cell-setup.hoc

/* ____________      CELL SET-UP PROCEEDURE      _____________ */


strdef sectype
objref CAN_temp, CAL_temp, CAT_temp, KAD_temp, KAP_temp, NA_temp


//RTH>> set distance ref
soma distance()

// Set passive membrane properties
Rm_trunk     = 36900 // Non-oblique dendritic specific membrane resistance.")
Rm_non_trunk = 36900 // Apical oblique specific membrane resistance.") 
Rm_basal     = 46000 // Basal specific membrane resistance.")
Rm_tip       = 36900 // Tip specific membrane resistance.")  
Rm_soma      = 20000 // Somatic specific membrane resistance.") 
Rm_axon      = 28000 // Axonal specific membrane resistance. ")   

Ra_basal     = 150 // Basal specific axial resistance.")
Ra_trunk     = 150 // Somatic specific axial resistance.")
Ra_non_trunk = 150 // Somatic specific axial resistance.")
Ra_soma      = 150 // Somatic specific axial resistance.")
Ra_tip       = 150 // Apical tip specific axial resistance.")
Ra_axon      = 50  // Axonal specific axial resistance. ")

Cm_default   = 1          // Default specific capacitance.")
Cm_axon      = Cm_default // Axonal specific capacitance. ")  
Cm_soma      = 1          // Somatic specific capacitance. ")     
Cm_soma      = 1.5        // Somatic specific capacitance. ")     
Cm_trunk     = 1.192      // Trunk specific capacitance.")         
Cm_trunk     = 1.5        // Trunk specific capacitance.")         
Cm_non_trunk = 1.192      // Oblique specific capacitance.")    
Cm_non_trunk = 1.5        // Oblique specific capacitance.")   
Cm_basal     = 1.144      // Basal specific capacitance.")       
Cm_tip       = 1.192      // Apical tip specific capacitance.")   

// SEVERELY affects experiment results
celsius      = 34 // Temperature of slice.")
        
//NDB >>>>  $o1.xopen_library("Terrence","cut-sections")
//          cut_sections(maximum_segment_length)
maximum_segment_length=75
forall {
    nseg=1+int(L/maximum_segment_length)
}
//<<<< NDB

//ORIG>>// make 3-d mapping of cell sections
//NDB >>>>    $o1.xopen_library("Terrence","map-segments-to-3d")
//           map_segments_to_3d()
forall {
	insert d3
	i=0
	x_d3(0)=x3d(0)
	y_d3(0)=y3d(0)
	z_d3(0)=z3d(0)

	for (x) if (x > 0 && x < 1) {
		while (arc3d(i)/L < x) { i += 1 }
		D=arc3d(i) - arc3d(i-1)
		if (D <= 0) {
			printf("\t\t * %s had a D < 0\n", secname())
		}
		alpha = (x*L - arc3d(i-1))/D
		x_d3(x)=x3d(i-1) + (x3d(i) - x3d(i-1))*alpha
		y_d3(x)=y3d(i-1) + (y3d(i) - y3d(i-1))*alpha
		z_d3(x)=z3d(i-1) + (z3d(i) - z3d(i-1))*alpha
	}

	x_d3(1)=x3d(n3d()-1)
	y_d3(1)=y3d(n3d()-1)
	z_d3(1)=z3d(n3d()-1)
}
//NDB <<<<

//ORIG>>// prepare to make a graph with cell configuration
//NDB >>>>    $o1.tmpo2=new Shape()
objref tmpo2
tmpo2=new Shape()
//NDB <<<<  


//ORIG>>// Set initial conductance values 
soma_caL =0.00006
soma_car =0.00003
gsomacar =0.00008
soma_caLH =0.0001 // 0.00017
soma_caT =0.0003
soma_km=0*0.001
potNa=50
mykca_init =0.9*1.5*0.03 //0.03 flag
soma_kca =0.7*4.5*0.0001//0.003 flag
soma_kap =7*0.0005
soma_hbar =1.8e-6
soma_kad =7*0.0005
gna=1.2*0.035 // 0.035
gkdr=2.2*0.015 //flag
gkd=0.005
gnadend=0.015
gkdrdend=2.2*0.015 //flag
gnanotrunk=0*0.01 // 0.035
gkdrnotrunk=2.2*0.015
AXKdr=1
AXNa=1
 
