// Author: Etay Hay 2014
// Dendritic excitability and gain control in recurrent cortical microcircuits (Hay and Segev, 2014, Cerebral Cortex)
//
// Cell template of L5 thick-tufted pyramidal cell (TTC)
//
// Modified by Tuomo Maki-Marttunen 2015-2016
//
begintemplate TTC
public init, biophys, geom_nseg, biophys_inhomo
public synlist, connect2target, APC
public locateSites, getLongestBranch, distributeSyn, distributeSyn2
public initRand,insertMCcons
public preconlist ,synLocList, rList, preTrainList, preTrainIndexList
public setnetworkparameters,initPreSynTrain,queuePreTrains,setpretrains
public pA
public soma, dend, apic, stimThreshold, ASCIIrpt, HDF5rpt, getAbsSecIndex
public all, somatic, apical, basal, nSecSoma, nSecApical, nSecBasal, nSecAll, SecSyn
public nsegs
public NsynsE, NsynsI
objref synlist, SecSyn, ASCIIrpt, HDF5rpt, APC
objref all, somatic, apical, basal
objref preconlist, syngroupIndexList, rList, preTrainList, preTrainIndexList
objref rd1
objref this
objref sref,fih
objref NsynsE, NsynsI
objref synvarVecList, treenameList
strdef tstr
create soma[1], dend[1], apic[2]
proc init() {localobj nl,import
all = new SectionList()
somatic = new SectionList()
basal = new SectionList()
apical = new SectionList()
apic[0] apical.append()
apic[1] apical.append()
soma[0] somatic.append()
dend[0] basal.append()
apic[0] all.append()
apic[1] all.append()
soma[0] all.append()
dend[0] all.append()
connect dend[0](0), soma[0](0)
connect apic[0](0), soma[0](1)
connect apic[1](0), apic[0](1)
access soma
soma insert pas
dend insert pas
apic[0] insert pas
apic[1] insert pas
nsegs = 5
soma {nseg = nsegs Ra = 100 diam = 13.47 L = 23.17 cm = 1 V = -80 e_pas = -90}
dend {nseg = nsegs Ra = 100 diam = 10.28 L = 282.13 cm = 2 V = -80 e_pas = -90}
apic[0] {nseg = nsegs Ra = 100 diam = 5.04 L = 700.0 cm = 2 V = -80 e_pas = -90}
apic[1] {nseg = nsegs Ra = 100 diam = 5.04 L = 600.53 cm = 2 V = -80 e_pas = -90}
soma {
insert Ca_LVAst
insert Ca_HVA
insert SKv3_1
insert SK_E2
insert K_Tst
insert K_Pst
insert Nap_Et2
insert NaTa_t
insert CaDynamics_E2
insert Ih
ek = -85
ena = 50
gIhbar_Ih = 0.0002
g_pas = 0.0000338
decay_CaDynamics_E2 = 460.0
gamma_CaDynamics_E2 = 0.000501
gCa_LVAstbar_Ca_LVAst = 0.00343
gCa_HVAbar_Ca_HVA = 0.000992
gSKv3_1bar_SKv3_1 = 0.693
gSK_E2bar_SK_E2 = 0.0441
gK_Tstbar_K_Tst = 0.0812
gK_Pstbar_K_Pst = 0.00223
gNap_Et2bar_Nap_Et2 = 0.00172
gNaTa_tbar_NaTa_t = 2.04
}
dend {
insert Ih
gIhbar_Ih = 0.0002
g_pas = 0.0000467
}
apic[0] {
insert Ca_LVAst
insert Ca_HVA
insert SKv3_1
insert SK_E2
insert NaTa_t
insert Im
insert CaDynamics_E2
insert Ih
ek = -85
ena = 50
decay_CaDynamics_E2 = 122
gamma_CaDynamics_E2 = 0.000509
gSK_E2bar_SK_E2 = 0.0012
gSKv3_1bar_SKv3_1 = 0.000261
gNaTa_tbar_NaTa_t = 0.0213
gImbar_Im = 0.0000675
g_pas = 0.0000589
gIhbar_Ih = 0.0004
gCa_LVAstbar_Ca_LVAst = 0.0187
gCa_HVAbar_Ca_HVA = 0.000555
}
apic[1] {
insert Ca_LVAst
insert Ca_HVA
insert SKv3_1
insert SK_E2
insert NaTa_t
insert Im
insert CaDynamics_E2
insert Ih
ek = -85
ena = 50
decay_CaDynamics_E2 = 122
gamma_CaDynamics_E2 = 0.000509
gSK_E2bar_SK_E2 = 0.0012
gSKv3_1bar_SKv3_1 = 0.000261
