cellects 0.4.14

Cell Expansion Computer Tracking Software.

Cellects: Cell Expansion Computer Tracking Software

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.

Figure 1: Cellects first window

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Installation (Short version)

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

Or, install via pip:

pip install cellects

Any difficulties? follow our complete installation tutorial

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Quick Start

Run in terminal:

cellects

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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]).

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Use Cases

See use cases for real-world examples:

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

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Contributing

We welcome contributions!

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

For developer workflows, see Contributing.

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License & Citation

GNU GPL3 License (see LICENSE).

To cite Cellects, use:

@article{boussard2024cellects,
  title={Cellects, a software to quantify cell expansion and motion},
  author={Boussard, Aur{\`e}le and Arrufat, Patrick and Dussutour, Audrey and P{\'e}rez-Escudero, Alfonso},
  journal={bioRxiv},
  pages={2024--03},
  year={2024},
  publisher={Cold Spring Harbor Laboratory}
}

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Testing

Run unit tests with:

pip install -e ".[test]"
pytest

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Resources

• Usage example (video)