//v_init=-70

//ORIG>>// Start inserting mechanisms in cell
sectype ="soma"
forsec "soma" {
	insert na3
	insert kdr
		gbar_na3=gna
		gkdrbar_kdr=gkdr
	ena         = potNa
	insert nap  //flag
		gnabar_nap = 0*.5*0.000014 
		K_nap = 4.5
		vhalf_nap = -60.4
	insert pas    // leak conductance
		g_pas = 1/Rm_soma       
		e_pas = -70
	Ra    = Ra_soma
	cm= Cm_soma
	insert h     // h current 
		gbar_h  = soma_hbar
		K_h     = 8.8
		vhalf_h = -82
	insert kap  // proximal A current
		gkabar_kap = soma_kap
	ek         = -80
	insert km  // m-type potassium current
		gbar_km    = soma_km
	ek         = -80 
	insert cal // HVA Ca++-L type current
		gcalbar_cal = 0.1*soma_caL
	insert cat // LVA Ca++-T type current
		gcatbar_cat = soma_caT
        //insert somacar // HVAm Ca++-R type current
    	//gcabar_somacar = gsomacar
	insert car // HVAm Ca++-R type current
	gcabar_car = gsomacar
	insert kca   // K(Ca) mAHP potassium type current
		cac_kca=0.00075 //0.0005
		gbar_kca = 0.5*soma_kca
	insert mykca // K(Ca) fAHP potassium type current
		gkbar_mykca = 5.5*mykca_init        
	insert cad  // calcium pump/buffering mechanism 
		taur_cad=20
	//insert cabalan  // calcium pump/buffering mechanism 
	tmpo2.color(2)            
}

//ORIG>>  Configure Axon

sectype="axon"
forsec axon_sec_list {	  
	insert nax
		gbar_nax=gna*AXNa
	insert kdr
		gkdrbar_kdr=gkdr*AXKdr
	ena         = potNa
	insert pas  // leak conductance
		g_pas      = 1/Rm_axon  
		e_pas       = -70
		Ra          = Ra_axon
		cm          = Cm_axon
	insert km  // m-type potassium current
		gbar_km     = 3*soma_km
		ek          = -80
	insert kap  // proximal A current
	   gkabar_kap = soma_kap
	   ek         = -80
}
    
//ORIG>>  Configure apical trunk
 
forsec apical_trunk_list {

	//ORIG>>// apical_h_insert_sig($o1)    // Inserting h-current
	//NDF>>>	apical_caR_caLH_insert($o1) // Inserting Ca++ R-type and Ca++ L-type currents
	for (x) {  
		xdist = find_vector_distance_precise(secname(),x)
		xdist=distance(x)
		insert car
		gcabar_car(x) = 0.1*soma_car
		insert calH
		if (xdist > 50) {            
			gcalbar_calH(x) = 2*soma_caLH    //4.6*soma_caLH
		} else {
			gcalbar_calH(x) = 0.1*soma_caLH               //0.1*soma_caLH
		}
	}
	//<<<NDF
	//NDF>>> apical_caT_insert($o1)      // Inserting Ca++ T-type current
	caT_distal_maxfactor = 4   //ORIG>> maximum cond. factor in dendrites
	caT_distal_distance  = 350 //ORIG>> distance in dendrites for maximum cond.
	for (x) {  
		xdist = find_vector_distance_precise(secname(),x)
		xdist = distance(x)
		fr = xdist/caT_distal_distance
		insert cat  
		if (xdist < 100) {
			gcatbar_cat(x) = 0
		} else {
			gcatbar_cat(x) = caT_distal_maxfactor*soma_caT*fr
		} 
	}
	//<<<NDF
	//NDF>>> apical_kca_insert($o1)      // Inserting K(Ca) sAHP and mAHP potassium currents
	kca_distal_maxfactor = 1   //ORIG>> maximum cond. factor in dendrites
	//ORIG>>// kca_distal_maxfactor = 0 //maximum cond. factor in dendrites
    kca_distal_distance  = 200 //ORIG>> distance in dendrites for maximum cond.
	for (x) {  
		xdist = find_vector_distance_precise(secname(),x)
		xdist = distance(x)
		fr = xdist/kca_distal_distance 
		insert cad    // calsium pump/buffering mechanism
			taur_cad=20
		insert kca    // slow AHP K++ current
			cac_kca=0.00075 //0.0005
		insert mykca  // medium AHP K++ current

