begintemplate ngfcell
public init, connect_sections, size_sections, append_sections
public mechinit, insert_mechs, set_biophys, get_root
public pre_list, connect_pre, is_art, is_connected, gid, randi
public soma, dend
public all, basal_list, apical_list, soma_list, axon_list, dendrite_list
public x, y, z, position, myroot, Vrest
public NumSoma, NumApical, NumBasal, NumAxon
// strings
strdef myroot
// objects
objref syn, pre_list, templist, rootlist, this
// external variables
external numCellTypes, cellType
// create the sections[segments]
NumSoma=1
NumApical=16
NumBasal=0
NumAxon=0
create soma[NumSoma], dend[NumApical]
proc init() {
gid = $1
randi = $2
// morphology
connect_sections() // local fcn: connect soma, dendrites, axon initial segment
size_sections() // local fcn: set the size dimensions of each section
define_shape() // builtin fcn: fill in 3d info for sections defined by only L and diam, translate 3d points for consistency with their connections
append_sections() // local fcn: append all sections to the section list
set_nseg() // local fcn: set the number of segments in each section
get_root() // local fcn: perform morphology checks
// electrophysiology
mechinit() // local fcn: set values for max conductances and reversal potentials of ion channels and other ephys parameters that are subject to fitting
insert_mechs() // local fcn: insert ion channels and actually set values determined in the mechinit fcn
set_chanparams() // local fcn: after all channels have been inserted, then their other parameters can be set
// synapses
pre_list = new List() // define a list for the presynaptic connections
define_synapses($3) // local fcn: define all possible synaptic connections received by this cell
}
proc connect_sections() { local i
connect dend[0](0), soma(1)
for i=0,3 {
connect dend[i+1](0), dend[i](1)
}
connect dend[5](0), soma(1)
for i=5,8 {
connect dend[i+1](0), dend[i](1)
}
connect dend[10](0), soma(0)
for i=10,11 {
connect dend[i+1](0), dend[i](1)
}
connect dend[13](0), soma(0)
for i=13,14 {
connect dend[i+1](0), dend[i](1)
}
}
proc size_sections() {
soma[0] {pt3dclear()
pt3dadd(0, 0, 0, 10) // distance from (0,0,0) = 0
pt3dadd(0, 10, 0, 10) // distance from (0,0,0) = 10
pt3dadd(0, 20, 0, 10) // distance from (0,0,0) = 20
}
dend[0] {pt3dclear()
pt3dadd(0, 20, 0, 4) // distance from (0,0,0) = 20
pt3dadd(19.4709, 66.053, 0, 4) // distance from (0,0,0) = 68.8631
pt3dadd(38.9418, 112.106, 0, 4) // distance from (0,0,0) = 118.677
}
dend[1] {pt3dclear()
pt3dadd(38.9418, 112.106, 0, 3) // distance from (0,0,0) = 118.677
pt3dadd(58.4128, 158.159, 0, 3) // distance from (0,0,0) = 168.601
pt3dadd(77.8837, 204.212, 0, 3) // distance from (0,0,0) = 218.56
}
dend[2] {pt3dclear()
pt3dadd(77.8837, 204.212, 0, 2) // distance from (0,0,0) = 218.56
pt3dadd(116.826, 296.318, 0, 2) // distance from (0,0,0) = 318.516
pt3dadd(155.767, 388.424, 0, 2) // distance from (0,0,0) = 418.494
}
dend[3] {pt3dclear()
