cortex_patterning

Repository of codes related to simulating the mathematical model and performing statistical analysis for Feng et al., Science Advances, 2021 (see https://doi.org/10.1126/sciadv.abf6808).

The collection of code here is for:

1. solving PDEs and processing output for models of cortical patterning/neural fate in brain development.
2. Processing cortical imaging data and computing statistics on this data - see the imaging_analysis folder.

Files with the .edp extension are for the freely available finite element PDE solver FreeFEM (https://freefem.org/).

• The ffmatlib folder contains codes needed to interpret FreeFEM meshes and solution output in MATLAB.
• ffmatlib.idp is a library which contains functions to write FreeFEM output to files (it should be in the same parent folder as the .edp file you want to run).

1D Simulations

These codes produce Math Supplement Figure 6 from Feng et al. (2021)

• 1D_gradient_linear.edp.edp
• matlab_plotting_script.m

2D Simulations

These codes produce Math Supplement Figure 7 from Feng et al. (2021)

• 2D_square_linear_gradient.edp
• plot2D_square.m

3D Simulations

These codes produce Math Supplement Figure 10 from Feng et al. (2021)

• 3D_simulation.edp
• plot3D_slice.m