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

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