{ "info": { "author": "", "author_email": "", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "License :: OSI Approved :: GNU General Public License (GPL)", "Operating System :: OS Independent", "Programming Language :: Cython", "Programming Language :: Python", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Topic :: Scientific/Engineering", "Topic :: Scientific/Engineering :: Physics", "Topic :: Utilities" ], "description": "LFPy\n====\n\nLFPy is a Python-module for calculation of extracellular potentials from multicompartment neuron models.\nIt relies on the NEURON simulator (http://www.neuron.yale.edu/neuron) and uses the\nPython interface (http://www.frontiersin.org/neuroinformatics/10.3389/neuro.11.001.2009/abstract) it provides.\n\nLFPy provides a set of easy-to-use Python classes for setting up your model, running your simulations and calculating the extracellular potentials arising from activity in your model neuron. If you have a model working in NEURON (www.neuron.yale.edu)\nalready, it is likely that it can be adapted to work with LFPy.\n\nThe extracellular potentials are calculated from transmembrane currents in multi-compartment neuron models using the line-source method (Holt & Koch, J Comp Neurosci 1999),\nbut a simpler point-source method is also available. The calculations assume that the neuron are surrounded by an infinite extracellular medium with homogeneous and frequency\nindependent conductivity, and compartments are assumed to be at least at a minimal distance from the electrode (which can be specified by the user). For more information on\nthe biophysics underlying the numerical framework used see this coming book chapter:\n\n- K.H. Pettersen, H. Linden, A.M. Dale and G.T. Einevoll: Extracellular spikes and current-source density, in *Handbook of Neural Activity Measurement*, edited by R. Brette and A. Destexhe, Cambridge, to appear (preprint PDF, 5.7MB http://arken.umb.no/~gautei/forskning/PettersenLindenDaleEinevoll-BookChapter-revised.pdf\n\nThe first release of LFPy (v1.x) was mainly designed for simulation extracellular potentials of single neurons, described in our paper on the package in Frontiers in Neuroinformatics entitled \"LFPy: A tool for biophysical simulation of extracellular potentials generated by detailed model neurons\".\nThe article can be found at http://dx.doi.org/10.3389%2Ffninf.2013.00041.\nSince version 2 (LFPy v2.x), the tool also facilitates simulations of extracellular potentials and current dipole moment from ongoing activity in recurrently connected networks of multicompartment neurons, prediction of EEG scalp surface potentials,\nMEG scalp surface magnetic fields, as described in the bioRXiv preprint \"Multimodal modeling of neural network activity: computing LFP, ECoG, EEG and MEG signals with LFPy2.0\" by Espen Hagen, Solveig Naess, Torbjoern V Ness, Gaute T Einevoll, found at https://doi.org/10.1101/281717.\n\nCiting LFPy:\n\n- LFPy v2.x: Hagen E, N\u00e6ss S, Ness TV and Einevoll GT (2018) Multimodal Modeling of Neural Network Activity: Computing LFP, ECoG, EEG, and MEG Signals With LFPy 2.0. Front. Neuroinform. 12:92. doi: 10.3389/fninf.2018.00092. https://dx.doi.org/10.3389/fninf.2018.00092\n- LFPy v1.x: Linden H, Hagen E, Leski S, Norheim ES, Pettersen KH and Einevoll GT (2013). LFPy: A tool for biophysical simulation of extracellular potentials generated by detailed model neurons. Front. Neuroinform. 7:41. doi: 10.3389/fninf.2013.00041. https://dx.doi.org/10.3389/fninf.2013.00041\n\nLFPy was developed in the Computational Neuroscience Group, Department of Mathemathical Sciences and Technology (http://www.nmbu.no/imt),\nat the Norwegian University of Life Sciences (http://www.nmbu.no),\nin collaboration with the Laboratory of Neuroinformatics (http://www.nencki.gov.pl/en/laboratory-of-neuroinformatics),\nNencki Institute of Experimental Biology (http://www.nencki.gov.pl), Warsaw, Poland. The effort was supported by\nInternational Neuroinformatics Coordinating Facility (http://incf.org), the Research Council of Norway (http://www.forskningsradet.no/english) (eScience, NevroNor) and EU-FP7 (BrainScaleS, http://www.brainscales.org).