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

//Deleting already existing dummy compartment (electrode position) 
if (section_exists("dummy")){

	access dummy
	delete_section() 
}


// Inserting extracellular and MEA electrode to all compartments
forall if (!issection(".*dummy.*")){	// Inserting extracellular electrode to all compartments and setting extracellular medium parameters
	if (!issection(".*myelin.*")){
	if (!issection(".*node.*")){
	if (!issection(".*branch.*")){
	insert extracellular    
	insert mea
}
}
}
}

// Initializing variables and functions for MEA calculation
objref mul_elec_x,mul_elec_y,mul_elec_z

mul_elec_x = new Vector()
mul_elec_x = new Vector()
mul_elec_x = new Vector()


Num_of_colum = 4
Num_of_row = 4


objref mul_x,mul_y,mul_z
mul_x = new Vector()
mul_y = new Vector()
mul_z = new Vector()


// Procedure to calculate MEA electrode position, this function detects NEURON model and places MEA electrodes in the vicinity 
proc auto_calc_mea_positions(){


	forall{ 
		if (issection(".*soma.*")){ //allowing only soma 
			xx_low = ((x3d(0)+x3d(1))/2)
			yy_low = ((y3d(0)+y3d(1))/2)
			zz_low = ((z3d(0)+z3d(1))/2)

			xx_high = ((x3d(0)+x3d(1))/2)
			yy_high = ((y3d(0)+y3d(1))/2)
			zz_high = ((z3d(0)+z3d(1))/2)
			break
		}
	}		


	forall{ 
		if (issection(".*soma.*")){ //allowing only soma 
			//print secname()

		
			/*x = (x3d(0) + x3d(1)) / 2
			y = (y3d(0) + y3d(1)) / 2 
			z = (z3d(0) + z3d(1)) / 2*/ 

			if (((x3d(0)+x3d(1))/2) < xx_low) {
				xx_low = ((x3d(0)+x3d(1))/2)
				print "xx_low=",xx_low
			}

			if (((y3d(0)+y3d(1))/2) < yy_low) {
				yy_low = ((y3d(0)+y3d(1))/2)
			}

			if (((z3d(0)+z3d(1))/2) < zz_low) {
				zz_low = ((z3d(0)+z3d(1))/2)
			}



			if (((x3d(0)+x3d(1))/2) > xx_high) {
				xx_high = ((x3d(0)+x3d(1))/2)
			}

			if (((y3d(0)+y3d(1))/2) > yy_high) {
				yy_high = ((y3d(0)+y3d(1))/2)
			}

			if (((z3d(0)+z3d(1))/2) > zz_high) {
				zz_high = ((z3d(0)+z3d(1))/2)
			}


		}
	}
}

//calling auto detect function
auto_calc_mea_positions()

//Setting mea electrode position
mul_start_point_x = ((xx_low+xx_high)/2) -  (2 * mul_elec_distance) + (mul_elec_distance/2) 
mul_start_point_y = ((yy_low+yy_high)/2) -  (2 * mul_elec_distance) + (mul_elec_distance/2)
mul_start_point_z = (zz_low+zz_high)/2

print "plane=",plane

// Script for shifting MEA electrodes to other planes
for (j = mul_start_point_y;j< (Num_of_row * mul_elec_distance) + mul_start_point_y;j = j + mul_elec_distance){
	for (i = mul_start_point_x; i<(Num_of_colum * mul_elec_distance) + mul_start_point_x; i = i + mul_elec_distance){	


		if (plane == 1){	//electrodes in x plane
			multi_setelec(mul_start_point_z,j,i) // for marking electrode position
			mul_x.append(mul_start_point_z)
			mul_y.append(j)
			mul_z.append(i)
		
		}
		if (plane == 2){	//electrodes in y plane
			multi_setelec(i,mul_start_point_z,j) // for marking electrode position
			mul_x.append(i)
			mul_y.append(mul_start_point_z)
			mul_z.append(j)


		}
		if (plane == 3){	//electrodes in z plane

			multi_setelec(i,j,mul_start_point_z) // for marking electrode position
			mul_x.append(i)
			mul_y.append(j)
			mul_z.append(mul_start_point_z)
		}
	}

}


// Funtion for calculating MEA LFP traces
func template_mea(){
		/*
		long_dist_x,$1
		long_dist_y,$2
		long_dist_z,$3
		sum_dist_comp,$4
		dist_comp,$5
		dist_comp_x,$6
		dist_comp_y,$7
		dist_comp_z,$8
		*/

		sum_HH = ($1 * $6) + ($2 * $7) + ($3 * $8)
				
		final_sum_HH = sum_HH / $4

		sum_temp1 = ($1*$1) + ($2*$2) + ($3*$3)
		r_sq = sum_temp1 -(final_sum_HH * final_sum_HH)
			
		Length_vector = final_sum_HH + $4
							


		if ((final_sum_HH<0)&&(Length_vector<=0)){


			phi=log((sqrt((final_sum_HH*final_sum_HH) + r_sq) - final_sum_HH)/(sqrt((Length_vector*Length_vector)+r_sq)-Length_vector))


		}else if((final_sum_HH>0)&&(Length_vector>0)){

			
			phi=log((sqrt((Length_vector*Length_vector)+r_sq) + Length_vector)/(sqrt((final_sum_HH*final_sum_HH)+r_sq) + final_sum_HH))
			
		}else{

			phi=log(((sqrt((Length_vector*Length_vector)+r_sq)+Length_vector) * (sqrt((final_sum_HH*final_sum_HH)+r_sq)-final_sum_HH))/r_sq)
						
		}


		initial_part_l = (1)/(4*PI*$4*sigma) * phi
		return initial_part_l

}


objref initial_part_line
initial_part_line = new Vector()


