • Merged pull requests: 20
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • bethac07 (51)
  • emiglietta (15)
  • ErinWeisbart (12)
  • gnodar01 (11)
  • braymp (9)
  • rsenft1 (6)
  • jenna-tomkinson (6)
  • d33bs (4)
  • ghbillings (4)
  • callum-jpg (3)
  • vkhodygo (3)
  • mdposkus (3)
  • 0x00b1 (3)
  • tischi (3)
  • capret (2)
Pull Request Authors
  • bethac07 (59)
  • gnodar01 (57)
  • sspathak (28)
  • callum-jpg (20)
  • DavidStirling (5)
  • ErinWeisbart (5)
  • leoank (5)
  • ShataDg (3)
  • Antsalacia (2)
  • JacobHayes (2)
  • bdiazroh (2)
  • Mas515 (1)
  • ximion (1)
  • fefossa (1)
  • alxndrkalinin (1)
Top Labels
Issue Labels
Bug (111) Needs verification (95) Enhancement (68) Feature request (56) Environment/Install (42) Documentation (11) linux specific (5) Future consideration (2) Easy (2) dependencies (1) OSX Specific (1) Breaking Change (1)
Pull Request Labels
Breaking Change (3) dependencies (1) Documentation (1)

Packages

  • Total packages: 6
  • Total downloads:
    • pypi 1,459 last-month
  • Total dependent packages: 3
    (may contain duplicates)
  • Total dependent repositories: 4
    (may contain duplicates)
  • Total versions: 193
  • Total maintainers: 6
pypi.org: cellprofiler
  • Versions: 21
  • Dependent Packages: 0
  • Dependent Repositories: 4
  • Downloads: 820 Last month
Rankings
Stargazers count: 2.2%
Forks count: 2.8%
Average: 5.8%
Dependent packages count: 7.4%
Dependent repos count: 7.7%
Downloads: 8.9%
Maintainers (6)
bcimini 0x00B1 alicelucas DavidStirling gnodar01 aether
Last synced: 10 months ago
proxy.golang.org: github.com/cellprofiler/cellprofiler
  • Versions: 35
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 9.0%
Average: 9.6%
Dependent repos count: 10.2%
Last synced: 10 months ago
proxy.golang.org: github.com/CellProfiler/CellProfiler
  • Versions: 35
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 9.0%
Average: 9.6%
Dependent repos count: 10.2%
Last synced: 10 months ago
pypi.org: cellprofiler-core-nightly

cellprofiler-core implements the bulk of CellProfiler's non-gui functionality

  • Homepage: https://cellprofiler.org/
  • Documentation: https://cellprofiler.org/manuals
  • License: The BSD 3-Clause License Copyright © 2003 - 2021 Broad Institute, Inc. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the Broad Institute, Inc. nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED “AS IS.” BROAD MAKES NO EXPRESS OR IMPLIED REPRESENTATIONS OR WARRANTIES OF ANY KIND REGARDING THE SOFTWARE AND COPYRIGHT, INCLUDING, BUT NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, CONFORMITY WITH ANY DOCUMENTATION, NON-INFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. IN NO EVENT SHALL BROAD, THE COPYRIGHT HOLDERS, OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF, HAVE REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF SUCH DAMAGE. If, by operation of law or otherwise, any of the aforementioned warranty disclaimers are determined inapplicable, your sole remedy, regardless of the form of action, including, but not limited to, negligence and strict liability, shall be replacement of the software with an updated version if one exists. Development of CellProfiler has been funded in whole or in part with federal funds from the National Institutes of Health, the National Science Foundation, and the Human Frontier Science Program.
  • Latest release: 5.0.0.dev265
    published 11 months ago
  • Versions: 34
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 228 Last month
Rankings
Dependent packages count: 9.5%
Average: 35.9%
Dependent repos count: 62.4%
Maintainers (2)
bcimini gnodar01
Last synced: 10 months ago
pypi.org: cellprofiler-library-nightly

cellprofiler-library implements CellProfiler's image processing and mathematical code, and is usable as a standalone library

