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 
*/


//Set default electrode position
elec_x = -100
elec_y = 50
elec_z = 0
place_mea_electrode = 0


objref MoveElec  
MoveElec = new Shape(0)  // Created morphology view plot, didn't map it to the screen


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 lfp
	
	local_xc_0 = xc[0] // extracellular capacitance
	local_xc_1 = xc[1] 

	local_xg_0 = xg[0] // extracellular conductance
	local_xg_1 = xg[1]

	local_xraxial_0 = xraxial[0] // extracellular axial resistance
	local_xraxial_1 = xraxial[1]
    	}
	}
	}
}

// Procedure to update extracellular medium parameters from UI
proc change_local_xc_0(){

	forall{
		xc[0]=$1	
	}	
}


proc change_local_xc_1(){

	forall{
		xc[1]=$1	
	}	
}


proc change_local_xg_0(){

	forall{
		xg[0]=$1	
	}	
}



proc change_local_xg_1(){

	forall{
		xg[1]=$1	
	}	
}


proc change_local_xraxial_0(){

	forall{
		xraxial[0]=$1	
	}	
}

proc change_local_xraxial_1(){

	forall{
		xraxial[1]=$1	
	}	
}


// Procedure for computing LFP via three schema, Point Source Approximation(PSA), Line Source Approximation (LSA), RC filter methods. 


proc re_insert_elec(){

	forall {    

	    if (ismembrane("lfp")) {	
		x = (x3d(0) + x3d(1)) / 2 
		y = (y3d(0) + y3d(1)) / 2 
		z = (z3d(0) + z3d(1)) / 2 
	
		sigma = 0.3

		if(elec_x==elec_y==elec_z==0){
			elec_z=1
		}

		dis = sqrt( ((elec_x - x)*(elec_x - x)) + ((elec_y - y)*(elec_y - y)) + ((elec_z - z)*(elec_z - z)))

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

		}
		point_part1 = (1 / (4 * 3.141 * dis * sigma)) * area(0.5)


		//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))

		//print "sum_dist_comp=",sum_dist_comp, secname(), area(0.5)

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

		}

		long_dist_x = (elec_x- x3d(1))
		long_dist_y = (elec_y- y3d(1))
		long_dist_z = (elec_z- z3d(1))

		sum_HH = (long_dist_x * dist_comp_x) + (long_dist_y * dist_comp_y) + (long_dist_z * dist_comp_z)
				
		final_sum_HH = sum_HH / sum_dist_comp

		sum_temp1 = (long_dist_x * long_dist_x) + (long_dist_y * long_dist_y) + (long_dist_z * long_dist_z)
		r_sq = sum_temp1 -(final_sum_HH * final_sum_HH)
			
		Length_vector = final_sum_HH + sum_dist_comp
							


		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)
						
		}


		line_part1 = 1/(4*PI*sum_dist_comp*sigma) * phi * area(0.5)


		// RC algorithm implementation
		capa = 1 // set to specific capacitance, Johnston and Wu 1995
		RC = sigma * capa
	
		time_const = dis / 240 // velo um/ms  // Nauhaus et al, 2009 calculated the propagation speed on average, 0.24 ± 0.20 m/s in monkeys and 0.31 ± 0.23 m/s in cats (mean ± s.d.) ie, 240 um/ms
		rc_part1 =  exp(-1 *(time_const/RC)) * area(0.5)

		for (x, 0) {


		
			setpointer transmembrane_current_lfp(x), i_membrane(x)
			
			initial_part_point_lfp(x) = point_part1
			
			initial_part_line_lfp(x) = line_part1

			initial_part_rc_lfp(x) = rc_part1
						
				
		}



	    }
	}

}


vrec = 0 
// function to sum field potential calculated for PSA schema
func fieldrec_point() { local sum
	sum = 0
	forall {
	  if (ismembrane("lfp")) {
		for (x,0) sum += lfp_point_lfp(x)
	  }
	}
	return sum
}

// function to sum field potential calculated for LSA schema
func fieldrec_line() { local sum
	sum = 0
	forall {
	  if (ismembrane("lfp")) {
		for (x,0) sum += lfp_line_lfp(x)
	  }
	}
	return sum
}


// function to sum field potential calculated for RC filter schema
func fieldrec_RC() { local sum
	sum = 0
	forall {
	  if (ismembrane("lfp")) {
		for (x,0) sum += lfp_rc_lfp(x)
	  }
	}
	return sum
}


proc init() { // Initializing all variables
        finitialize(v_init)
        fcurrent()
	Point_source = fieldrec_point()
	Line_source = fieldrec_line()
	Simple_RC_filter = fieldrec_RC()
}

proc advance() {
        fadvance()
	Point_source = fieldrec_point()
	Line_source = fieldrec_line()
	Simple_RC_filter = fieldrec_RC()
}

//Recording summed LFP using NEURON's record function
objref total_lfp
total_lfp = new Vector()
total_lfp.record(&Line_source)


objref total_point
total_point = new Vector()
total_point.record(&Point_source)

objref total_RC
total_RC = new Vector()
total_RC.record(&Simple_RC_filter)


xopen("move_electrode.hoc")

// Initializing tool interface 
xopen("tool_interface.hoc")

// Funtion to display electrode position
func change_electrode_pos() {
	
	if($1 == 2) {
		
		setelec($2, $3, 0)	
		//drawelec($2, $3, 0)
		print "x, y = ",$2,$3	
	}				
	
	return (0)
	
}	


/*Single electrode location may be set both manually and interactively. To set manually, the user needs to provide values for x,y,z of electrode location in panel D. Interactive LFP electrode implemented using NEURON's menu tool. To access this funtionality, the user needs to move the mouse pointer on "Morphology view" window and right click on the plot, then select "LFP_electrode" and move mouse pointer to move electrode and click on the point on the plot area to record the extracellular potential from that point.
*/

MoveElec.menu_tool("LFP_electrode", "change_electrode_pos","1")



// Write the calculated LFP as files in "LFP_traces" directory
objref f
proc file_write(){
	f = new File()

	f.wopen("LFP_traces/Line_source.dat") 
		for i=0, total_lfp.size()-1 { 

			f.printf("%e",total_lfp.x[i]) 
			f.printf("\n")
		}
	f.close()	



	f.wopen("LFP_traces/Point_source.dat") 
		for i=0, total_point.size()-1 { 

			f.printf("%e",total_point.x[i]) 
			f.printf("\n")
		}
	f.close()


	f.wopen("LFP_traces/RC.dat") 
		for i=0, total_RC.size()-1 { 

			f.printf("%e",total_RC.x[i]) 
			f.printf("\n")
		}
	f.close()
	xpanel("Simulation complete!", 0)
	xlabel("Traces are saved to LFP_traces directory. Run GNU Octave/Matlab scripts to save as .ps for later use.")
	xpanel(494,468)
}


// Funtion to set electrode location for Multi Electrode Array simualtion (MEA)
proc run_multi_button(){

	if (place_mea_electrode == 1){
		mea_run_control()
		
	}else{
		xpanel("")
		xlabel("Please set electrode location by clicking on \"Set Multiple Electrodes\". Run MEA simulation!")
		xpanel(494,468)

	}
}


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