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dks577.append.hoc
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dks577.append.hoc
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// --------------------------------------------------------------
// Select which dendrites get na/kd channels
// --------------------------------------------------------------
n_axon_seg = 5
// n_axon_seg = 25
create myelin[n_axon_seg],node[n_axon_seg]
objectvar active, apical, basal, distal, dend, axon
soma distance()
dend = new SectionList()
forsec "dend" dend.append()
// distal dendrites
distal = new SectionList()
forsec "dend9" if (distance(0) > 550) distal.append()
// apical
apical = new SectionList()
forsec "dend9" apical.append()
// basal dendrites
basal = new SectionList()
forsec "dend" basal.append()
forsec apical basal.remove()
axon = new SectionList()
hill axon.append()
iseg axon.append()
forsec "myelin" axon.append()
forsec "node" axon.append()
// active sections
active = new SectionList()
forall active.append()
forsec "myelin" active.remove()
// --------------------------------------------------------------
// Other geometry-specific locations
// --------------------------------------------------------------
objref dsite
dend9[76] dsite = new SectionRef()
site_loc = 0.5 // distance = 416 um
// synapses
objref synloc
synloc = new SectionList()
forsec distal synloc.append()
// along ap
objref path
path = new SectionList()
dend9[76] path.append()
dend9[72] path.append()
dend9[68] path.append()
dend9[62] path.append()
dend9[56] path.append()
dend9[50] path.append()
dend9[48] path.append()
dend9[38] path.append()
dend9[30] path.append()
dend9[24] path.append()
dend9[8] path.append()
dend9[0] path.append()
// oblique
objref oblique
oblique = new SectionList()
forsec apical oblique.append()
forsec distal oblique.remove()
forsec path oblique.remove()
// --------------------------------------------------------------
// correct diameter of apical
// --------------------------------------------------------------
double x[199],y[199],z[199],d[199]
proc diam_interp() { local d0,d1
d0 = $1
d1 = $2
for i=0,n3d()-1 {
x[i]=x3d(i) y[i]=y3d(i) z[i]=z3d(i)
}
if (numarg() > 2) {
n = $3
} else {
n = n3d()
}
max = n3d()
pt3dclear()
for i=0,n-1 {
pt3dadd(x[i],y[i],z[i],i/n*d1+(1-i/n)*d0)
}
for i=n,max-1 {
pt3dadd(x[i],y[i],z[i],i/n*d1+(1-i/n)*d0)
}
}
proc shrink() { local factor
factor = $1
n = n3d()
for i=0,n-1 {
x[i]=x3d(i) y[i]=y3d(i) z[i]=z3d(i) d[i]=diam3d(i)
}
pt3dclear()
for i=0,n-1 {
pt3dadd(x[i]*factor,y[i]*factor,z[i]*factor,d[i]*factor)
}
}
// --------------------------------------------------------------
// discretization
// --------------------------------------------------------------
max_len_dend = 50
forsec dend {
n = L / max_len_dend
if (n < 1) n = 1
nseg = n+1
}
// give more segments to path
max_len_path = 10
forsec path {
n = L / max_len_path
if (n < 1) n = 1
nseg = n+1
}
// --------------------------------------------------------------
// Axon geometry
// --------------------------------------------------------------
// hillock
// hillock is only a few microns long (2-4) and tapered diam from 4 to 1-2 um
// then initial segment follows, can be 100-150 um long with diam of ~ 1 um
// myelin starts after initial segment
// initial segment
// Farinas & DeFelipe J Comp Neurol 1991:
// L diam
// cocallosal 21.6 +- 4.10 1.06 +- 0.18
// ispsilateral 22.24 +- 1.58 1.06 +- 0.12
hill {
L = 10
nseg = 10
diam(0:1) = 4:1 // taper
}
iseg { // initial segment between hillock + myelin
L = 15
nseg = 10
// for(x) diam(x) = 3.5*exp(-(x*L+hill.L)/5)+.5
diam = 1
}
// construct myelinated axon with nodes of ranvier
for i=0,n_axon_seg-1 {
myelin[i] { // myelin element
nseg = 25
L = 100
diam = 1.5
}
node[i] { // nodes of Ranvier
nseg = 1
L = 1.0
diam = 1.0 // nodes are thinner than axon
}
}
iseg connect myelin[0](0), 1
myelin[0] connect node[0](0), 1
for i=0,n_axon_seg-2 {
node[i] connect myelin[i+1](0), 1
myelin[i+1] connect node[i+1](0), 1
}
access soma
// --------------------------------------------------------------
// Spines
// --------------------------------------------------------------
fold_spines = 0
spine_area = 0.83 // um^2 -- Harris
// spines per linear um
// Larkman (1991) JCN
sd_apical = 6.3
sd_oblique = 1.5
sd_basal = 1.43
sd_distal = 0.91
proc add_spines() { local a
spine_dens = $2
forsec $o1 {
a =0
for(x) a=a+area(x)
if (fold_spines) {
// Folding factor
// Jack et al (1989), Marjor et al (1994)
F = (L*spine_area*spine_dens + a)/a
L = L * F^(2/3)
for(x) diam(x) = diam(x) * F^(1/3)
} else {
F = 1 + L*spine_area*spine_dens/a
cm = c_m * F
g_pas = F/rm
}
}
}