// ----------------------------------------------------------------------------
// membrane.hoc
// loads the full cell morphology, inserts passive
// membrane properties, corrects membrane resistance
// and capacitance for spines, and corrects (roughly)
// for temperature if needed
//
// 2007-06-17, Christoph Schmidt-Hieber, University of Freiburg
//
// accompanies the publication:
// Schmidt-Hieber C, Jonas P, Bischofberger J (2007)
// Subthreshold Dendritic Signal Processing and Coincidence Detection
// in Dentate Gyrus Granule Cells. J Neurosci 27:8430-8441
//
// send bug reports and suggestions to christoph.schmidt-hieber@uni-freiburg.de
//
// 2007-08-31: adheres to NetworkReadyCell policy
//
// ----------------------------------------------------------------------------
// load gui or stdrun:
load_file("stdrun.hoc")
load_file("./../share/genutils.hoc")
load_file("./../share/calcSpines.hoc")
load_file("./../share/fixnseg.hoc")
begintemplate cell_6
public is_art
public init, topol, basic_shape, subsets, geom, biophys, geom_nseg, biophys_inhomo
public synlist, x, y, z, position, connect2target
public somaLoc,distalDendLoc,proxDendLoc,synDendLoc,spineCount,n_sections,n_axon
public section, axon
public all,den,axo
external verbose,debug_mode,accuracy,calc_spines
external q10_cm,q10_g_pas,q10_Ra,tempScale,geom_nseg_shared,lambda_f
objref somaLoc,distalDendLoc,proxDendLoc,synDendLoc,spineCount,this,synlist
proc init() {
topol()
if (debug_mode) print "Loaded cell, n_sections=",n_sections
subsets()
geom()
biophys()
geom_nseg()
synlist = new List()
synapses()
x = y = z = 0 // only change via position
n_sections = 0
n_axon = 0
}
// dummy compartments, will be updated later:
create axon[1],section[1]
proc init_spines() {
forall insert spines
section[0] count_spines = 0
section[1] count_spines = 10
section[2] count_spines = 2
section[3] count_spines = 112+91+36
section[4] count_spines = 135
section[5] count_spines = 137+93
section[6] count_spines = 43+123+57
section[7] count_spines = 47
section[8] count_spines = 133+100+84
section[9] count_spines = 56+133+82
section[10] count_spines = 10
section[11] count_spines = 5
section[12] count_spines = 149+153+29
section[13] count_spines = 68
section[14] count_spines = 104+120
section[15] count_spines = 81+73
section[16] count_spines = 87+112+103
forall calc_spines()
}
proc init_pas() {
forall {
insert pas
e_pas=0
cm = 1.09686 * tempScale(q10_cm) * scale_spines
g_pas = 2.76876e-05 * tempScale(q10_g_pas) * scale_spines
Ra = 320.159 * tempScale(q10_Ra)
}
}
proc basic_shape() {localobj morphoFile
strdef sectionLabel
morphoFile = new File()
morphoFile.ropen("./cell_6/morpho.txt")
n_sections = morphoFile.scanvar()
create section[n_sections]
n_axon = morphoFile.scanvar()
create axon[n_axon]
forall pt3dclear()
while (!morphoFile.eof()) {
morphoFile.scanstr(sectionLabel)
if (strcmp(sectionLabel,"S")==0) {
section[morphoFile.scanvar()] pt3dadd(morphoFile.scanvar(),morphoFile.scanvar(),morphoFile.scanvar(),morphoFile.scanvar())
} else {
axon[morphoFile.scanvar()] pt3dadd(morphoFile.scanvar(),morphoFile.scanvar(),morphoFile.scanvar(),morphoFile.scanvar())
}
}
morphoFile.close()
// define soma:
section[0] somaLoc = new Location(0.5)
// define dendritic sites:
section[12] distalDendLoc = new Location(0.8)
section[1] proxDendLoc = new Location(0.05)
section[5] synDendLoc = new Location(0.8)
access somaLoc.secRef.sec
}
proc topol() {
basic_shape()
connect axon[1](0.0), axon[0](1.0)
connect axon[2](0.0), axon[1](1.0)
connect axon[3](0.0), axon[2](1.0)
connect axon[4](0.0), axon[3](1.0)
connect axon[5](0.0), axon[4](1.0)
connect axon[6](0.0), axon[4](1.0)
connect axon[7](0.0), axon[3](1.0)
connect axon[8](0.0), axon[2](1.0)
connect axon[9](0.0), axon[1](1.0)
connect axon[10](0.0), axon[9](1.0)
connect axon[11](0.0), axon[9](1.0)
connect axon[12](0.0), axon[0](1.0)
connect axon[13](0.0), axon[12](1.0)
connect axon[14](0.0), axon[12](1.0)
connect axon[0](0.0), section[0](0.0)
connect section[1](0.0), section[0](1.0)
connect section[2](0.0), section[1](1.0)
connect section[3](0.0), section[2](1.0)
connect section[4](0.0), section[2](1.0)
connect section[5](0.0), section[4](1.0)
connect section[6](0.0), section[4](1.0)
connect section[7](0.0), section[1](1.0)
connect section[8](0.0), section[7](1.0)
connect section[9](0.0), section[7](1.0)
connect section[10](0.0), section[0](1.0)
connect section[11](0.0), section[10](1.0)
connect section[12](0.0), section[11](1.0)
connect section[13](0.0), section[11](1.0)
connect section[14](0.0), section[13](1.0)
connect section[15](0.0), section[13](1.0)
connect section[16](0.0), section[10](1.0)
init_spines()
}
objref all,den,axo
proc subsets() { local i
objref all,den,axo
all = new SectionList()
for i=0, n_sections-1 section[i] all.append()
for i=0, n_axon-1 axon[i] all.append()
den = new SectionList()
for i=1, n_sections-1 section[i] den.append()
axo = new SectionList()
for i=0, n_axon-1 axon[i] axo.append()
}
proc geom() {
}
proc geom_nseg() {
geom_nseg_shared()
// increase nseg even further (tribute to Josef):
if (accuracy >= 1) {
forall nseg*=3
}
}
proc biophys() {
init_pas()
}
proc biophys_inhomo(){}
proc position() { local i
somaLoc.secRef.sec 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 = $3
}
obfunc connect2target() { localobj nc //$o1 target point process, optional $o2 returned NetCon
axon[0] nc = new NetCon(&v(0), $o1)
nc.threshold = 10
if (numarg() == 2) { $o2 = nc } // for backward compatibility
return nc
}
objref syn_
proc synapses() {
}
func is_art() { return 0 }
endtemplate cell_6