// Setting MEA electrode position and pointing each electrode to respective pointer in mea.mod
proc set_electrode(){

forall {    

	    if (ismembrane("mea")) {	
		x = (x3d(0) + x3d(1)) / 2 
		y = (y3d(0) + y3d(1)) / 2 
		z = (z3d(0) + z3d(1)) / 2 

		//calculate length of the compartment
	
		
		dist_comp = sqrt( ((x3d(1) - x3d(0))*(x3d(1) - x3d(0))) + ((y3d(1) - y3d(0))*(y3d(1) - y3d(0))) + ((z3d(1) - z3d(0))*(z3d(1) - z3d(0))))
		dist_comp_x = (x3d(1) - x3d(0)) //* 1e-6
		dist_comp_y = (y3d(1) - y3d(0)) //* 1e-6
		dist_comp_z = (z3d(1) - z3d(0)) //* 1e-6

		sum_dist_comp = sqrt((dist_comp_x*dist_comp_x) + (dist_comp_y*dist_comp_y) + (dist_comp_z*dist_comp_z))


		if(sum_dist_comp<(diam/2)){ // setting radius limit
					sum_dist_comp = (diam/2) + 0.1

		}
		for ee=0,15{
				
			long_dist_x = (mul_x.x[ee] - x3d(1))
			long_dist_y = (mul_y.x[ee] - y3d(1))
			long_dist_z = (mul_z.x[ee] - z3d(1))
			val = template_mea(long_dist_x,long_dist_y,long_dist_z,sum_dist_comp,dist_comp,dist_comp_x,dist_comp_y,dist_comp_z)
			initial_part_line.append(val*area(0.5))

		}	
	

		for (x, 0) {
		
		
			setpointer transmembrane_current_m_mea(x), i_membrane(x)

			initial_part_line0_mea(x) = initial_part_line.x[0]
			initial_part_line1_mea(x) = initial_part_line.x[1]
			initial_part_line2_mea(x) = initial_part_line.x[2]
			initial_part_line3_mea(x) = initial_part_line.x[3]
			
			initial_part_line4_mea(x) = initial_part_line.x[4]
			initial_part_line5_mea(x) = initial_part_line.x[5]
			initial_part_line6_mea(x) = initial_part_line.x[6]
			initial_part_line7_mea(x) = initial_part_line.x[7]

			initial_part_line8_mea(x) = initial_part_line.x[8]
			initial_part_line9_mea(x) = initial_part_line.x[9]
			initial_part_line10_mea(x) = initial_part_line.x[10]
			initial_part_line11_mea(x) = initial_part_line.x[11]

			initial_part_line12_mea(x) = initial_part_line.x[12]
			initial_part_line13_mea(x) = initial_part_line.x[13]
			initial_part_line14_mea(x) = initial_part_line.x[14]
			initial_part_line15_mea(x) = initial_part_line.x[15]
	
							
		}

	    }
	}

}


set_electrode()
xopen("mea_field_sum.hoc")

//Initializing vectors
proc init() {
        finitialize(v_init)
        fcurrent()
	mea_line0 = mea_fieldrec_line0()
	mea_line1 = mea_fieldrec_line1()
	mea_line2 = mea_fieldrec_line2()
	mea_line3 = mea_fieldrec_line3()
	mea_line4 = mea_fieldrec_line4()
	mea_line5 = mea_fieldrec_line5()
	mea_line6 = mea_fieldrec_line6()
	mea_line7 = mea_fieldrec_line7()
	mea_line8 = mea_fieldrec_line8()
	mea_line9 = mea_fieldrec_line9()
	mea_line10 = mea_fieldrec_line10()
	mea_line11 = mea_fieldrec_line11()
	mea_line12 = mea_fieldrec_line12()
	mea_line13 = mea_fieldrec_line13()
	mea_line14 = mea_fieldrec_line14()
	mea_line15 = mea_fieldrec_line15()
}

proc advance() {
        fadvance()
	mea_line0 = mea_fieldrec_line0()
	mea_line1 = mea_fieldrec_line1()
	mea_line2 = mea_fieldrec_line2()
	mea_line3 = mea_fieldrec_line3()
	mea_line4 = mea_fieldrec_line4()
	mea_line5 = mea_fieldrec_line5()
	mea_line6 = mea_fieldrec_line6()
	mea_line7 = mea_fieldrec_line7()
	mea_line8 = mea_fieldrec_line8()
	mea_line9 = mea_fieldrec_line9()
	mea_line10 = mea_fieldrec_line10()
	mea_line11 = mea_fieldrec_line11()
	mea_line12 = mea_fieldrec_line12()
	mea_line13 = mea_fieldrec_line13()
	mea_line14 = mea_fieldrec_line14()
	mea_line15 = mea_fieldrec_line15()
}



//Recording summed MEA LFP traces using NEURON's record function
objref mea_rec[16]
proc run_multi(){

	set_electrode()
		
	for pp=0,15{
		mea_rec[pp] = new Vector()
	}
	mea_rec[0].record(&mea_line0)
	mea_rec[1].record(&mea_line1)
	mea_rec[2].record(&mea_line2)
	mea_rec[3].record(&mea_line3)
	mea_rec[4].record(&mea_line4)
	mea_rec[5].record(&mea_line5)
	mea_rec[6].record(&mea_line6)
	mea_rec[7].record(&mea_line7)
	mea_rec[8].record(&mea_line8)
	mea_rec[9].record(&mea_line9)
	mea_rec[10].record(&mea_line10)
	mea_rec[11].record(&mea_line11)
	mea_rec[12].record(&mea_line12)
	mea_rec[13].record(&mea_line13)
	mea_rec[14].record(&mea_line14)
	mea_rec[15].record(&mea_line15)

	run()
	
}




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