Enhanced perfusion following exposure to radiotherapy: a theoretical investigation

An archive of code used to generate simulations and figures for the paper 'Enhanced perfusion following exposure to radiotherapy: a theoretical investigation'. Please use the following citation:

Köry J, Narain V, Stolz BJ, Kaeppler J, Markelc B, et al. (2024) Enhanced perfusion following exposure to radiotherapy: A theoretical investigation. PLOS Computational Biology 20(2): e1011252. https://doi.org/10.1371/journal.pcbi.1011252

Simulations

• Simulations were generated using Microvessel Chaste, an add-on to Chaste.
• To run the code, follow the installation instructions here but use the MicrovesselChaste folder from this repo instead.
• The simulations in this paper were generated by the file MicrovesselChaste/test/simulation/flow/TestEnhancedPerfusionFollowingExposureToRadiotherapy.hpp.

Data

• The simulation data can be generated by the code described above.
• For the experimental data, see the manuscript and this repository.

Analysis

The Python files used to analyse the simulation data and produce figures can be found in the directory Scripts.

• All metrics for the forking network are generated by calculate_nonrandom_forking_metrics_individual_killing.py
• All metrics for the hexagonal network are generated by calculate_hex_metrics_individual_killing.py
• All functions (including TDA analysis) are defined in get_paraview_data.py
• For the TDA function alone, see TDA/Script.py
• Diameter distributions for the hexagonal network are generated by generate_hexagonal_radii_distributions.py

Note

In the code, 'PQ' refers to the perfusion quotient, which is synonymous with 'PF' (the perfusion fraction).

Citation

Enhanced perfusion following exposure to radiotherapy: a theoretical investigation Jakub Köry, Vedang Narain, Bernadette J. Stolz, Jakob Kaeppler, Bostjan Markelc, Ruth J. Muschel, Philip K. Maini, Joe M. Pitt-Francis, Helen M. Byrne bioRxiv 2023.06.12.544532; doi: https://doi.org/10.1101/2023.06.12.544532