pt3dadd(155.767, 388.424, 0, 1.5) // distance from (0,0,0) = 418.494
pt3dadd(175.238, 434.477, 0, 1.5) // distance from (0,0,0) = 468.486
pt3dadd(194.709, 480.531, 0, 1.5) // distance from (0,0,0) = 518.48
}
dend[4] {pt3dclear()
pt3dadd(194.709, 480.531, 0, 1) // distance from (0,0,0) = 518.48
pt3dadd(214.18, 526.584, 0, 1) // distance from (0,0,0) = 568.475
pt3dadd(233.651, 572.637, 0, 1) // distance from (0,0,0) = 618.47
}
dend[5] {pt3dclear()
pt3dadd(0, 20, 0, 4) // distance from (0,0,0) = 20
pt3dadd(-19.4709, 66.053, 0, 4) // distance from (0,0,0) = 68.8631
pt3dadd(-38.9418, 112.106, 0, 4) // distance from (0,0,0) = 118.677
}
dend[6] {pt3dclear()
pt3dadd(-38.9418, 112.106, 0, 3) // distance from (0,0,0) = 118.677
pt3dadd(-58.4128, 158.159, 0, 3) // distance from (0,0,0) = 168.601
pt3dadd(-77.8837, 204.212, 0, 3) // distance from (0,0,0) = 218.56
}
dend[7] {pt3dclear()
pt3dadd(-77.8837, 204.212, 0, 2) // distance from (0,0,0) = 218.56
pt3dadd(-116.826, 296.318, 0, 2) // distance from (0,0,0) = 318.516
pt3dadd(-155.767, 388.424, 0, 2) // distance from (0,0,0) = 418.494
}
dend[8] {pt3dclear()
pt3dadd(-155.767, 388.424, 0, 1.5) // distance from (0,0,0) = 418.494
pt3dadd(-175.238, 434.477, 0, 1.5) // distance from (0,0,0) = 468.486
pt3dadd(-194.709, 480.531, 0, 1.5) // distance from (0,0,0) = 518.48
}
dend[9] {pt3dclear()
pt3dadd(-194.709, 480.531, 0, 1) // distance from (0,0,0) = 518.48
pt3dadd(-214.18, 526.584, 0, 1) // distance from (0,0,0) = 568.475
pt3dadd(-233.651, 572.637, 0, 1) // distance from (0,0,0) = 618.47
}
dend[10] {pt3dclear()
pt3dadd(0, 0, 0, 2) // distance from (0,0,0) = 0
pt3dadd(-19.4709, -46.0531, 0, 2) // distance from (0,0,0) = 50
pt3dadd(-38.9418, -92.1061, 0, 2) // distance from (0,0,0) = 100
}
dend[11] {pt3dclear()
pt3dadd(-38.9418, -92.1061, 0, 1.5) // distance from (0,0,0) = 100
pt3dadd(-58.4128, -138.159, 0, 1.5) // distance from (0,0,0) = 150
pt3dadd(-77.8837, -184.212, 0, 1.5) // distance from (0,0,0) = 200
}
dend[12] {pt3dclear()
pt3dadd(-77.8837, -184.212, 0, 1) // distance from (0,0,0) = 200
pt3dadd(-97.3546, -230.265, 0, 1) // distance from (0,0,0) = 250
pt3dadd(-116.826, -276.318, 0, 1) // distance from (0,0,0) = 300
}
dend[13] {pt3dclear()
pt3dadd(0, 0, 0, 2) // distance from (0,0,0) = 0
pt3dadd(19.4709, -46.053, 0, 2) // distance from (0,0,0) = 50
pt3dadd(38.9419, -92.1061, 0, 2) // distance from (0,0,0) = 100
}
dend[14] {pt3dclear()
pt3dadd(38.9419, -92.1061, 0, 1.5) // distance from (0,0,0) = 100
pt3dadd(58.4128, -138.159, 0, 1.5) // distance from (0,0,0) = 150
pt3dadd(77.8837, -184.212, 0, 1.5) // distance from (0,0,0) = 200
}
dend[15] {pt3dclear()
pt3dadd(77.8837, -184.212, 0, 1) // distance from (0,0,0) = 200
pt3dadd(97.3546, -230.265, 0, 1) // distance from (0,0,0) = 250
pt3dadd(116.826, -276.318, 0, 1) // distance from (0,0,0) = 300
}
}
objref all, basal_list, apical_list, dendrite_list, soma_list, axon_list
proc append_sections() { local i
objref all, basal_list, apical_list, dendrite_list, soma_list, axon_list
