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bioRxiv · 10.1101/2024.03.26.586795

Cellects, a software to quantify cell expansion and motion

Boussard, A.·Arrufat, P.·Dussutour, A.·Perez-Escudero, A.
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Abstract

Cellects is a user-friendly and open-source software for automated quantification of biological growth, motion, and morphology from 2D image data and time-lapse sequences (2D + t), acquired under a wide range of experimental conditions and biological systems (from fungal colonies to unicellular branching networks). The software is available as a stand-alone version, featuring a graphical interface that supports interactive parameter tuning, visualization, validation, and batch processing. The analysis pipeline can be extended and customized using a dedicated Python API. The typical inputs and outputs are as follows. Cellects is designed to process grayscale or color images originating from standard microscopy, macroscopic imaging setups, or camera-based platforms. The software supports single or multiple organisms growing or moving in one or several arenas and can analyze multiple folders sequentially. All quantitative results (area, circularity, orientation axes, centroid trajectories, oscillations, network topology...) are exported as standardized .csv files suitable for downstream statistical analysis, ensuring reproducibility and integration into existing workflows.

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Boussard, A., Arrufat, P., Dussutour, A., Perez-Escudero, A.. 2024-03-29. Cellects, a software to quantify cell expansion and motion. https://doi.org/10.1101/2024.03.26.586795

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