//------------------------------------------------------------------------------------------
//
// Title: modelCellReConstruction.hoc
// Author: Ronald van Elburg (RonaldAJ at vanElburg eu)
//
// Affiliation:
// Department of Artificial Intelligence
// Groningen University
//
// NEURON model specification for the paper:
//
// Ronald A.J. van Elburg and Arjen van Ooyen (2010) `Impact of dendritic size and
// dendritic topology on burst firing in pyramidal cells',
// PLoS Comput Biol 6(5): e1000781. doi:10.1371/journal.pcbi.1000781.
//
// Please consult Readme.txt or instructions on the usage of this file.
//
// This software is released under the GNU GPL version 3:
// http://www.gnu.org/copyleft/gpl.html
//
// The modelcode was partially derived from the code for:
//
// Z. F. Mainen and T. J. Sejnowski (1996) Influence of dendritic
// structure on firing pattern in model neocortical neurons.
// Nature 382: 363-366.
//
// Available from http://senselab.med.yale.edu/ModelDB , accession number 2488
//
//
objref sh, st, axonal, dendritic
strdef demofactorydir, tstrFileName
sprint(demofactorydir,"%s", getcwd())
// load_proc("nrnmainmenu")
load_file("nrngui.hoc")
load_file("hoc/mep.hoc")
load_file("hoc/LTree.hoc")
// load dll if not already loaded automatically and set defaults for parameters that can be overwritten by calling code
isDefined=name_declared("cad")
if(isDefined!=1){
nrn_load_dll("nrnmech.dll")
}
isDefined=name_declared("interactive")
if(isDefined==0){
interactive=0
}
print "interactive: ",interactive
isDefined=name_declared("rallify_cell")
if(isDefined==0){
rallify_cell=0
}
print "rallify_cell: ",rallify_cell
isDefined=name_declared("use_dlambda")
if(isDefined==0){
use_dlambda=0
}
print "use_dlambda: ",use_dlambda
isDefined=name_declared("segmentlength")
if(isDefined!=5){
segmentlength=50
}
print "segmentlength: ",segmentlength
create soma
access soma
//tstop = 9000
steps_per_ms = 40
dt = 0.025
objref CV_Ode
create cvode_dummy
cvode_dummy {
CV_Ode= new CVode()
CV_Ode.active(1)
}
// --------------------------------------------------------------
// passive & active membrane
// --------------------------------------------------------------
ra = 150
rm = 30000
c_m = 0.75
cm_myelin = 0.04
g_pas_node = 0.02
v_init = -70
celsius = 37
Ek = -90
Ena = 60
gna_dend = 20
gna_node = 30000
gna_soma = gna_dend
gkv_axon = 2000
gkv_soma = 200
gca = .3
gkm = .1
gkca = 3
gca_soma = gca
gkm_soma = gkm
gkca_soma = gkca
// --------------------------------------------------------------
// Axon geometry
//
// Similar to Mainen et al (Neuron, 1995)
// --------------------------------------------------------------
n_axon_seg = 5
create soma,iseg,hill,myelin[2],node[2]
proc create_axon() {
create iseg,hill,myelin[n_axon_seg],node[n_axon_seg]
soma {
equiv_diam = sqrt(area(.5)/(4*PI))
}
if (numarg()) equiv_diam = $1
iseg { // initial segment between hillock + myelin
L = 15
nseg = 5
diam = equiv_diam/10 // see Sloper and Powell 1982, Fig.71
}
hill {
L = 10
nseg = 5
diam(0:1) = 4*iseg.diam:iseg.diam
}
// construct myelinated axon with nodes of ranvier
for i=0,n_axon_seg-1 {
myelin[i] { // myelin element
nseg = 5
L = 100
diam = iseg.diam
}
node[i] { // nodes of Ranvier
nseg = 1
L = 1.0
diam = iseg.diam*.75 // nodes are thinner than axon
}
}
soma connect hill(0), 0.5
hill connect iseg(0), 1
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
}
}
// --------------------------------------------------------------
// Spines
// --------------------------------------------------------------
// Based on the "Folding factor" described in
// Jack et al (1989), Major et al (1994)
// note, this assumes active channels are present in spines
// at same density as dendrites
spine_dens = 1
// just using a simple spine density model due to lack of data on some
// neuron types.
