Cellects: Cell Expansion Computer Tracking Software

Coverage

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.

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!

Fork the repository and create a new branch.
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

Usage example (video)

Metadata

Release files for cellects 1.1.20

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for cellects 1.1.20
File	Size	Uploaded
cellects-1.1.20.tar.gz	851.5 kB	Oct 3, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for cellects 1.1.20
File	Interpreter	ABI	Platform	Reset
cellects-1.1.20-py3-none-any.whl 802.2 kB Oct 3, 2026	Python 3	none	any	Details

Total release size: 1.7 MB

Release files / cellects-1.1.20.tar.gz

Download URL	cellects-1.1.20.tar.gz
Size	851.5 kB
Tags	Source
SHA-256 checksum How to use checksums	`00cc91b38d3761315850713e8cc7fda1e7a826071e59b46abf74a364449ae95d`
BLAKE2b-256 checksum How to use checksums	`cf332fa669f9d994d250135aca3deac14292ab8de98753a7d0422ab339ddaa28`
Upload date	Oct 3, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/7.0.0 CPython/3.13.14`

Provenance

Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/Aurele-B/Cellects
Publishing commit: github.com/Aurele-B/Cellects/tree/7440bc2e85a17524610299d61207c94be3a5ba9e

Workflow

Publishing configuration: github.com/Aurele-B/Cellects/blob/7440bc2e85a17524610299d61207c94be3a5ba9e/.github/workflows/release.yml
Publishing logs: github.com/Aurele-B/Cellects/actions/runs/37122627363/attempts/1

Artifact

Subject: cellects-1.1.20.tar.gz
SHA-256 checksum: 00cc91b38d3761315850713e8cc7fda1e7a826071e59b46abf74a364449ae95d Verifying attestations

Release files / cellects-1.1.20-py3-none-any.whl

Download URL	cellects-1.1.20-py3-none-any.whl
Size	802.2 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`a46527f017c1f0de8fb31a0c90b7a7ed717055428c238fe10f6424d0cf3c7dac`
BLAKE2b-256 checksum How to use checksums	`85c2fabe39ac12ce1848f09167282d475f8702a79e6a0db7fea74c55b411e9a3`
Upload date	Oct 3, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/7.0.0 CPython/3.13.14`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/Aurele-B/Cellects
Publishing commit: github.com/Aurele-B/Cellects/tree/7440bc2e85a17524610299d61207c94be3a5ba9e

Workflow

Publishing configuration: github.com/Aurele-B/Cellects/blob/7440bc2e85a17524610299d61207c94be3a5ba9e/.github/workflows/release.yml
Publishing logs: github.com/Aurele-B/Cellects/actions/runs/37122627363/attempts/1

Artifact

Subject: cellects-1.1.20-py3-none-any.whl
SHA-256 checksum: a46527f017c1f0de8fb31a0c90b7a7ed717055428c238fe10f6424d0cf3c7dac Verifying attestations