Chaste - Cancer Heart And Soft Tissue Environment - main public repository.

Spheroid models of morphogenesis for the GPU.

"Scutoids are a geometrical solution to three-dimensional packing of epithelia" - https://www.nature.com/articles/s41467-018-05376-1.

vertex model implementation to simulate biological tissue in 3D

vertex model for simulating two-dimensional epithelial tissues

Ontology of human developmental anatomy

Matlab scripts to recreate figures of the JR Soc Interface article "Model reduction enables Turing instability analysis of large reaction-diffusion models"

Analysis scripts for the Ebbing et manuscript: "Spatially-resolved transcriptomics in C. elegans identifies sex-specific differences in gene expression patterns"

Python code to model the syncytial development of a cricket in 3D. Additional Mathematica Code for rendering mesh2 objects in povray.

Deep Learning Based Models for Preimplantation Mouse and Human Development

Analysis scripts for the Vertesy 2018 paper: "Parental haplotype specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells"

Analysis of junctional protein localization patterns in epithelial tissues

"Theoretical tool bridging cell polarities with development of robust morphologies" published in eLife (2018)

Custom codes for Flysta3D paper.

a mathematica implementation of the cellular-potts model

deep-learning for metadata extraction from the C. elegans embryo

Expression of Wnt signaling components in the brachiopod Terebratalia transversa

EpiGraph is a Fiji plugin that combines computational geometry and graph theory to measure the degree of arrangement in any computational or natural tessellation.