Beams Simple and Fast LIGHT simulation (bsf_light) - light simulation tool using a beam-spread-function approach

Replication and improvement of original model introduced by Yona et al. 2016 [1]. Replication details and model published in [2].

software requirements:

• Requires python 3.13, dependencies will be installed automatically. See /bsf_light/setup.py file for more details.

Tested on Ubuntu 20.04 LTS and 22.04.4 LTS.

Pip installation:

• pip install bsf-light

• install additional dependency: pip install pandas

Run simulations and reproduce figures:

• Run in bash console: bash run_all.sh

Use code for modeling light propagation in cortical tissue

1. Define simulation parameters, example can be found under bsf_light/examples/default.yml and under https://github.com/CSNG-MFF/bsf_light in params/default.yml

2. Use commandline to run simulation using the run-script provided in bsf_light/examples/run.py and under https://github.com/CSNG-MFF/bsf_light in scripts/run.py, providing the parameter-file defined in step 1. and the location where simulation output shall be written to: python scripts/run.py PARAMETER_FILE OUTPUT_LOCATION, e.g., python scripts/run.py params/defaults.yml result.pickle will run the simulation using default parameters and write results to result.pickle.

References

[1] G. Yona, N. Meitav, I. Kahn, S. Shoham, Realistic Numerical and Analytical Modeling of Light Scattering in Brain Tissue for Optogenetic Applications. eNeuro 3, ENEURO.0059-15.2015 (2016).

[2] D. Berling, J. Střeleček, T. Iser, J. Antolík, An open-source replication for fast and accessible light propagation modeling in brain tissue. In revision at PLOS ONE. 2025.