https://github.com/oftatkofta/cellocity

Scientific software for analysis of confluent cell dynamics.
https://github.com/oftatkofta/cellocity

analysis cell-dynamics microscopy microscopy-data time-series-analysis vector-analysis

Last synced: 5 months ago
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Scientific software for analysis of confluent cell dynamics.

• Host: GitHub
• URL: https://github.com/oftatkofta/cellocity
• Owner: Oftatkofta
• License: gpl-3.0
• Created: 2019-07-04T10:06:25.000Z (almost 7 years ago)
• Default Branch: master
• Last Pushed: 2025-05-09T14:18:45.000Z (about 1 year ago)
• Last Synced: 2026-01-04T11:12:01.237Z (5 months ago)
• Topics: analysis, cell-dynamics, microscopy, microscopy-data, time-series-analysis, vector-analysis
• Language: Python
• Homepage: https://cellocity.readthedocs.io/en/latest/
• Size: 91.7 MB
• Stars: 7
• Watchers: 0
• Forks: 3
• Open Issues: 1
• Metadata Files:
  • Readme: readme.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE

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README

          
# 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](https://cellocity.readthedocs.io/en/latest/).

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](https://joss.theoj.org/papers/10.21105/joss.02818/status.svg)](https://doi.org/10.21105/joss.02818)