Modelling Cell Shape in 3D Structured Environments: A Quantitative Comparison with Experiments

This repository contains experimental data and computer scripts for the following publication: Link R, Jaggy M, Bastmeyer M, Schwarz US (2024) Modelling cell shape in 3D structured environments: A quantitative comparison with experiments. PLoS Comput Biol 20(4): e1011412. https://doi.org/10.1371/journal.pcbi.1011412

There are two directories, “data” and “scripts”.

 1)     Directory data

 WRL-files for experimental data generated with Imaris from Zeiss image files.

The WRL-files can be converted to STL-files with MeshLab (https://www.meshlab.net).

The STL-files can be converted to FE-files for the SurfaceEvolver with our script CreateFeFile.py.

 The WRL-files are named according to the scaffolds:

L*.wrl cells in L-shaped scaffolds (n=6).

V*.wrl cells in V-shaped scaffolds (n=7).

TRight*.wrl cells in right-triangle scaffolds (n=3).

TEqui*.wrl cells in equilateral-triangle scaffolds (n=4).

2)     Directory scripts

ClusterSurfaceLinearPlugin: New CompuCell3D plugin needed to calculate linear surface energy functional for cells with nucleus (using the cluster concept).

CompuCell3DScript: Hamiltonian_Comparison.cc3d is the main script for our simulations, uses the directory “Simulation”.

CreateFeFile.py: generates surface evolver FE-file from STL-file. A STL-file can be generated from a WRL-file e.g. with MeshLab (https://www.meshlab.net). 

SphericalHarmonicsAnalysis.ipynb: Python notebook that calculates the Fourier spectrum and Delta_30, needs WRL-file as input.