//**************************************************************************
// Begin cell template for MSP_Cell
// load cell template - builds the cell topology, including inserting
// channels and synapses
begintemplate MSP_Cell
public is_art
public init, topol, basic_shape, subsets, geom, memb
public synlist, x, y, z, position, connect2target
public soma, dend1, dend2, dend3, dend4, dend1_1, dend1_2
public dend2_1, dend2_2, dend4_1, dend4_2, dend3_2, dend3_1
public all, Prox_Dend, Mid_Dend, Dist_Dend
public leaf
public gaba, ampa, nmda
create soma, dend1, dend2, dend3, dend4, dend1_1[3], dend1_2[3]
create dend2_1[3], dend2_2[3], dend4_1[3], dend4_2[3], dend3_2[3], dend3_1[3]
objref synlist, leaf, gaba[300], ampa[300], nmda[300]
proc init() {
topol()
subsets()
geom()
biophys()
forall {Ra = $1 CM = $2}
geom_nseg()
compts = 0
forall {print secname(), " ", nseg compts = compts + nseg}
print compts, " compartments"
synlist = new List()
leaf = new List()
synloops()
x = y = z = 0 // only change via position
}
proc topol() { local i
connect dend1(0), soma(1)
connect dend2(0), soma(1)
connect dend3(0), soma(0)
connect dend4(0), soma(0)
connect dend1_1(0), dend1(1)
for i = 1, 2 connect dend1_1[i](0), dend1_1(1)
connect dend1_2(0), dend1(1)
for i = 1, 2 connect dend1_2[i](0), dend1_2(1)
connect dend2_1(0), dend2(1)
for i = 1, 2 connect dend2_1[i](0), dend2_1(1)
connect dend2_2(0), dend2(1)
for i = 1, 2 connect dend2_2[i](0), dend2_2(1)
connect dend4_1(0), dend4(1)
for i = 1, 2 connect dend4_1[i](0), dend4_1(1)
connect dend4_2(0), dend4(1)
for i = 1, 2 connect dend4_2[i](0), dend4_2(1)
connect dend3_2(0), dend3(1)
for i = 1, 2 connect dend3_2[i](0), dend3_2(1)
connect dend3_1(0), dend3(1)
for i = 1, 2 connect dend3_1[i](0), dend3_1(1)
basic_shape()
}
proc basic_shape() {
soma {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(15, 0, 0, 1)}
dend1 {pt3dclear() pt3dadd(15, 0, 0, 1) pt3dadd(45, -29, 0, 1)}
dend2 {pt3dclear() pt3dadd(15, 0, 0, 1) pt3dadd(45, 30, 0, 1)}
dend3 {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(-29, -29, 0, 1)}
dend4 {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(-29, 30, 0, 1)}
dend1_1 {pt3dclear() pt3dadd(45, -29, 0, 1) pt3dadd(45, -59, 0, 1)}
dend1_2 {pt3dclear() pt3dadd(45, -29, 0, 1) pt3dadd(90, -29, 0, 1)}
dend2_1 {pt3dclear() pt3dadd(45, 30, 0, 1) pt3dadd(90, 30, 0, 1)}
dend2_2 {pt3dclear() pt3dadd(45, 30, 0, 1) pt3dadd(60, 75, 0, 1)}
dend4_1 {pt3dclear() pt3dadd(-29, 30, 0, 1) pt3dadd(-44, 75, 0, 1)}
dend4_2 {pt3dclear() pt3dadd(-29, 30, 0, 1) pt3dadd(-74, 30, 0, 1)}
dend3_2 {pt3dclear() pt3dadd(-29, -29, 0, 1) pt3dadd(-74, -29, 0, 1)}
dend3_1 {pt3dclear() pt3dadd(-29, -29, 0, 1) pt3dadd(-44, -59, 0, 1)}
dend1_1[1] {pt3dclear() pt3dadd(45, -59, 0, 1) pt3dadd(30, -89, 0, 1)}
dend1_1[2] {pt3dclear() pt3dadd(45, -59, 0, 1) pt3dadd(75, -74, 0, 1)}
dend1_2[1] {pt3dclear() pt3dadd(90, -29, 0, 1) pt3dadd(120, -14, 0, 1)}
dend1_2[2] {pt3dclear() pt3dadd(90, -29, 0, 1) pt3dadd(120, -59, 0, 1)}
dend2_1[1] {pt3dclear() pt3dadd(90, 30, 0, 1) pt3dadd(120, 15, 0, 1)}
dend2_1[2] {pt3dclear() pt3dadd(90, 30, 0, 1) pt3dadd(105, 60, 0, 1)}
dend2_2[1] {pt3dclear() pt3dadd(60, 75, 0, 1) pt3dadd(90, 90, 0, 1)}
dend2_2[2] {pt3dclear() pt3dadd(60, 75, 0, 1) pt3dadd(45, 105, 0, 1)}
dend4_1[1] {pt3dclear() pt3dadd(-44, 75, 0, 1) pt3dadd(-14, 105, 0, 1)}
