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cellprofiler-plugins

Community-contributed and experimental CellProfiler modules.

https://github.com/cellprofiler/cellprofiler-plugins

Science Score: 44.0%

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
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.1%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Community-contributed and experimental CellProfiler modules.

Basic Info
Statistics
  • Stars: 68
  • Watchers: 9
  • Forks: 70
  • Open Issues: 28
  • Releases: 1
Created about 13 years ago · Last pushed 6 months ago
Metadata Files
Readme Citation

README.md

CellProfiler-plugins

A home for community-contributed, experimental, and dependency-heavy CellProfiler modules.

Plugins advance the capabilities of CellProfiler but are not officially supported in the same way as modules. A module may be in CellProfiler-plugins instead of CellProfiler itself because: - it is under active development - it has a niche audience - it is not documented to CellProfiler's standards - it only works with certain version of CellProfiler - it requires extra libraries or other dependencies we are unable or unwilling to require for CellProfiler - it has been contributed by a community member

Please see our CellProfiler-plugins documentation for more information about installation, currently supported plugins, and how to contribute.

Troubleshooting

If CellProfiler won't open after setting the CellProfiler Plugins folder (and it returns error: no commands supplied in the terminal), it is likely because you have set the CellProfiler Plugins folder to the parent folder of the plugins repository (CellProfiler-plugins), not the folder that contains plugins (CellProfiler-plugins/active_plugins).

In order to get CellProfiler to open, remove setup.py from the CellProfiler-plugins folder. Open CellProfiler. Change the CellProfiler Plugins path to the correct path and close CellProfiler. Return setup.py to the parent folder.
OR
Alternatively, you can edit the PluginDirectory line of your config to the correct path and then reload CellProfiler. On Mac, you can find the config at /Users/{username}/Library/Preferences/CellProfilerLocal.cfg

For other troubleshooting information, please see the Troubleshooting page of our documentation.

Owner

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

Software for quantitative analysis of biological images

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If using CellProfiler Plugins in a pipeline used in a publication, please cite our CellProfiler-Plugins paper. Additionally, some plugins require citation themselves if used. You can determine which plugins require citation by reading the Help information for each plugin, accessible through CellProfiler, or by using the Citation generator built into CellProfiler (since CellProfiler 5)."
type: software
authors:
  - name: 'Imaging Platform, Broad Institute of Harvard and MIT'
    city: Cambridge
    country: US
repository: https://github.com/CellProfiler/CellProfiler-plugins
title: "CellProfiler plugins"
doi: https://doi.org/10.1111/jmi.13223
date-released: 2023
preferred-citation:
  type: article
  authors:
  - family-names: "Weisbart"
    given-names: "Erin"
    orcid: "https://orcid.org/0000-0002-6437-2458"
  - family-names: "Tromans-Coia"
    given-names: "Callum"
    orcid: "https://orcid.org/0000-0002-5518-8915"
  - family-names: "Diaz-Rohrer"
    given-names: "Barbara"
    orcid: "https://orcid.org/0000-0002-4748-7077"
  - family-names: "Stirling"
    given-names: "David R."
    orcid: "https://orcid.org/0000-0001-6802-4103"
  - family-names: "Garcia-Fossa"
    given-names: "Fernanda"
    orcid: "https://orcid.org/0000-0003-2308-0149"
  - family-names: "Senft"
    given-names: "Rebecca A."
    orcid: "https://orcid.org/0000-0003-0081-4170"
  - family-names: "Hiner"
    given-names: "Mark C."
    orcid: "https://orcid.org/0000-0001-9404-7579"
  - family-names: "de Jesus"
    given-names: "Marcelo B."
    orcid: "https://orcid.org/0000-0003-0812-1491"
  - family-names: "Eliceiri"
    given-names: "Kevin W."
    orcid: "https://orcid.org/0000-0001-8678-670X"
  - family-names: "Cimini"
    given-names: "Beth A."
    orcid: "https://orcid.org/0000-0001-9640-9318"
  doi: "https://doi.org/10.1111/jmi.13223"
  journal: "Journal of Microscopy"
  title: "CellProfiler plugins – An easy image analysis platform integration for containers and Python tools."
  year: 2023

GitHub Events

Total
  • Issues event: 17
  • Watch event: 9
  • Delete event: 9
  • Issue comment event: 34
  • Push event: 39
  • Pull request review comment event: 5
  • Pull request review event: 9
  • Pull request event: 26
  • Fork event: 3
  • Create event: 11
Last Year
  • Issues event: 17
  • Watch event: 9
  • Delete event: 9
  • Issue comment event: 34
  • Push event: 39
  • Pull request review comment event: 5
  • Pull request review event: 9
  • Pull request event: 26
  • Fork event: 3
  • Create event: 11

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 11
  • Total pull requests: 14
  • Average time to close issues: over 1 year
  • Average time to close pull requests: 5 months
  • Total issue authors: 8
  • Total pull request authors: 7
  • Average comments per issue: 1.36
  • Average comments per pull request: 1.29
  • Merged pull requests: 9
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 5
  • Pull requests: 11
  • Average time to close issues: 5 days
  • Average time to close pull requests: 24 days
  • Issue authors: 4
  • Pull request authors: 4
  • Average comments per issue: 0.4
  • Average comments per pull request: 1.18
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ErinWeisbart (6)
  • braymp (3)
  • MikeLippincott (2)
  • Pvannd (1)
  • ML33M (1)
  • viksyn2 (1)
  • jenna-tomkinson (1)
  • emiglietta (1)
  • obruck (1)
  • bethac07 (1)
  • Yesha012025 (1)
  • sugan89 (1)
  • kmshort (1)
  • J-M-Dundee (1)
Pull Request Authors
  • ErinWeisbart (11)
  • bethac07 (6)
  • gnodar01 (4)
  • emiglietta (4)
  • wllgrnt (2)
  • GaiaGerbaka (1)
  • sugan89 (1)
  • fefossa (1)
  • binliunls (1)
  • rsenft1 (1)
  • ShataDg (1)
Top Labels
Issue Labels
enhancement (4)
Pull Request Labels

Dependencies

.github/workflows/deploy.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • peaceiris/actions-gh-pages v3.6.1 composite
.github/workflows/test.yml actions
  • actions/cache v3 composite
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
.github/workflows/test_cellpose.yml actions
  • actions/cache v3 composite
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
.github/workflows/test_stardist.yml actions
  • actions/cache v3 composite
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
dockerfiles/RunCellpose/Dockerfile docker
  • pytorch/pytorch 1.13.0-cuda11.6-cudnn8-runtime build
setup.py pypi