all = new SectionList()
basal_list = new SectionList()
apical_list = new SectionList()
soma_list = new SectionList()
axon_list = new SectionList()
dendrite_list = new SectionList()
soma all.append()
soma soma_list.append()
for i=0,15 {
dend[i] all.append()
dend[i] dendrite_list.append()
}
for i=0,9 {
dend[i] apical_list.append()
}
for i=10,15 {
dend[i] basal_list.append()
}
}
external lambda_f
proc set_nseg() {
forsec all { nseg = int((L/(0.1*lambda_f(100))+.9)/2)*2 + 1 }
}
proc mechinit() {
// resting membrane potential. Must lie between Na+ and K+ reversal potentials
Vrest=-65
// Temperature of simulation
celsius = 34.0
// Membrane resistance in ohm*cm2
RmDend = 5555 //1/0.00018
RmSoma = 5555 //1/0.00018
// Membrane capacitance in uF/cm2
CmSoma= 1.4
CmDend = 1.4
// Axial resistance in ohm*cm
RaDend= 100
RaSoma= 100
// Calcium concentrations in mM
ca_outside = 2
ca_inside = 5.e-6 // 50.e-6
catau = 10
// reversal potentials in mV
ekval = -90
enaval = 55
eHCNval = -30
ecaval = 8.314*(273.15+celsius)/(2*9.649e4)*log(ca_outside/ca_inside)*1000 // about 170, otherwise set to 130
if (Vrest<ekval) Vrest=ekval // Cell cannot rest lower than K+ reversal potential
if (Vrest>enaval) Vrest=enaval // Cell cannot rest higher than Na+ reversal potential
eleakval = Vrest
// max ion channel conductances in mho/cm2
gNav = 0.15 // soma: // 0.12 //original 0.030 to .055 ; lm: //0.5 //original 0.015
gKdr = 0.013 // Delayed rectifier potassium
gKvA = 0.00015 // Proximal A-type potassium
gHCN = 0.00002 // HCN (hyperpolarization-activated cyclic nucleotide-gated channel)
gCavN = 0.0008 // T-type calcium
gCavL = 0.005 // L-type calcium
gKvCaB = 0.0000002 // Big potassium channel: voltage and calcium gated
gKCaS = 0.000002 // Small potassium channel: calcium gated
gNasoma=3.7860265
gNadend=0.25918894
gKvA=5.2203905e-06
kdrf=0.15514516
kdrfdend = 0.0021817289
gleak=8.470825e-05
gCavL=0.056108352
gCavN=0.00058169587
gKvCaB=1.0235317e-06
gKCaS=4.5152237e-07
myRa = 14 //75
CM = 1.8 //1.8
offset1=20
offset2=20
offset3=13.5816
offset4=13.35371
slope1=0.68266
slope2=0.56966
slope3=1.18592
slope4=49.4896
offset5=9
offset6=9
slope5=.07
slope6=.264
}
proc insert_mechs() {
forsec all {
insert iconc_Ca
catau_iconc_Ca = 10
caiinf_iconc_Ca = 5.e-6
insert ch_KvAngf
gmax_ch_KvAngf = gKvA
insert ch_CavN // HAV-N- Ca channel
gmax_ch_CavN = gCavN
insert ch_CavL
gmax_ch_CavL=gCavL
insert ch_KCaS
gmax_ch_KCaS=gKCaS
insert ch_KvCaB
gmax_ch_KvCaB =gKvCaB
cm=CM
}
soma {
insert ch_Navngf
gmax_ch_Navngf=gNasoma //0.10*gna_scale
offset1_ch_Navngf=offset1
offset2_ch_Navngf=offset2
offset3_ch_Navngf=offset3
offset4_ch_Navngf=offset4
slope1_ch_Navngf=slope1
slope2_ch_Navngf=slope2
slope3_ch_Navngf=slope3
slope4_ch_Navngf=slope4
ena = 55
insert ch_Kdrfastngf
gmax_ch_Kdrfastngf=kdrf
offset5_ch_Kdrfastngf=offset5
offset6_ch_Kdrfastngf=offset6
slope6_ch_Kdrfastngf=slope6
slope5_ch_Kdrfastngf=slope5
// insert ch_Kdrslow
// gmax_ch_Kdrslow=kdrf
insert ch_leak
