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, √Črdi 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 GLU cell; Hippocampus CA1 pyramidal GLU 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 GLU cell; Cerebellum interneuron granule GLU cell;
/*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 
*/


// This scipt is a part of MEA electrode implementation, script for plotting mea traces
// calling functions for mea calculation
run_multi()

objref mv1,mv2
objref mh1,mh2,mh3,mh4

// script for interface partition
mv1=new VBox()
mv2=new VBox()
mh1=new HBox()
mh2=new HBox()
mh3=new HBox()
mh4=new HBox()

objref m_e_g[16]

proc make_plots(){
	for i=$1,$2{
	m_e_g[i] = new Graph()



	m_e_g[i].beginline()		
		for k=0,mea_rec[i].size()-1{			
			m_e_g[i].line((k*dt), mea_rec[i].x[k])	

		}
	m_e_g[i].flush()	
	//g.color(index)	
	m_e_g[i].exec_menu("View = plot")
	
	}
}


mv1.intercept(1)
	
	mv2.intercept(1)

		xpanel("Control Panel")
		xlabel("                                                  ===== Multiple electrode recording ===== ")
		xlabel("")
		//xbutton("Save Traces as MEA.dat","mea_file_write()")
		xpanel()

	mv2.intercept(0)
	mv2.map()

	mh1.intercept(1)		//row 1
		make_plots(12,15)
	mh1.intercept(0)
	mh1.map()

	mh2.intercept(1)		//row 2
		make_plots(8,11)
	mh2.intercept(0)
	mh2.map()

	mh3.intercept(1)		//row 3
		make_plots(4,7)
	mh3.intercept(0)
	mh3.map()

	mh4.intercept(1)		//row 3
		make_plots(0,3)
	mh4.intercept(0)
	mh4.map()



mv1.intercept(0)
mv1.map("LFP Simulation tool", 1, 1, 800, 800)



objref f
proc mea_file_write(){
	f = new File()

	f.wopen("LFP_traces/MEA.dat") 
		
	for k=0,mea_rec[0].size()-1{
			for i=0,15{
				f.printf("%e\t",mea_rec[i].x[k]) 
			}
			f.printf("\n")
	}
	f.close()	


	xpanel("Simulation complete!")
		xlabel("Traces are saved to LFP_traces directory. Run GNU Octave/Matlab script to save as .ps") 
	xpanel(500,300)

}

// Calling function for writing mea traces
mea_file_write()

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