dend4_1[2] {pt3dclear() pt3dadd(-44, 75, 0, 1) pt3dadd(-74, 90, 0, 1)}
dend4_2[1] {pt3dclear() pt3dadd(-74, 30, 0, 1) pt3dadd(-89, 60, 0, 1)}
dend4_2[2] {pt3dclear() pt3dadd(-74, 30, 0, 1) pt3dadd(-104, 15, 0, 1)}
dend3_2[1] {pt3dclear() pt3dadd(-74, -29, 0, 1) pt3dadd(-104, -14, 0, 1)}
dend3_2[2] {pt3dclear() pt3dadd(-74, -29, 0, 1) pt3dadd(-104, -59, 0, 1)}
dend3_1[1] {pt3dclear() pt3dadd(-44, -59, 0, 1) pt3dadd(-29, -89, 0, 1)}
dend3_1[2] {pt3dclear() pt3dadd(-44, -59, 0, 1) pt3dadd(-89, -74, 0, 1)}
}
objref all, Prox_Dend, Mid_Dend, Dist_Dend
proc subsets() { local i
objref all, Prox_Dend, Mid_Dend, Dist_Dend
all = new SectionList()
soma all.append()
dend1 all.append()
dend2 all.append()
dend3 all.append()
dend4 all.append()
for i=0, 2 dend1_1[i] all.append()
for i=0, 2 dend1_2[i] all.append()
for i=0, 2 dend2_1[i] all.append()
for i=0, 2 dend2_2[i] all.append()
for i=0, 2 dend4_1[i] all.append()
for i=0, 2 dend4_2[i] all.append()
for i=0, 2 dend3_2[i] all.append()
for i=0, 2 dend3_1[i] all.append()
Prox_Dend = new SectionList()
dend1 Prox_Dend.append()
dend2 Prox_Dend.append()
dend3 Prox_Dend.append()
dend4 Prox_Dend.append()
Mid_Dend = new SectionList()
dend1_1 Mid_Dend.append()
dend1_2 Mid_Dend.append()
dend2_1 Mid_Dend.append()
dend2_2 Mid_Dend.append()
dend4_1 Mid_Dend.append()
dend4_2 Mid_Dend.append()
dend3_2 Mid_Dend.append()
dend3_1 Mid_Dend.append()
Dist_Dend = new SectionList()
for i=1, 2 dend1_1[i] Dist_Dend.append()
for i=1, 2 dend1_2[i] Dist_Dend.append()
for i=1, 2 dend2_1[i] Dist_Dend.append()
for i=1, 2 dend2_2[i] Dist_Dend.append()
for i=1, 2 dend4_1[i] Dist_Dend.append()
for i=1, 2 dend4_2[i] Dist_Dend.append()
for i=1, 2 dend3_2[i] Dist_Dend.append()
for i=1, 2 dend3_1[i] Dist_Dend.append()
}
// Wilson 1992 Single Neuron Computation
// dendritic diam(um) * (1+spine/dend ratio)
// also O'Donnell 1993 Synapse
// Koch/Segev Methods in Neuronal Modeling pg 122-3, 1998
proc geom() {
forsec Prox_Dend { L = 20 diam = 2.25 }
forsec Mid_Dend {L = 24.23 diam = 1.10} // { L = 20 diam = 1 * (1+0.3) }
forsec Dist_Dend {L = 395.2 diam = 0.72} // { L = 190 diam = 0.5 * (1+2) }
soma { L = 16 diam = 16 }
}
//**********
// use d_lambda function (see neuron website) to assign segments/nodes
func lambda_f() { local i, x1, x2, d1, d2, lam
if (n3d() < 2) {
return 1e5*sqrt(diam/(4*PI*$1*Ra*cm))
}
// above was too inaccurate with large variation in 3d diameter
// so now we use all 3-d points to get a better approximate lambda
x1 = arc3d(0)
d1 = diam3d(0)
lam = 0
for i=1, n3d()-1 {
x2 = arc3d(i)
d2 = diam3d(i)
lam += (x2 - x1)/sqrt(d1 + d2)
x1 = x2 d1 = d2
}
// length of the section in units of lambda
lam *= sqrt(2) * 1e-5*sqrt(4*PI*$1*Ra*cm)
return L/lam
}
proc geom_nseg() {
freq = 100 // Hz, frequency at which AC length constant will be computed
d_lambda = 0.15
forall { nseg = int((L/(d_lambda*lambda_f(freq))+0.9)/2)*2 + 1 }
}
//**********
proc biophys() {
forsec Prox_Dend {
insert pas
insert naf
insert nap
insert kir
insert kas
insert kaf
insert bkkca
insert skkca
insert caldyn
insert caL
insert caL13
insert cadyn
insert can
insert caq
insert car
insert cat
}
forsec Mid_Dend {
insert pas
insert naf
insert nap
insert kir
insert kas
insert kaf
insert bkkca
insert skkca
insert caldyn
insert caL
insert caL13
insert cadyn
insert can
insert caq