\n\nFor updated information on LFPy and online documentation, see the LFPy homepage (http://lfpy.readthedocs.io).\n\nThis scientific software is released under the GNU Public License GPLv3.\n\nCode status\n===========\n[![PyPI version](https://badge.fury.io/py/LFPy.svg)](https://badge.fury.io/py/LFPy)\n[![Build Status](https://travis-ci.org/LFPy/LFPy.svg?branch=master)](https://travis-ci.org/LFPy/LFPy)\n[![Coverage Status](https://coveralls.io/repos/github/LFPy/LFPy/badge.svg?branch=master)](https://coveralls.io/github/LFPy/LFPy?branch=master)\n[![Documentation Status](https://readthedocs.org/projects/lfpy/badge/?version=latest)](http://lfpy.readthedocs.io/en/latest/?badge=latest)\n[![DOI](https://zenodo.org/badge/78627256.svg)](https://zenodo.org/badge/latestdoi/78627256)\n\nConda-forge release info\n========================\n\n| Name | Downloads | Version | Platforms |\n| --- | --- | --- | --- |\n| [![Conda Recipe](https://img.shields.io/badge/recipe-lfpy-green.svg)](https://anaconda.org/conda-forge/lfpy) | [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/lfpy.svg)](https://anaconda.org/conda-forge/lfpy) | [![Conda Version](https://img.shields.io/conda/vn/conda-forge/lfpy.svg)](https://anaconda.org/conda-forge/lfpy) | [![Conda Platforms](https://img.shields.io/conda/pn/conda-forge/lfpy.svg)](https://anaconda.org/conda-forge/lfpy) |\n\nRequirements\n============\n\nTo install LFPy you will need the following:\n\n- Python modules numpy, scipy, matplotlib, h5py, mpi4py, Cython\n- NEURON (from http://www.neuron.yale.edu, v7.6.4 or newer) and corresponding Python module. The following should execute without error in a Python console:\n\n import neuron\n neuron.test()\n\n- Cython (C-extensions for python, http://cython.org) to speed up simulations of extracellular fields\n\n\nInstallation\n============\n\nThere are few options to install LFPy:\n\n1. From the Python Package Index with only local access using pip:\n\n pip install LFPy --user\n\n as sudoer (in general not recommended as system Python files may be overwritten):\n\n sudo pip install LFPy\n\n Upgrading LFPy from the Python package index (without attempts at upgrading dependencies):\n\n pip install --upgrade --no-deps LFPy --user\n\n LFPy release candidates can be installed as:\n\n pip install --pre --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple LFPy --user\n\n\n2. From the Python Package Index with only local access using easy_install:\n\n easy_install --user LFPy\n\n As sudoer:\n\n sudo easy_install LFPy\n\n3. From source:\n\n tar -xzf LFPy-x.x.tar.gz\n cd LFPy-x.x\n (sudo) python setup.py develop (--user)\n\n4. Development version from the GitHub repository:\n\n git clone https://github.com/LFPy/LFPy.git\n cd LFPy\n (sudo) pip install -r requirements.txt (--user) # install dependencies\n (sudo) python setup.py develop (--user)\n\n5. Anaconda Python (macos/linux):\n\n conda install lfpy neuron=*=mpi* # installs LFPy and Neuron in the current conda environment\n\n or\n\n conda create -n lfpy lfpy neuron=*=mpi* # creates new conda environment with LFPy and Neuron\n\nUninstall\n=========\n\nTo remove installed LFPy files it should suffice to issue (repeat until no more LFPy files are found):\n\n (sudo) pip uninstall LFPy\n\n\nDocumentation\n=============\n\nTo generate the html documentation using Sphinx, issue from the LFPy source code directory:\n\n sphinx-build -b html /doc \n\nThe main html file is in ``/index.html``. 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