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Cellocity

Cellocity: A Python package for analysis of confluent cell layer dynamics - Published in JOSS (2021)

https://github.com/oftatkofta/cellocity

Science Score: 95.0%

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
    Found 4 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org
  • ✓
    Committers with academic emails
    1 of 4 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

analysis cell-dynamics microscopy microscopy-data time-series-analysis vector-analysis
Last synced: 6 months ago · JSON representation

Repository

Scientific software for analysis of confluent cell dynamics.

Basic Info
Statistics
  • Stars: 7
  • Watchers: 0
  • Forks: 3
  • Open Issues: 1
  • Releases: 11
Topics
analysis cell-dynamics microscopy microscopy-data time-series-analysis vector-analysis
Created over 6 years ago · Last pushed 10 months ago
Metadata Files
Readme Contributing License

readme.md

Cellocity

Cellocity is a python package that allows the user to perform Optical Flow and PIV analysis on microscopy data. It is intended to be helpful in both the exploratory and in the data acquisition phases of a cell layer dynamics project. In the exploratory phase, several different algorithms, settings, and preprocessing functions can be evaluated. In the acquisition phase, a pipeline can be "hard coded" for processing of multiple data sets through a pre-determined series of steps.

Velocity and vector analysis of microscopy data

Cellocity can create vector field visualizations, speed graphs, and multiple advanced vector field analyses, such as calculating the instantaneous order parameter, alignment index and correlation lengths of migrating cells.

Documentation & Software validation

Documentation is available at Read the Docs. There you can also find an extensive chapter on the validation of the Cellocity software.

Citing Cellocity

If you want to cite Cellocity in your work you can use our JOSS publication DOI

Owner

  • Name: Jens Eriksson
  • Login: Oftatkofta
  • Kind: user
  • Location: Sweden
  • Company: Uppsala University

JOSS Publication

Cellocity: A Python package for analysis of confluent cell layer dynamics
Published
January 28, 2021
DOI
Volume 6, Issue 57, Page 2818
Authors
Jens Eriksson ORCID
Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University
Daniel Styrström
Daniel Styrström Consulting
Mikael E. Sellin ORCID
Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University
Editor
Juan Nunez-Iglesias ORCID
Tags
microscopy dynamics confluent cell layer
View PDF Review Thread Software Archive

GitHub Events

Total
  • Issues event: 1
  • Watch event: 1
  • Issue comment event: 2
  • Push event: 13
Last Year
  • Issues event: 1
  • Watch event: 1
  • Issue comment event: 2
  • Push event: 13

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 290
  • Total Committers: 4
  • Avg Commits per committer: 72.5
  • Development Distribution Score (DDS): 0.072
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Jens Eriksson O****a 269
Mikael E. Sellin 7****n 19
jrijn j****n@g****m 1
Daniel S. Katz d****z@i****g 1
Committer Domains (Top 20 + Academic)
ieee.org: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 4
  • Total pull requests: 19
  • Average time to close issues: 25 days
  • Average time to close pull requests: about 14 hours
  • Total issue authors: 3
  • Total pull request authors: 4
  • Average comments per issue: 4.0
  • Average comments per pull request: 0.11
  • Merged pull requests: 16
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 4.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jrijn (2)
  • fabricesenger (1)
  • YunanYe (1)
Pull Request Authors
  • MikaelSellin (11)
  • Oftatkofta (5)
  • jrijn (2)
  • danielskatz (1)
Top Labels
Issue Labels
enhancement (2) bug (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 48 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 9
  • Total maintainers: 1
pypi.org: cellocity

Velocity and vector analysis of microscopy data

  • Versions: 9
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 48 Last month
Rankings
Dependent packages count: 10.0%
Forks count: 16.8%
Average: 19.1%
Stargazers count: 20.3%
Dependent repos count: 21.7%
Downloads: 26.7%
Maintainers (1)
oftakofta
Last synced: 6 months ago

Dependencies

docs/requirements.txt pypi
  • OpenPIV ==0.22.2
  • cython >=0.29.19
  • docutils >=0.16
  • matplotlib >=3.2.1
  • numpy >=1.18.1
  • opencv-python >4.2.0
  • pandas >=1.0.1
  • seaborn >=0.10.1
  • tifffile ==2020.2.16
setup.py pypi
  • OpenPIV ==0.22.2
  • cython >=0.29.19
  • docutils >=0.16
  • matplotlib >=3.2.1
  • numpy >=1.18.1
  • opencv-python >4.2.0
  • pandas >=1.0.1
  • seaborn >=0.10.1
  • sphinxcontrib-bibtex ==1.0.0
  • tifffile ==2020.2.16
.github/workflows/python-publish.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite