Metadata-Version: 2.1
Name: bsf_light
Version: 1.0.0
Summary: Beams Simple and Fast LIGHT simulation (bsf_light) - Fast light simulation for brain tissue using a beam-spread-function approach
Author: David Berling
Author-email: berling@ksvi.mff.cuni.cz
Requires-Python: >=3.13
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy>=2.1.3
Requires-Dist: scipy>=1.14.1
Requires-Dist: pyyaml>=6.0.2
Requires-Dist: matplotlib>=3.9.2

# 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.

