ECM simulations

A collection of scripts for computing eigenfunctions on geometrical models of C elegans embryos using NGSolve.

Setup

Install uv, then create the environment:

uv sync

Then, you should be able to run the examples using:

uv run python <filename>  # just console output, no GUI
uv run netgen <filename>  # console output and GUI

The .py scripts in the scripts/ directory are text representations of notebook files courtesy of jupytext. When you open them in jupyter (right-click and choose 'Open With > Jupytext notebook'), they will be automatically converted to interactive notebooks, which you can find in the notebooks/ directory. Saving a notebook will also automatically update the associated .py file.

C. elegans CLI scripts

scripts/celegans/process_all_geometries.py and scripts/celegans/process_all_genes.py are plain CLI scripts (not jupytext notebooks). Run -h on either for the full list of options.

Generate meshes and harmonics for every time step of an embryo model. They are stored in a single HDF5 file with a sibling .xdmf file that can be opened in ParaView:

uv run python scripts/celegans/process_all_geometries.py <path_to_celegans_models.h5> \
    --output-file results/embryo_harmonics.h5 --n-harmonics 300 --mesh-size 5

Compute harmonic coefficients for all genes and tissues from the meshes/harmonics produced above:

uv run python scripts/celegans/process_all_genes.py <path_to_celegans_genedata.h5> results/embryo_harmonics.h5 \
    --output-file harmonic_coefficients.h5