Modeling single neuron LFPs and extracellular potentials with LFPsim (Parasuram et al. 2016)

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Accession:190140
LFPsim - Simulation scripts to compute Local Field Potentials (LFP) from cable compartmental models of neurons and networks implemented in the NEURON simulation environment.
References:
1 . Parasuram H, Nair B, D'Angelo E, Hines M, Naldi G, Diwakar S (2016) Computational Modeling of Single Neuron Extracellular Electric Potentials and Network Local Field Potentials using LFPsim. Front Comput Neurosci 10:65 [PubMed]
2 . Diwakar S, Medini C, Nair M, Parasuram H, Vijayan A, Nair B (2017) Computational Neuroscience of Timing, Plasticity and Function in Cerebellum Microcircuits (Chapter 12) Computational Neurology and Psychiatry, Springer Series in Bio-/Neuroinformatics, Érdi P:et al, ed. pp.343
Model Information (Click on a link to find other models with that property)
Model Type: Extracellular;
Brain Region(s)/Organism:
Cell Type(s): Cerebellum interneuron granule cell; Hippocampus CA1 pyramidal cell;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Extracellular Fields; Methods;
Implementer(s): Parasuram, Harilal [harilalp@am.amrita.edu]; Diwakar, Shyam [shyam at amrita.edu];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal cell; Cerebellum interneuron granule cell; 
20170201 In this version of LFPsim, the ion channel distribution
density and size of the individual compartments were considered in the
LFP calculation. This modification was supplied by S Diwakar in
response to user comments. It does not change the paper or the LFP
reconstructions.

This is the README for the model associated with the paper:

Parasuram H, Nair B, D'Angelo E, Hines M, Naldi G, Diwakar
S. Computational Modeling of Single Neuron Extracellular Electric
Potentials and Network Local Field Potentials using LFPsim,
Front. Comp. Neurosc., June 13, 2016, 10.3389/fncom.2016.00065
available at
http://journal.frontiersin.org/article/10.3389/fncom.2016.00065/abstract

LFPsim - Simulation scripts to compute Local Field Potentials (LFP)
from cable compartmental models of neurons and networks implemented in
NEURON simulation environment.

LFPsim works reliably on biophysically detailed multi-compartmental
neurons with ion channels in some or all compartments.

Last updated 12-March-2016
Developed by : Harilal Parasuram & Shyam Diwakar
Computational Neuroscience & Neurophysiology Lab, School of Biotechnology, Amrita University, India.
Email: harilalp@am.amrita.edu; shyam@amrita.edu
www.amrita.edu/compneuro 
*/

How to run LFPsim
=================

1. Copy all LFPsim files and the directory into your NEURON model
directory downloaded from ModelDB. Copy lfp.mod and mea.mod from
LFPsim to the mechanism directory of the NEURON model.

2. Compile the model; if you had already compiled the model without
LFPsim, include the LFPsim mod files and re-compile using "nrnivmodl"
or "mknrndll".

3. Load your neuron or network model in NEURON.

4. On the terminal type: xopen("extracellular_electrode.hoc") to
initiate LFPsim GUI interface.

5. Set the electrode properties in the GUI.

6. Run the simulation to reconstruct LFP.

A detailed step-by-step procedure is also listed in the
How-To-LFPsim.pdf document.

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