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bioRxiv · 10.1101/2025.09.02.673513

3DTubularVoronoi: a Voronoi-Based Framework for Estimating Equilibrium Cellular Packing in 3D Tubular Epithelia

Guitou, L.·Serrano, E. T.·Conejero, J. A.·Buceta, J.
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Abstract

Epithelial tube morphogenesis is fundamental to organ development and functioning, yet accurately modeling its intricate 3D organization and dynamics remains a challenge. In particular, current computational tools fail to capture the spontaneous emergence of non-transient scutoids, a geometric feature essential for accommodating curvature in epithelia. Here, we introduce 3DTubularVoronoi, a novel simulation framework for modeling epithelial tube morphogenesis and determining their stable cell packing organization depending on mechanical parameters. The model employs a Voronoi tessellation strategy combined with an energy minimization approach using the Metropolis-Hasting algorithm. 3DTubularVoronoi enables realistic epithelial tube simulations, accounting for scutoid formation and dynamic rearrangements. This tool provides an open-source, user-friendly solution for exploring gland morphogenesis and offering insights into developmental biology and tissue engineering. Availabilityhttps://github.com/TheSiMBioSysI2SysBio/3DTubularVoronoi

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Guitou, L., Serrano, E. T., Conejero, J. A., Buceta, J.. 2025-09-06. 3DTubularVoronoi: a Voronoi-Based Framework for Estimating Equilibrium Cellular Packing in 3D Tubular Epithelia. https://doi.org/10.1101/2025.09.02.673513

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