Cellects: Cell Expansion Computer Tracking Software

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Description

Cellects is a user-friendly software for automated computation of biological growth, motion and morphology from 2D images and time-lapse sequences (2D + t). Its graphical interface has a minimalist design which ensures users can perform essential image analysis tasks without prior expertise. Cellects’ main strengths are its broad scope of action, automated computation of a variety of geometrical descriptors, easy installation and user-friendly interface.

Cellects first window
Figure 1: Cellects first window

Installation (Short version)

Install on Windows .exe and macOS (silicon only) .dmg

Or, install via pip:

pip install cellects

Any difficulties? follow our complete installation tutorial

Quick Start

Run in terminal:

cellects

Documentation

Cellects' workflow is described in a complete documentation. It includes:

  • What is Cellects: Purpose of the software, usable data and introduction of its user manual
  • Setting up a first analysis: Step-by-step workflows for data localization, image analysis and video tracking
  • Improving the analysis: Customization options, batch processing, parameter tuning.
  • Use cases: Real-world cases using the GUI (interface) and the API (scripts).
  • Contributing: Report bugs and feature requests; contribute; testing and documentation processes.
  • API Reference: Auto-generated from source code docstrings (see [Build Documentation]).

Use Cases

See use cases for real-world examples:

  • Automated Physarum polycephalum tracking using GUI
  • Automated Physarum polycephalum tracking using API
  • Colony growth tracking

Contributing

We welcome contributions!

  1. Fork the repository and create a new branch.
  2. Submit issues/PRs via GitHub.

For developer workflows, see Contributing.

License & Citation

GNU GPL3 License (see LICENSE).

To cite Cellects, use:

@article{boussard2026cellects,
  title={Cellects, a software to quantify cell expansion and motion},
  author = {Boussard, Aur{\`e}le and Petit, Manuel and Arrufat, Patrick and Dussutour, Audrey and P{\'e}rez-Escudero, Alfonso},
  journal={bioRxiv},
  pages={2026--02},
  year = {2026},
  doi = {10.1101/2024.03.26.586795},
  publisher={Cold Spring Harbor Laboratory}
}

Testing

Run unit tests with:

pip install -e ".[test]"
pytest

Resources

Project links

Data verified by PyPI on Sep 5, 2026
Data provided by the project maintainers, verified at the time the release was uploaded to PyPI.

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Newer release available (1.1.19)

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for Aurele-B from gravatar.com Aurele-B

Credits

Author: Aurèle Boussard

GitHub Statistics

Data verified by PyPI on Sep 5, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

GNU General Public License v3 (GPLv3) (GNU GENERAL PUBLIC LICENSE)

Requires

Python <3.15, >=3.11

Provides Extra

test doc

Classifiers

Report project as malware

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