// Author: Etay Hay, 2011
// Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of
// Dendritic and Perisomatic Active Properties
// (Hay et al., PLoS Computational Biology, 2011)
//
// Model of L5 Pyramidal Cell, constrained both for BAC firing and Current Step Firing
// Copied and adapted some needed functions to work with LFPy from file
// models/L5PCtemplate.hoc
//
// 30.01.2012 ehagen@umb.no
// Fixed problem of looping over the section lists
//
// 08.06.2012 ehagen@umb.no
objref this
proc geom_nseg() {local nSec, L1, L2, D1, D2, nSeg1, nSeg2
soma area(.5) // make sure diam reflects 3d points
nSec = 0
forsec all {
nseg = 1 + 2*int(L/40)
nSec = nSec + 1
}
nSecAll = nSec
nSec = 0
soma { nSec = nSec + 1}
nSecSoma = nSec
nSec = 0
apic { nSec = nSec + 1}
nSecApical= nSec
nSec = 0
dend { nSec = nSec + 1}
nSecBasal = nSec
nSec = 0
axon { nSec = nSec + 1}
nSecAxonalOrig = nSecAxonal = nSec
}
proc distribute_channels() {local dist,val,base,maxLength
base = $8
soma distance()
maxLength = getLongestBranch($s1)
forsec $s1 {
if(0==strcmp($s2,"Ra")){
Ra = $8
} else {
for(x) {
if ($3==3) {
dist = distance(x)
} else {
dist = distance(x)/maxLength
}
val = calculate_distribution($3,dist,$4,$5,$6,$7,$8)
sprint(tstr,"%s(%5.10f) = %5.10f",$s2,x,val)
execute(tstr)
}
}
}
}
// $s1 section
func getLongestBranch(){local maxL,d localobj distallist,sref
sprint(tstr,"%s distance()",$s1)
execute(tstr,this)
if(0==strcmp($s1,"axon")){
sprint(tstr,"%s[0] distance(1)",$s1)
execute(tstr,this)
}
maxL = 0
d = 0
distallist = new SectionList()
forsec $s1 {
sref = new SectionRef()
if (sref.nchild==0) distallist.append()
}
forsec distallist{
d = distance(1)
if(maxL<d) maxL = d
}
// for the soma case
if (maxL == 0) {
$s1 {
maxL = L
}
}
return maxL
}
// $1 is the distribution type:
// 0 linear, 1 sigmoid, 2 exponential
// 3 step for absolute distance (in microns)
func calculate_distribution() {local value
if ($1==0) {value = $3 + $2*$4}
if ($1==1) {value = $3 + ($4/(1+exp(($2$5)/$6)))}
if ($1==2) {value = $3 + $6*exp($4*($2$5))}
if ($1==3) {
if (($2 > $5) && ($2 < $6)) {
value = $3
} else {
value = $4
}
}
value = value*$7
return value
}
// deleting axon, keeping only first 60 micrometers
proc delete_axon(){
axon {delete_section()}
create axon[2]
access axon[0]{
L= 30
diam = 1
nseg = 1+2*int(L/40)
}
access axon[1]{
L= 30
diam = 1
nseg = 1+2*int(L/40)
}
nSecAxonal = 2
connect axon(0), soma(0.5)
connect axon[1](0), axon[0](1)
access soma
}
