bsf-light 1.0.0

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

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:

• python 3.x
• numpy
• matplotlib
• scipy
• pyyaml

Tested on Ubuntu 20.04 LTS and 22.04.4 LTS.

Pip installation:

pip install bsf_light

Use code for modeling light propagation in cortical tissue

1. Define simulation parameters, example can be found under 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 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 run.py PARAMETER_FILE OUTPUT_LOCATION

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] To be announced.