methods to calculate extracellular signals of neural activity from spike events from spiking neuron networks
Project description
# Module hybridLFPy
Python module implementating a hybrid model scheme for predictions of extracellular potentials (local field potentials, LFPs) of spiking neuron network simulations.
## Project Status
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.45185.svg)](https://doi.org/10.5281/zenodo.45185) [![Documentation Status](https://readthedocs.org/projects/hybridlfpy/badge/?version=latest)](https://hybridLFPy.readthedocs.io/en/latest/?badge=latest) [![Upload Python Package](https://github.com/INM-6/hybridLFPy/workflows/Upload%20Python%20Package/badge.svg)](https://pypi.org/project/hybridLFPy) [![Python pytest](https://github.com/INM-6/hybridLFPy/workflows/Python%20pytest/badge.svg)](https://github.com/INM-6/hybridLFPy/actions/workflows/python-pytest.yml) [![License](http://img.shields.io/:license-GPLv3+-green.svg)](http://www.gnu.org/licenses/gpl-3.0.html)
## Development
The module hybridLFPy was mainly developed in the Computational Neuroscience Group (http://compneuro.umb.no), Department of Mathemathical Sciences and Technology (http://www.nmbu.no/imt), at the Norwegian University of Life Sciences (http://www.nmbu.no), Aas, Norway, in collaboration with Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6), Juelich Research Centre and JARA, Juelich, Germany (http://www.fz-juelich.de/inm/inm-6/EN/).
## Citation
Should you find hybridLFPy useful for your research, please cite the following paper: ` Espen Hagen, David Dahmen, Maria L. Stavrinou, Henrik Lindén, Tom Tetzlaff, Sacha J. van Albada, Sonja Grün, Markus Diesmann, Gaute T. Einevoll; Hybrid Scheme for Modeling Local Field Potentials from Point-Neuron Networks, Cerebral Cortex, Volume 26, Issue 12, 1 December 2016, Pages 4461–4496, https://doi.org/10.1093/cercor/bhw237 `
Bibtex source: ` @article{doi:10.1093/cercor/bhw237, author = {Hagen, Espen and Dahmen, David and Stavrinou, Maria L. and Lindén, Henrik and Tetzlaff, Tom and van Albada, Sacha J. and Grün, Sonja and Diesmann, Markus and Einevoll, Gaute T.}, title = {Hybrid Scheme for Modeling Local Field Potentials from Point-Neuron Networks}, journal = {Cerebral Cortex}, volume = {26}, number = {12}, pages = {4461-4496}, year = {2016}, doi = {10.1093/cercor/bhw237}, URL = { + http://dx.doi.org/10.1093/cercor/bhw237}, eprint = {/oup/backfile/content_public/journal/cercor/26/12/10.1093_cercor_bhw237/2/bhw237.pdf} } `
## License
This software is released under the General Public License (see the [LICENSE](https://github.com/INM-6/hybridLFPy/blob/master/LICENSE) file).
## Warranty
This software comes without any form of warranty.
## Installation
First download all the hybridLFPy source files using git (http://git-scm.com). Open a terminal window and type: ` cd $HOME/where/to/put/hybridLFPy git clone https://github.com/INM-6/hybridLFPy.git `
To use hybridLFPy from any working folder without copying files, run: ` (sudo) pip install -e . (--user) `
Installing it is also possible, but not recommended as things might change with future pulls from the repository: ` (sudo) pip install . (--user) `
### examples folder
Some example script(s) on how to use this module
### docs folder
Source files for autogenerated documentation using Sphinx (https://www.sphinx-doc.org).
To compile documentation source files in this directory using sphinx, use: ` sphinx-build -b html docs documentation `
### Dockerfile
The provided Dockerfile provides a Docker container recipe for x86_64 hosts with all dependencies required to run simulation files provided in examples. To build and run the container locally, get Docker from https://www.docker.com and issue the following (replace <image-name> with a name of your choosing):
$ docker build -t <image-name> -< Dockerfile $ docker run -it -p 5000:5000 <image-name>:latest
The –mount option can be used to mount a folder on the host to a target folder as:
$ docker run –mount type=bind,source=”$(pwd)”,target=/opt/hybridLFPy -it -p 5000:5000 <image-name>
Then, code examples may be run as:
$ cd /opt/hybridLFPy/examples $ nrnivmodl # compile local .mod (NMODL) files $ mpirun –allow-run-as-root python3 example_brunel.py
## Online documentation
The sphinx-generated html documentation can be accessed at https://hybridLFPy.readthedocs.io
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