gNaTa_tbar_NaTa_t = 0.0213
gImbar_Im = 0.0000675
g_pas = 0.0000589
gIhbar_Ih = 0.0004
gCa_LVAstbar_Ca_LVAst = 0.0187
gCa_HVAbar_Ca_HVA = 0.000555
}
geom_nseg()
area(0.5)
distance()
access soma
synlist = new List()
preconlist = new List()
stimThreshold =0
preTrainList = new List()
preTrainIndexList = new List()
syngroupIndexList = new List()
synvarVecList = new List()
pA = 0.5
}
proc setnetworkparameters(){
rcpWeightFactor = $1 //how stronger reciprocal connections are on average
EsynConductance = $2
IsynConductance = $3
NsynE = $4
NsynI = $5
contactsNumE = $6
weight_AMPA = $7
weight_factor_NMDA = $8
weight_GABA = $9
gNoiseCoeff = $10
}
proc geom() {
}
proc geom_nseg() {local nSec, L1, L2, D1, D2, nSeg1, nSeg2
soma area(.5) // make sure diam reflects 3d points
nSec = 0
forsec all {
nseg = 1 + 2*int(L/40)
nSec = nSec + 1
}
nSecAll = 5
nSecSoma = 1
nSecApical = 2
nSecBasal = 1
}
proc connect2target() { //$o1 target point process, $o2 returned NetCon
soma $o2 = new NetCon(&v(1), $o1)
$o2.threshold = -30
}
// $s1 section
func getLongestBranch(){local maxL,d localobj distallist,sref
sprint(tstr,"%s distance()",$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
}
// $s1 section
// $2 distance x in micrometers
// return list of [1,2] vectors - of the appropriate section and the location in each vector
obfunc locateSites() {local maxL,site,d0,d1,siteX,i localobj vv,ll
ll = new List()
sprint(tstr,"%s distance()",$s1)
execute(tstr,this)
maxL = getLongestBranch($s1)
site = $2
i = 0
forsec $s1 {
if (distance(0) < distance(1)) {
d0 = distance(0)
d1 = distance(1)
} else {
d1 = distance(0)
d0 = distance(1)
}
if (site <= d1 && site >= d0) {
siteX = (site-d0)/(d1-d0)
secNum = i
vv = new Vector()
ll.append(vv.append(secNum,siteX))
}
i = i+1
}
return ll
}
//========================================================================================
//================================= microcircuit related stuff============================
//========================================================================================
// $1 some number that is function of the TTC index
//
// Have each TTC with unique sites, but certain portion of inputs identical to root TTC
proc initRand() {
rList = new List() //for stochastic synapses
rd1 = new Random($1) // unique to this TTC
rd1.uniform(0,1)
}
double siteVec[2]
proc distributeSyn() {local sitenum,i, segInd, compInd localobj sl
strdef treename,cmd2
NsynsE = new List()
NsynsI = new List()
for i = 0, 2 {
NsynsE.append(new Vector(nsegs))
NsynsI.append(new Vector(nsegs))
}
lengthA = apic[0].L + apic[1].L
lengthB = dend.L
pA = lengthA/(lengthA + lengthB)
for(i=0;i<2*3*nsegs;i+=1) {
syngroupIndexList.append(new Vector())
}
for(i=0;i<(NsynE+NsynI);i+=1){
if (rd1.repick()<pA){
treename = "apic"
compInd = 1
} else {
treename = "dend"
compInd = 0
}
sl = locateSites(treename,rd1.repick()*getLongestBranch(treename))
sitenum = int((sl.count()-1)*rd1.repick())
compInd = compInd + sl.o[sitenum].x[0] // if we are at apical, and sl.o[sitenum].x[0]=1, then compInd = 2, otherwise 1 at apical, and 0 at basal
segInd = int(sl.o[sitenum].x[1]*nsegs)
if (i<NsynE) {
