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

Data from the paper

https://doi.org/10.5281/zenodo.23121341

Resources

Usage example (video)

Metadata

Release files for cellects 1.1.21

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 1.1.21
File	Size	Uploaded
cellects-1.1.21.tar.gz	851.6 kB	Oct 14, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for cellects 1.1.21
File	Interpreter	ABI	Platform	Reset
cellects-1.1.21-py3-none-any.whl 802.3 kB Oct 14, 2026	Python 3	none	any	Details

Total release size: 1.7 MB

Release files / cellects-1.1.21.tar.gz

Download URL	cellects-1.1.21.tar.gz
Size	851.6 kB
Tags	Source
SHA-256 checksum How to use checksums	`fffa06cfe20b0c4965545184541ba4ba1b4dc6d39937813fa9e0a98fb24b5c81`
BLAKE2b-256 checksum How to use checksums	`a1251bae2348db3fb78521b34015b44a1f0c145e2a2c38a20954e99c710a0257`
Upload date	Oct 14, 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/af527b24bc3a601821a449a5946bbe635326062c

Workflow

Publishing configuration: github.com/Aurele-B/Cellects/blob/af527b24bc3a601821a449a5946bbe635326062c/.github/workflows/release.yml
Publishing logs: github.com/Aurele-B/Cellects/actions/runs/38598691515/attempts/1

Artifact

Subject: cellects-1.1.21.tar.gz
SHA-256 checksum: fffa06cfe20b0c4965545184541ba4ba1b4dc6d39937813fa9e0a98fb24b5c81 Verifying attestations

Release files / cellects-1.1.21-py3-none-any.whl

Download URL	cellects-1.1.21-py3-none-any.whl
Size	802.3 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`0e2e4876a91697ebd2c98c60df0c0c79d491cf5f09d90d70762bc2222bccadac`
BLAKE2b-256 checksum How to use checksums	`4adafa2b5ac875888df2e14bce64b83e3fb4c341416b6b8a2e9f9f9a1be0b713`
Upload date	Oct 14, 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/af527b24bc3a601821a449a5946bbe635326062c

Workflow

Publishing configuration: github.com/Aurele-B/Cellects/blob/af527b24bc3a601821a449a5946bbe635326062c/.github/workflows/release.yml
Publishing logs: github.com/Aurele-B/Cellects/actions/runs/38598691515/attempts/1

Artifact

Subject: cellects-1.1.21-py3-none-any.whl
SHA-256 checksum: 0e2e4876a91697ebd2c98c60df0c0c79d491cf5f09d90d70762bc2222bccadac Verifying attestations