insert car
insert cat
}
forsec Dist_Dend {
insert pas
insert naf
insert nap
insert kir
insert kas
insert kaf
insert bkkca
insert skkca
insert caldyn
insert caL
insert caL13
insert cadyn
insert can
insert caq
insert car
insert cat
}
soma {
insert pas
insert naf
insert nap
insert kir
insert kas
insert kaf
insert krp
insert bkkca
insert skkca
insert caldyn
insert caL
insert caL13
insert cadyn
insert can
insert caq
insert car
insert cat
}
}
proc position() { local i
soma 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 = $3
}
proc connect2target() { //$o1 target point process, $o2 returned NetCon
soma $o2 = new NetCon(&v(1), $o1)
}
func is_art() { return 0 }
proc synloops() {
//***************************
//Build AMPA synapses
// Inner dends AMPA
for i = 0, 0 { // 0 in soma, 1 in each prox dend
dend1 ampa[i] = new AMPAt(0.5) synlist.append(ampa[i])
}
for i = 0, 0 {
dend2 ampa[i] = new AMPAt(0.5) synlist.append(ampa[i])
}
for i = 0, 0 {
dend3 ampa[i] = new AMPAt(0.5) synlist.append(ampa[i])
}
for i = 0, 0 {
dend4 ampa[i] = new AMPAt(0.5) synlist.append(ampa[i])
}
//Second level dends
for i = 0, 1 { // 2 in each mid dend
onode = (i+1)/3 // 0.33, 0.66
dend1_1 ampa[i] = new AMPAt(onode) synlist.append(ampa[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend1_2 ampa[i] = new AMPAt(onode) synlist.append(ampa[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend2_1 ampa[i] = new AMPAt(onode) synlist.append(ampa[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend2_2 ampa[i] = new AMPAt(onode) synlist.append(ampa[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend3_1 ampa[i] = new AMPAt(onode) synlist.append(ampa[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend3_2 ampa[i] = new AMPAt(onode) synlist.append(ampa[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend4_1 ampa[i] = new AMPAt(onode) synlist.append(ampa[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend4_2 ampa[i] = new AMPAt(onode) synlist.append(ampa[i])
}
//Outer_level Dends
for i = 0, 3 { // 4 in each distal dend
onode = (i+1)/5 // 0.2, 0.4, 0.6, 0.8
dend1_1[1] ampa[i] = new AMPAt(onode) synlist.append(ampa[i])
}
for i = 0, 3 {
onode = (i+1)/5
dend1_1[2] ampa[i] = new AMPAt(onode) synlist.append(ampa[i])
}
for i = 0, 3 {
onode = (i+1)/5
dend1_2[1] ampa[i] = new AMPAt(onode) synlist.append(ampa[i])
}
for i = 0, 3 {
onode = (i+1)/5
dend1_2[2] ampa[i] = new AMPAt(onode) synlist.append(ampa[i])
}
for i = 0, 3 {
onode = (i+1)/5
dend2_1[1] ampa[i] = new AMPAt(onode) synlist.append(ampa[i])
}
for i = 0, 3 {
onode = (i+1)/5
dend2_1[2] ampa[i] = new AMPAt(onode) synlist.append(ampa[i])
}
for i = 0, 3 {
onode = (i+1)/5
dend2_2[1] ampa[i] = new AMPAt(onode) synlist.append(ampa[i])
}
for i = 0, 3 {
onode = (i+1)/5
dend2_2[2] ampa[i] = new AMPAt(onode) synlist.append(ampa[i])
}
for i = 0, 3 {
onode = (i+1)/5
dend3_1[1] ampa[i] = new AMPAt(onode) synlist.append(ampa[i])
}
for i = 0, 3 {
onode = (i+1)/5
dend3_1[2] ampa[i] = new AMPAt(onode) synlist.append(ampa[i])
}
for i = 0, 3 {
onode = (i+1)/5
dend3_2[1] ampa[i] = new AMPAt(onode) synlist.append(ampa[i])
}
for i = 0, 3 {
onode = (i+1)/5
dend3_2[2] ampa[i] = new AMPAt(onode) synlist.append(ampa[i])
}
for i = 0, 3 {
onode = (i+1)/5
dend4_1[1] ampa[i] = new AMPAt(onode) synlist.append(ampa[i])
}
for i = 0, 3 {
onode = (i+1)/5