		if (xdist < kca_distal_distance && xdist > 50) {       
			gbar_kca(x) = 5*soma_kca
			gkbar_mykca = 2*mykca_init
		} else {
			gbar_kca(x) = 0.5*soma_kca
			gkbar_mykca = 0.5*mykca_init
		}
	}
	//<<<NDF
	//ORIG>>// A_insert($o1)               // Inserting A-current
	insert h
	insert kap
	insert kad 
	for (x){ 
		xdist = distance(x)
		if (xdist>500) {xdist=500}
		gbar_h(x) = soma_hbar*(1+3*xdist/100)
		if (xdist > 100){
			if (xdist>300) {ndist=300} else {ndist=xdist}
			vhalf_h(x)=-81-8*(ndist-100)/200
			gkabar_kad(x) = soma_kad*(1+xdist/100)
			gkabar_kap(x)=0
		} else {
			vhalf_h(x)=-81
			gkabar_kap(x) = soma_kap*(1+xdist/100)
			gkabar_kad(x)=0
		}
	}
	insert na3
		gbar_na3=gnadend
	insert nap //flag
		gnabar_nap = 0*.5*0.000014 
		K_nap = 4.5
		vhalf_nap = -60.4
	insert kdr
		gkdrbar_kdr=gkdr
	ena         = potNa
	insert km  // m-type potassium current
		gbar_km    = soma_km
	ek         = -80 
	insert pas // leak conductance
		g_pas     =  1/Rm_trunk  
		g_pas     =  1/Rm_soma //flag  
		e_pas          = -70
	Ra             = Ra_trunk
	cm             = Cm_trunk
	//ORIG>>>// Rm_sigmoid($o1)   // configure Rm along apical trunk
	//ORIG>>>//  Ra_sigmoid($o1)   // configure Ra along apical trunk
	tmpo2.color(4)
}
 

// Configure the apical-non-trunk section: insert basic mechanisms  
 
sectype = "apical non-trunk"
forsec apical_non_trunk_list {
	//ORIG>>//         apical_h_insert_sig($o1)    // Inserting h-current
	//NDF>>>	apical_caR_caLH_insert($o1) // Inserting Ca++ R-type and Ca++ L-type currents
	for (x) {  
		xdist = find_vector_distance_precise(secname(),x)
		xdist=distance(x)
		insert car
		gcabar_car(x) = 0.1*soma_car

		insert calH
		if (xdist > 50) {            
			gcalbar_calH(x) = 2*soma_caLH    //4.6*soma_caLH
		} else {
			gcalbar_calH(x) = 0.1*soma_caLH               //0.1*soma_caLH
		}
	}
	//<<<NDF
	//NDF>>> apical_caT_insert($o1)      // Inserting Ca++ T-type current
	caT_distal_maxfactor = 4  // ORIG>> maximum cond. factor in dendrites")
	caT_distal_distance  = 350 // ORIG>> distance in dendrites for maximum cond.")
	for (x) {  
		xdist = find_vector_distance_precise(secname(),x)
		xdist=distance(x)
		fr = xdist/caT_distal_distance
		insert cat  
		if (xdist < 100) {
			gcatbar_cat(x) = 0
		} else {
			gcatbar_cat(x) = caT_distal_maxfactor*soma_caT*fr
		} 
    }
	//<<<NDF
	//NDF>>> apical_kca_insert($o1)      // Inserting K(Ca) sAHP and mAHP potassium currents
	kca_distal_maxfactor = 1 // ORIG>> maximum cond. factor in dendrites")
	// ORIG>>//kca_distal_maxfactor = 0 // maximum cond. factor in dendrites
	kca_distal_distance = 200 // ORIG>> distance in dendrites for maximum cond.")
  
