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LFPy documentation
==================

.. image:: logo_liten.png

What is LFPy?
=============

LFPy is a `Python <http://www.python.org>`_-module for calculating extracellular potentials from multicompartment neuron models.
It relies on the `NEURON simulator <http://www.neuron.yale.edu/neuron/>`_ and the 
`Python interface to NEURON <http://www.frontiersin.org/neuroinformatics/10.3389/neuro.11.001.2009/abstract>`_ it provides.


LFPy relies on calculating compartmental membrane currents using the `NEURON <www.neuron.yale.edu>`_-simulator under the hood, and
provides a set of easy-to-use Python-classes for setting up your model, and run your simulations and have simultaneous
model predicitions of the extracellular potentials arising from activity of your model neuron. If you have a model working in `NEURON <www.neuron.yale.edu>`_
already, it is likely that it can be adapted to work with LFPy.


The extracellular potentials are calculated using the following assumptions:
 * The extracellular potential is zero for every compartment when calculating membrane currents
 * The transmembrane current of each compartment are treates as either point- or line-sources in the extracellular space
 * Extracellular potential can not be calculated inside the model cell's volume, LFPy adjust the distance to each compartment to it's radius if the extracellular distance is less than this radius
 * Infinite and homogenous extracellular conductivity of the extracellular conductivity
 * Linear and frequency independent extracellular medium
 * Linear superposition of the extracellular potential contribution from all current-sources.


LFPy was developed in the `Computational Neuroscience Group <http://compneuro.umb.no>`_, `Department of Mathemathical Sciences and Technology <http://www.umb.no/imt>`_,
at the `Norwegian University of Life Sciences <http://www.umb.no>`_ ,
in collaboration with the `Laboratory of Neuroinformatics <http://www.nencki.gov.pl/en/laboratory-of-neuroinformatics>`_, 
`Nencki Institute of Experimental Biology <http://www.nencki.gov.pl>`_, Warsaw, Poland. The effort was supported by 
`International Neuroinformatics Coordinating Facility <http://incf.org>`_ (`INCF <http://incf.org>`_) and the e-science program of `The Research Council of Norway <http://www.forskningsradet.no/english/>`_.



Contents
========
.. toctree::
    :maxdepth: 3
   
    information
    tutorial
    using
    classes
    contributors
..    citations

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`