dend4_1[2] ampa[i] = new AMPAt(onode) synlist.append(ampa[i])
}
for i = 0, 3 {
onode = (i+1)/5
dend4_2[1] ampa[i] = new AMPAt(onode) synlist.append(ampa[i])
}
for i = 0, 3 {
onode = (i+1)/5
dend4_2[2] ampa[i] = new AMPAt(onode) synlist.append(ampa[i])
}
//***************************
//***************************
//Build NMDA synapses
// Inner dends NMDA
for i = 0, 0 { // 0 in soma, 1 in each prox dend
dend1 nmda[i] = new NMDAt(0.5) synlist.append(nmda[i])
}
for i = 0, 0 {
dend2 nmda[i] = new NMDAt(0.5) synlist.append(nmda[i])
}
for i = 0, 0 {
dend3 nmda[i] = new NMDAt(0.5) synlist.append(nmda[i])
}
for i = 0, 0 {
dend4 nmda[i] = new NMDAt(0.5) synlist.append(nmda[i])
}
//Second level dends
for i = 0, 1 { // 2 in each mid dend
onode = (i+1)/3
dend1_1 nmda[i] = new NMDAt(onode) synlist.append(nmda[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend1_2 nmda[i] = new NMDAt(onode) synlist.append(nmda[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend2_1 nmda[i] = new NMDAt(onode) synlist.append(nmda[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend2_2 nmda[i] = new NMDAt(onode) synlist.append(nmda[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend3_1 nmda[i] = new NMDAt(onode) synlist.append(nmda[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend3_2 nmda[i] = new NMDAt(onode) synlist.append(nmda[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend4_1 nmda[i] = new NMDAt(onode) synlist.append(nmda[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend4_2 nmda[i] = new NMDAt(onode) synlist.append(nmda[i])
}
//Outer_level Dends
for i = 0, 3 { // 4 in each dist dend
onode = (i+1)/5 // 0.2, 0.4, 0.6, 0.8
dend1_1[1] nmda[i] = new NMDAt(onode) synlist.append(nmda[i])
}
for i = 0, 3 {
onode = (i+1)/5 // 0.2, 0.4, 0.6, 0.8
dend1_1[2] nmda[i] = new NMDAt(onode) synlist.append(nmda[i])
}
synloops_1() // continue in next proc to avoid to large a proc error
} //end synloops
proc synloops_1() {
for i = 0, 3 {
onode = (i+1)/5 // 0.2, 0.4, 0.6, 0.8
dend1_2[1] nmda[i] = new NMDAt(onode) synlist.append(nmda[i])
}
for i = 0, 3 {
onode = (i+1)/5 // 0.2, 0.4, 0.6, 0.8
dend1_2[2] nmda[i] = new NMDAt(onode) synlist.append(nmda[i])
}
for i = 0, 3 {
onode = (i+1)/5 // 0.2, 0.4, 0.6, 0.8
dend2_1[1] nmda[i] = new NMDAt(onode) synlist.append(nmda[i])
}
for i = 0, 3 {
onode = (i+1)/5 // 0.2, 0.4, 0.6, 0.8
dend2_1[2] nmda[i] = new NMDAt(onode) synlist.append(nmda[i])
}
for i = 0, 3 {
onode = (i+1)/5 // 0.2, 0.4, 0.6, 0.8
dend2_2[1] nmda[i] = new NMDAt(onode) synlist.append(nmda[i])
}
for i = 0, 3 {
onode = (i+1)/5 // 0.2, 0.4, 0.6, 0.8
dend2_2[2] nmda[i] = new NMDAt(onode) synlist.append(nmda[i])
}
for i = 0, 3 {
onode = (i+1)/5 // 0.2, 0.4, 0.6, 0.8
dend3_1[1] nmda[i] = new NMDAt(onode) synlist.append(nmda[i])
}
for i = 0, 3 {
onode = (i+1)/5 // 0.2, 0.4, 0.6, 0.8
dend3_1[2] nmda[i] = new NMDAt(onode) synlist.append(nmda[i])
}
for i = 0, 3 {
onode = (i+1)/5 // 0.2, 0.4, 0.6, 0.8
dend3_2[1] nmda[i] = new NMDAt(onode) synlist.append(nmda[i])
}
for i = 0, 3 {
onode = (i+1)/5 // 0.2, 0.4, 0.6, 0.8
dend3_2[2] nmda[i] = new NMDAt(onode) synlist.append(nmda[i])
}
for i = 0, 3 {
onode = (i+1)/5 // 0.2, 0.4, 0.6, 0.8
dend4_1[1] nmda[i] = new NMDAt(onode) synlist.append(nmda[i])
}
for i = 0, 3 {
onode = (i+1)/5 // 0.2, 0.4, 0.6, 0.8