	for (x) {  
		xdist = find_vector_distance_precise(secname(),x)
		xdist=distance(x)
		fr = xdist/kca_distal_distance 
		insert cad    // calsium pump/buffering mechanism
		taur_cad=20
		insert kca    // slow AHP K++ current
		cac_kca=0.00075 //0.0005
		insert mykca  // medium AHP K++ current

		if (xdist < kca_distal_distance && xdist > 50) {       
			gbar_kca(x) = 5*soma_kca
			gkbar_mykca = 2*mykca_init
		} else {
			gbar_kca(x) = 0.5*soma_kca
			gkbar_mykca = 0.5*mykca_init
		}
	}
	//<<<NDF
	//ORIG>>//        A_insert($o1)               // Inserting A-current
			 
	insert h
	insert kap
	insert kad 

	for (x){
		xdist = distance(x)
		if (xdist>500) {xdist=500}
		gbar_h(x) = soma_hbar*(1+3*xdist/100)
		if (xdist > 100){
			if (xdist>300) {ndist=300} else {ndist=xdist}
			vhalf_h(x)=-81-8*(ndist-100)/200
			gkabar_kad(x) = soma_kad*(1+xdist/100)
			gkabar_kap(x) = 0
		} else {
			vhalf_h(x)=-81
			gkabar_kap(x) = soma_kap*(1+xdist/100)
			gkabar_kad(x) = 0
		}
	}
	insert na3
		gbar_na3    = gnadend
	insert nap //flag
		gnabar_nap = 0*.5*0.000014 
		K_nap = 4.5
		vhalf_nap = -60.4
	insert kdr
		gkdrbar_kdr = gkdr
	ena         = potNa
	insert km  // m-type potassium current
		gbar_km    = soma_km
	ek         = -80 

	insert pas // passive properties
		g_pas     =  1/Rm_non_trunk 
		e_pas     = -70                     
	Ra        = Ra_non_trunk
	cm        = Cm_non_trunk
	//ORIG>>//Rm_sigmoid($o1)   // configure Rm along apical trunk
	//ORIG>>//Ra_sigmoid($o1)   // configure Ra along apical trunk
	tmpo2.color(3)
}

//ORIG>>//khoblique_peri_decay($o1)  // Configure the apical oblique dendrites

// Configure the basal dendrites

sectype = "basal tree"
forsec basal_tree_list {
	insert na3dend
	insert nap
		gnabar_nap = 0*.5*0.000014 //flag 
		K_nap = 4.5
		vhalf_nap = -60.4
	insert kap 
		gkabar_kap = 0.0025036
	insert h                
		gbar_h = soma_hbar
	//ORIG>>//ek = -80 
	insert kdr
		gbar_na3dend=gnadend
		gkdrbar_kdr=gkdrdend
	ena         = potNa

	insert pas // passive properties
		g_pas          = 6.458e-05 // 1/Rm_basal  
		e_pas          = -70
	Ra             = Ra_basal
	cm             = Cm_basal
	//ORIG>>//  Ra_sigmoid($o1) // configure Ra
	tmpo2.color(5)
}

//ORIG>>//khbasal_fixed($o1) // Configure basal dendrites         
   
forsec "soma" { g_pas= 1/Rm_soma} // force Rm at all soma sections

//ORIG>>// forall if (ismembrane("kdr") ) {  
//ORIG>>//           ek         = -77      //-77 
//ORIG>>//      }
forall if(ismembrane("ca_ion")) {
	eca =140
	ion_style("ca_ion",0,1,0,0,0)
	vshift_ca = 0
}
  



//ORIG>>// Print a postcript file in the generic directory with the cell configuration
//NTB>>> sprint(tmp_str2, "%s/configure_sections.eps", $o1.generic_dir)
//      $o1.tmpo2.printfile($o1.tmp_str2)
tmpo2.printfile("experiment/configure_sections.eps")
//<<<NTB

//NTB>>> econ.xopen_library("Terrence","current-balance") 
//ORIG>>//current_balance(v_init)
//<<<NTB

//ORIG>>//Carmen's change previous origin was at 0 end of apical dendrite[65]
soma distance()