  • Homepage: https://cellprofiler.org/
  • Documentation: https://cellprofiler.org/manuals
  • License: The BSD 3-Clause License Copyright © 2003 - 2021 Broad Institute, Inc. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the Broad Institute, Inc. nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED “AS IS.” BROAD MAKES NO EXPRESS OR IMPLIED REPRESENTATIONS OR WARRANTIES OF ANY KIND REGARDING THE SOFTWARE AND COPYRIGHT, INCLUDING, BUT NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, CONFORMITY WITH ANY DOCUMENTATION, NON-INFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. IN NO EVENT SHALL BROAD, THE COPYRIGHT HOLDERS, OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF, HAVE REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF SUCH DAMAGE. If, by operation of law or otherwise, any of the aforementioned warranty disclaimers are determined inapplicable, your sole remedy, regardless of the form of action, including, but not limited to, negligence and strict liability, shall be replacement of the software with an updated version if one exists. Development of CellProfiler has been funded in whole or in part with federal funds from the National Institutes of Health, the National Science Foundation, and the Human Frontier Science Program.
  • Latest release: 5.0.0.dev265
    published 11 months ago
  • Versions: 34
  • Dependent Packages: 2
  • Dependent Repositories: 0
  • Downloads: 246 Last month
Rankings
Dependent packages count: 9.5%
Average: 35.9%
Dependent repos count: 62.4%
Maintainers (2)
bcimini gnodar01
Last synced: 10 months ago
pypi.org: cellprofiler-nightly

CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

  • Homepage: https://cellprofiler.org/
  • Documentation: https://cellprofiler.org/manuals
  • License: The BSD 3-Clause License Copyright © 2003 - 2021 Broad Institute, Inc. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the Broad Institute, Inc. nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED “AS IS.” BROAD MAKES NO EXPRESS OR IMPLIED REPRESENTATIONS OR WARRANTIES OF ANY KIND REGARDING THE SOFTWARE AND COPYRIGHT, INCLUDING, BUT NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, CONFORMITY WITH ANY DOCUMENTATION, NON-INFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. IN NO EVENT SHALL BROAD, THE COPYRIGHT HOLDERS, OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF, HAVE REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF SUCH DAMAGE. If, by operation of law or otherwise, any of the aforementioned warranty disclaimers are determined inapplicable, your sole remedy, regardless of the form of action, including, but not limited to, negligence and strict liability, shall be replacement of the software with an updated version if one exists. Development of CellProfiler has been funded in whole or in part with federal funds from the National Institutes of Health, the National Science Foundation, and the Human Frontier Science Program.
  • Latest release: 5.0.0.dev265
    published 11 months ago
  • Versions: 34
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 165 Last month
Rankings
Dependent packages count: 9.5%
Average: 35.9%
Dependent repos count: 62.4%
Maintainers (2)
bcimini gnodar01
Last synced: 10 months ago

Dependencies

setup.py pypi
  • Jinja2 >=2.11.2
  • Pillow >=7.1.0
  • boto3 >=1.12.28
  • cellprofiler-core ==4.2.1
  • centrosome ==1.2.0
  • docutils ==0.15.2
  • h5py *
  • imageio >=2.5
  • inflect >=2.1
  • joblib >=0.13
  • mahotas >=1.4
  • matplotlib ==3.1.3
  • mysqlclient ==1.4.6
  • numpy >=1.20.1
  • prokaryote ==2.4.4
  • python-bioformats ==4.0.5
  • python-javabridge ==4.0.3
  • pyzmq *
  • requests >=2.22
  • scikit-image >=0.17.2
  • scikit-learn >=0.20
  • scipy >=1.4.1
  • sentry-sdk ==0.18.0
  • six *
  • wxPython ==4.1.0
.github/workflows/release.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/create-release v1 composite
  • actions/download-artifact v1 composite
  • actions/setup-java v3 composite
  • actions/setup-python v2 composite
  • actions/upload-artifact v1 composite
  • actions/upload-artifact v2 composite
  • actions/upload-release-asset v1 composite
.github/workflows/test.yml actions
  • actions/cache v3 composite
  • actions/checkout v2 composite
  • actions/setup-java v1 composite
  • actions/setup-python v2 composite
environment.yml conda
  • boto3
  • docutils
  • h5py
  • imageio
  • inflect
  • joblib
  • mahotas
  • matplotlib
  • mysqlclient
  • numpy
  • psutil
  • pyzmq
  • scikit-image
  • scipy
  • scyjava