dend4_1[2] nmda[i] = new NMDAt(onode) synlist.append(nmda[i])
}
for i = 0, 3 {
onode = (i+1)/5 // 0.2, 0.4, 0.6, 0.8
dend4_2[1] nmda[i] = new NMDAt(onode) synlist.append(nmda[i])
}
for i = 0, 3 {
onode = (i+1)/5 // 0.2, 0.4, 0.6, 0.8
dend4_2[2] nmda[i] = new NMDAt(onode) synlist.append(nmda[i])
}
//***************************
//***************************
//Build GABA synapses
// soma GABA
for i = 0, 15 { // 16 in soma
soma gaba[i] = new GABAt(0.5) synlist.append(gaba[i])
}
// Inner dends GABA
for i = 0, 2 { // 3 each
dend1 gaba[i] = new GABAt(0.5) synlist.append(gaba[i])
}
for i = 0, 2 {
dend2 gaba[i] = new GABAt(0.5) synlist.append(gaba[i])
}
for i = 0, 2 {
dend3 gaba[i] = new GABAt(0.5) synlist.append(gaba[i])
}
for i = 0, 2 {
dend4 gaba[i] = new GABAt(0.5) synlist.append(gaba[i])
}
//Second level dends
for i = 0, 2 { // 3 each
dend1_1 gaba[i] = new GABAt(0.5) synlist.append(gaba[i])
}
for i = 0, 2 {
dend1_2 gaba[i] = new GABAt(0.5) synlist.append(gaba[i])
}
for i = 0, 2 {
dend2_1 gaba[i] = new GABAt(0.5) synlist.append(gaba[i])
}
for i = 0, 2 {
dend2_2 gaba[i] = new GABAt(0.5) synlist.append(gaba[i])
}
for i = 0, 2 {
dend3_1 gaba[i] = new GABAt(0.5) synlist.append(gaba[i])
}
for i = 0, 2 {
dend3_2 gaba[i] = new GABAt(0.5) synlist.append(gaba[i])
}
for i = 0, 2 {
dend4_1 gaba[i] = new GABAt(0.5) synlist.append(gaba[i])
}
for i = 0, 2 {
dend4_2 gaba[i] = new GABAt(0.5) synlist.append(gaba[i])
}
//Outer_level Dends
for i = 0, 1 { // 2 each
onode = (i+1)/3 // 0.33, 0.66
dend1_1[1] gaba[i] = new GABAt(onode) synlist.append(gaba[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend1_1[2] gaba[i] = new GABAt(onode) synlist.append(gaba[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend1_2[1] gaba[i] = new GABAt(onode) synlist.append(gaba[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend1_2[2] gaba[i] = new GABAt(onode) synlist.append(gaba[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend2_1[1] gaba[i] = new GABAt(onode) synlist.append(gaba[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend2_1[2] gaba[i] = new GABAt(onode) synlist.append(gaba[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend2_2[1] gaba[i] = new GABAt(onode) synlist.append(gaba[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend2_2[2] gaba[i] = new GABAt(onode) synlist.append(gaba[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend3_1[1] gaba[i] = new GABAt(onode) synlist.append(gaba[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend3_1[2] gaba[i] = new GABAt(onode) synlist.append(gaba[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend3_2[1] gaba[i] = new GABAt(onode) synlist.append(gaba[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend3_2[2] gaba[i] = new GABAt(onode) synlist.append(gaba[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend4_1[1] gaba[i] = new GABAt(onode) synlist.append(gaba[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend4_1[2] gaba[i] = new GABAt(onode) synlist.append(gaba[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend4_2[1] gaba[i] = new GABAt(onode) synlist.append(gaba[i])
}
for i = 0, 1 {
onode = (i+1)/3
dend4_2[2] gaba[i] = new GABAt(onode) synlist.append(gaba[i])
}
//**************************
} // end synloops()
endtemplate MSP_Cell
//**************************************************************************