gmax_ch_leak = gleak
}
access soma
distance()
forsec dendrite_list {
for (x,0) {
if (distance(x)<100) {
insert ch_Navngf
gmax_ch_Navngf=gNadend //0.08*gna_scale
offset1_ch_Navngf=offset1
offset2_ch_Navngf=offset2
offset3_ch_Navngf=offset3
offset4_ch_Navngf=offset4
slope1_ch_Navngf=slope1
slope2_ch_Navngf=slope2
slope3_ch_Navngf=slope3
slope4_ch_Navngf=slope4
ena = 55
insert ch_Kdrfastngf
gmax_ch_Kdrfastngf=kdrfdend //.007
offset5_ch_Kdrfastngf=offset5
offset6_ch_Kdrfastngf=offset6
slope6_ch_Kdrfastngf=slope6
slope5_ch_Kdrfastngf=slope5
}
}
}
forsec dendrite_list {
insert ch_leak
gmax_ch_leak = gleak
}
}
proc set_chanparams() {
forsec all {Ra=myRa}
forsec all {ek=-90 eca=130
e_ch_leak =-60
cao_iconc_CaZ=2
//cao_ccanl=2
} // make catau slower70e-3 cao=2 cai=50.e-6
}
proc connect_pre() { // $o1 target point process, $o2 returned NetCon
soma $o2 = new NetCon (&v(1), $o1)
$o2.threshold = -15
}
func is_art() { return 0 }
proc position(){ local i
forall {
for i = 0, n3d()-1 {
pt3dchange(i, $1-x+x3d(i), $2-y+y3d(i), $3-z+z3d(i), diam3d(i))
}
}
x = $1 y = $2 z = $3
}
proc get_root() {local i localobj sref
rootlist = new SectionList()
rootlist.allroots()
i=0
forsec all {
sref = new SectionRef()
if (sref.has_parent==0) {
myroot = secname()
i=i+1
}
for(x,0) {
if (diam(x) <=0.01) print "WARNING: tiny diameter of ", diam(x), " um at ", secname(), ", point ", x, "!"
if (diam3d(x) <=0.01) print "WARNING: tiny 3d diameter of ", diam3d(x), " um at ", secname(), ", point ", x, "!"
}
if (L <=0.001) print "WARNING: tiny length of ", L, " um at ", secname(), "!"
}
if (i>1) {
print "WARNING: cell ", gid, " has ", i, " root sections!"
}
}
strdef myStr
objref newSecRef, syn
proc define_synapses() {
ind = $1
i = 0
access soma[0]
{distance()}
for celltype = 0, numCellTypes-1 {
templist = new List ()
for r=0, cellType[ind].SynList[celltype].count()-1 {
execute(cellType[ind].SynList[celltype].object(r).NewSynStr, this) // sets newSecRef
forsec newSecRef {
for (x,0) {
execute(cellType[ind].SynList[celltype].object(r).CondStr, this)
if (y==1) {
execute(cellType[ind].SynList[celltype].object(r).SynStr, this)
if (cellType[ind].SynList[celltype].object(r).GABAabFlag==0) {
syn.tau1 = cellType[ind].SynList[celltype].object(r).tau1
syn.tau2 = cellType[ind].SynList[celltype].object(r).tau2
syn.e = cellType[ind].SynList[celltype].object(r).efirst
if (strcmp(cellType[ind].SynList[celltype].object(r).SynType,"MyExp2Sidnw")==0) {
execute(cellType[ind].SynList[celltype].object(r).Scaling, this)
}
} else {
syn.tau1a = cellType[ind].SynList[celltype].object(r).tau1a
syn.tau2a = cellType[ind].SynList[celltype].object(r).tau2a
syn.ea = cellType[ind].SynList[celltype].object(r).ea
syn.tau1b = cellType[ind].SynList[celltype].object(r).tau1b
syn.tau2b = cellType[ind].SynList[celltype].object(r).tau2b
syn.eb = cellType[ind].SynList[celltype].object(r).eb
}
syn.sid = i
templist.append(syn)
i = i + 1
}
}
}
}
pre_list.append(templist)
findme = 1
}
}
endtemplate ngfcell
