Parameter estimation for Hodgkin-Huxley based models of cortical neurons (Lepora et al. 2011)

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Simulation and fitting of two-compartment (active soma, passive dendrite) for different classes of cortical neurons. The fitting technique indirectly matches neuronal currents derived from somatic membrane potential data rather than fitting the voltage traces directly. The method uses an analytic solution for the somatic ion channel maximal conductances given approximate models of the channel kinetics, membrane dynamics and dendrite. This approach is tested on model-derived data for various cortical neurons.
1 . Lepora NF, Overton PG, Gurney K (2012) Efficient fitting of conductance-based model neurons from somatic current clamp. J Comput Neurosci 32:1-24 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism:
Cell Type(s): Neocortex L5/6 pyramidal GLU cell; Neocortex L2/3 pyramidal GLU cell; Neocortex fast spiking (FS) interneuron; Neocortex spiking regular (RS) neuron; Neocortex spiking low threshold (LTS) neuron;
Channel(s): I Na,t; I L high threshold; I T low threshold; I K; I M;
Gap Junctions:
Simulation Environment: GENESIS; MATLAB;
Model Concept(s): Parameter Fitting; Simplified Models; Parameter sensitivity;
Implementer(s): Lepora, Nathan [n.lepora at];
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; Neocortex L2/3 pyramidal GLU cell; I Na,t; I L high threshold; I T low threshold; I K; I M;
// genesis - sample currents from dendrite

// Output format
addglobal str out_form "%0.15g"
setclock 2 100 // prevents carriage returns from sim_chan

// set voltages: creates tables V_1...V_n (n=nV) of voltages
function set_voltage(files)
if ({strcmp {files} "none"})
	int j, nV={getarg {arglist {files}} -count}
	for (j=1; j<={nV}; j=j+1)
		create table "time"
		call "time" TABCREATE 1 0 1 // default to be overwritten
		str file = {getarg {arglist {files}} -arg {j}}		
		file2tab {file} "time" table -table2 "dummy"
		float tdivs = {getfield time table->xdivs}
		create table "V_"{j}
		call "V_"{j} TABCREATE 1 0 1 // default to be overwritten
		setfield "V_"{j} step_mode 2 stepsize 0
		file2tab {file} "V_"{j} table -xy {tdivs} 
		echo "set V_"{j}" for" {file}
	echo "voltage not specified in file"

// output results: output_sim <dir> <file> <object> <var1> <var2> ...
function output_sim(dir,file,object,var)	
	str dir, file, object, var
	if (!{exists {file}})  	// create & open asc_file if doesn't exist
		create asc_file {file}
		setfield {file} filename {dir}/{file} leave_open 1 append 1 float_format {out_form}
		call {file} OUT_OPEN	// (careful - think acts as toggle)
    useclock {file} 1
	int i, nv=({argc}-3)
	for (i=1; i<={nv}; i=i+1)	// write header describing vars
		str var = {argv {3+i}}		
		call {file} OUT_WRITE "%" {object} {var}
	for (i=1; i<={nv}; i=i+1)	// iterate through variables	
		str var = {argv {3+i}}	// ... and add message to asc_file
		addmsg {object} {file} SAVE {var}

// Main Script

// set voltage
set_voltage {files_voltage}

// some vars
float pi = 3.14, SA = pi*len*dia, SA1 = pi*len1*dia1, XA = pi*dia*dia/4, XA1 = pi*dia1*dia1/4

// Make the cell
create neutral /cell
create compartment /cell/soma 
create compartment /cell/dend 
setfield /cell/soma dia {dia}  len {len}  Em {Em0} Cm {CM0*SA}  Rm {RM0/SA}  Ra {RA0*len/XA}
setfield /cell/dend dia {dia1} len {len1} Em {Em0} Cm {CM0*SA1} Rm {RM0/SA1} Ra {RA0*len1/XA1}

// Simulation variables
float V0 = {getfield V_1 table->table[0]} 
float tmax = {getfield V_1 table->xmax} 
float dt = {getfield V_1 table->dx} 
setclock 1 {dt}

// Initial voltage input
create table V_0
call V_0 TABCREATE 1 1 1 
setfield V_0 step_mode 1 table->table[0] {V0} table->table[1] {V0}

// Initialise sim 
setclock 0 {100*dt}
addmsg V_0 /cell/dend AXIAL output
step 100 -t 
deletemsg /cell/dend 0 -incoming -find V_0 AXIAL

// Save initial state
save /cell/## {dir_out}/ 

// Output voltages from each compartment
output_sim {dir_out} data_Vd.dat /cell/dend Vm

// Run sim
int i
for (i=1; i<={countelementlist /V_#}-1; i=i+1)
	restore {dir_out}/
	addmsg "V_"{i} /cell/dend AXIAL output
	setclock 0 {dt}
	step {tmax} -t
	deletemsg /cell/dend 0 -incoming -find "V_"{i} AXIAL


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