spine_area = 0.83 // um^2 -- K Harris
proc add_spines() { local area_section
forsec $o1 {
area_section =0
for(x,0) { area_section=area_section+area(x) } // Calculate area and update diameters
F = (L*spine_area*spine_dens + area_section)/area_section
L = L * F^(2/3)
// make sure no compartments exceed 50 uM length
nseg = L/segmentlength + 1
for(x,0) {
area(x) // Call area function to update diameters
diam(x) = diam(x) * F^(1/3) // Change diameters using updated values
}
}
}
// --------------------------------------------------------------
// Init_cell
// --------------------------------------------------------------
proc init_cell() {
// passive
forall {
insert pas
Ra = ra
cm = c_m
g_pas = 1/rm
e_pas = v_init
}
// exceptions along the axon
forsec "myelin" cm = cm_myelin
forsec "node" g_pas = g_pas_node
// na+ channels
forall insert na
forsec dendritic gbar_na = gna_dend
forsec "myelin" gbar_na = gna_dend
hill.gbar_na = gna_node
iseg.gbar_na = gna_node
forsec "node" gbar_na = gna_node
// kv delayed rectifier channels
iseg { insert kv gbar_kv = gkv_axon }
hill { insert kv gbar_kv = gkv_axon }
soma { insert kv gbar_kv = gkv_soma }
// dendritic channels
forsec dendritic {
insert km gbar_km = gkm
insert kca gbar_kca = gkca
insert ca gbar_ca = gca
insert cad
}
soma {
gbar_na = gna_soma
insert km gbar_km = gkm_soma
insert kca gbar_kca = gkca_soma
insert ca gbar_ca = gca_soma
insert cad
}
forall if(ismembrane("k_ion")) ek = Ek
forall if(ismembrane("na_ion")) {
ena = Ena
// seems to be necessary for 3d cells to shift Na kinetics -5 mV
vshift_na = -5
}
forall if(ismembrane("ca_ion")) {
eca = 140
ion_style("ca_ion",0,1,0,0,0)
vshift_ca = 0
}
}
// --------------------------------------------------------------
// Load_3dcell
// --------------------------------------------------------------
proc load_3dcell() {
forall delete_section()
objref KSyn, KSynList, sh, st, axonal, dendritic
sprint(tstrFileName,"%s\%s",demofactorydir, $s1)
xopen(tstrFileName)
access soma
dendritic = new SectionList()
forsec "dend" {
dendritic.append()
}
// show cell
sh = new PlotShape()
sh.size(-300,300,-300,300)
soma nseg=(L/segmentlength)+1
if (!aspiny) {
add_spines(dendritic,spine_dens)
}else{
forsec dendritic {
nseg=(L/segmentlength)+1
}
}
create_axon()
init_cell()
st=new IClamp(.5)
st.dur = tstop
st.del = 100
}
/* proc AdjustModel()
remove_basal = $1
passive_basal = $2
passive_apical = $3
passive_soma = $4
remove_axon = $5
*/
proc AdjustModel(){local remove_basal,passive_basal,passive_apical,passive_soma,remove_axon localobj basal_dends
remove_basal = $1
passive_basal = $2
passive_apical = $3
passive_soma = $4
remove_axon = $5
if(remove_basal==1){
basal_dends = new SectionList()
forsec "dend" {
basal_dends.append()
}
forsec "dend11" {
basal_dends.remove()
}
forsec basal_dends {
disconnect()
delete_section()
}
}
if(passive_basal==1){
basal_dends = new SectionList()
forsec "dend" {
basal_dends.append()
}
forsec "dend11" {
basal_dends.remove()
}
forsec basal_dends {
uninsert ca
uninsert cad
uninsert kca
uninsert na
uninsert km
}
}
if(passive_apical==1){
forsec "dend11" {
uninsert ca
uninsert cad
uninsert kca
uninsert na
uninsert km
}
}
if(passive_soma==1){
forsec "soma" {
uninsert na
uninsert kv
}
}
if(remove_axon==1){
forsec "hill" {
disconnect()
delete_section()
}
forsec "iseg" {
disconnect()
delete_section()
}
forsec "myelin" {
disconnect()
delete_section()
}
forsec "node" {
disconnect()
delete_section()
}
}
}
proc ModifyBasalChannelDensity(){local x_factor localobj basal_dends
x_factor=$1
basal_dends = new SectionList()
forsec "dend" {
basal_dends.append()
}
forsec "dend11" {
basal_dends.remove()
}
forsec basal_dends {
// uninsert kca
gbar_kca = x_factor*gkca
// uninsert na
gbar_na = x_factor*gna_dend
// uninsert km
gbar_km = x_factor*gkm
}
}
proc ModifyHillockChannelDensity(){local y_factor localobj hillsecs
y_factor=$1
hillsecs = new SectionList()
forsec "hill" {
hillsecs.append()
}
forsec "iseg" {
hillsecs.append()
}
forsec hillsecs {
// uninsert kca
gbar_na = y_factor*gna_node
// uninsert na
gbar_kv = y_factor*gkv_axon
}
}
nrnmainmenu()
nrncontrolmenu()
// Load default model
proc fig1d() {
load_3dcell("cells/j4a.hoc")
st.amp = 0.2
}
aspiny = 1
L_factor=1
D_factor=1
XFactor=1
bMoveBranches=0
bDendriticStimulation=0
objref KSyn, KSynList
bPrintTree=0
pruneDend11=0
pruneProbability=0
seed=0
pruneDepth=0
pruneSeed=0
remove_basal=0
passive_basal=0
passive_apical=0
passive_soma=0
remove_axon=0
ST_AMP=0.2
ST_DEL=100
ST_DUR=500
modBasalChannelDensity=0
remCaDepChannelsFromSoma=0
modHillockChannelDensity=0
fig1d()
load_file("hoc/prune.hoc")
proc customModifications(){
}
func volume(){local v
v=0
forall {
v=v+diam*diam*PI/2*L
}
return v
}
strdef loopstr, epsfilename
// Overwrite standard MRC_PrepareModel function
proc MRC_PrepareModel(){
fig1d()
AdjustModel(remove_basal,passive_basal,passive_apical,passive_soma,remove_axon)
if(modBasalChannelDensity==1){
ModifyBasalChannelDensity(XFactor)
}
if(remCaDepChannelsFromSoma==1){
uninsert kca
uninsert cad
uninsert ca
}
if(pruneDend11==1){
prune_endsegments_rndn("dend11",pruneProbability,pruneDepth,pruneSeed)
}
if(modHillockChannelDensity==1){
ModifyHillockChannelDensity(YFactor)
}
sh.exec_menu("View = plot")
sh.exec_menu("Show Diam")
st.del=ST_DEL
st.amp=ST_AMP
st.dur=ST_DUR
customModifications()
if(bPrintTree==1){
sprint(epsfilename,"%s.eps",loopstr)
sh.printfile(epsfilename)
}
}