NsynsE.o[compInd].x[segInd] = NsynsE.o[compInd].x[segInd] + 1
syngroupIndexList.o[compInd*nsegs+segInd].append(i)
} else {
NsynsI.o[compInd].x[segInd] = NsynsI.o[compInd].x[segInd] + 1
syngroupIndexList.o[3*nsegs + compInd*nsegs+segInd].append(i)
}
}
}
proc distributeSyn2() {local sitenum,syni,preconi,i,i1, segInd, compInd localobj sl,nilstim
strdef cmd2
//objref treenameList
treenameList = new List()
treenameList.append(new String("dend[0]"))
treenameList.append(new String("apic[0]"))
treenameList.append(new String("apic[1]"))
for(i=0;i<NsynsE.count();i+=1){
sprint(cmd2,"access %s",treenameList.o[i].s)
execute(cmd2,this)
sprint(cmd2,"%s sref = new SectionRef()",treenameList.o[i].s)
execute(cmd2,this)
for(iseg=0;iseg<NsynsE.o[i].size();iseg+=1) {
segx = (0.5+iseg)/NsynsE.o[i].size()
sref {
synlist.append(new ProbAMPANMDA2groupdet(segx))
syni = synlist.count()-1 //synapse index
rList.append(new Random(int(1000000*rd1.repick())))
rList.o[syni].negexp(1)
synlist.o[syni].setRNG(rList.o[syni])
synlist.o[syni].tau_r_AMPA = 0.3
synlist.o[syni].tau_d_AMPA = 3
synlist.o[syni].tau_r_NMDA = 2
synlist.o[syni].tau_d_NMDA = 65
synlist.o[syni].e = 0
synlist.o[syni].Dep = 800
synlist.o[syni].Fac = 0
synlist.o[syni].Use = 0.6
synlist.o[syni].u0 = 0
synlist.o[syni].gmax = EsynConductance*gNoiseCoeff
synlist.o[syni].weight_factor_NMDA = weight_factor_NMDA
Nsyns_thissyn = NsynsE.o[i].x[iseg]
synvarVecList.append(new Vector(3*Nsyns_thissyn))
for i1=0,Nsyns_thissyn-1 {
synvarVecList.o[synvarVecList.count()-1].x(i1) = 0
synvarVecList.o[synvarVecList.count()-1].x(Nsyns_thissyn+i1) = 1
synvarVecList.o[synvarVecList.count()-1].x(2*Nsyns_thissyn+i1) = 0
}
synlist.o[syni].setVec(synvarVecList.o[synvarVecList.count()-1])
preconlist.append(new NetCon(nilstim, synlist.o[syni]))
preconi = preconlist.count()-1 //connection index
preconlist.o[preconi].weight = weight_AMPA
preconlist.o[preconi].delay = 0
}
}
}
for(i=0;i<NsynsI.count();i+=1){
sprint(cmd2,"access %s",treenameList.o[i].s)
execute(cmd2,this)
sprint(cmd2,"%s sref = new SectionRef()",treenameList.o[i].s)
execute(cmd2,this)
for(iseg=0;iseg<NsynsI.o[i].size();iseg+=1) {
segx = (0.5+iseg)/NsynsI.o[i].size()
sref {
synlist.append(new ProbUDFsyn2groupdet(segx))
syni = synlist.count()-1 //synapse index
rList.append(new Random(int(1000000*rd1.repick())))
rList.o[syni].negexp(1)
synlist.o[syni].setRNG(rList.o[syni])
synlist.o[syni].tau_r = 1
synlist.o[syni].tau_d = 20
synlist.o[syni].e = -80
synlist.o[syni].Dep = 800
synlist.o[syni].Fac = 0
synlist.o[syni].Use = 0.25
synlist.o[syni].u0 = 0
synlist.o[syni].gmax = IsynConductance*gNoiseCoeff
Nsyns_thissyn = NsynsI.o[i].x[iseg]
synvarVecList.append(new Vector(3*Nsyns_thissyn))
for i1=0,Nsyns_thissyn-1 {
synvarVecList.o[synvarVecList.count()-1].x(i1) = 0
synvarVecList.o[synvarVecList.count()-1].x(Nsyns_thissyn+i1) = 1
synvarVecList.o[synvarVecList.count()-1].x(2*Nsyns_thissyn+i1) = 0
}
synlist.o[syni].setVec(synvarVecList.o[synvarVecList.count()-1])
preconlist.append(new NetCon(nilstim, synlist.o[syni]))
preconi = preconlist.count()-1 //connection index
preconlist.o[preconi].weight = weight_GABA
preconlist.o[preconi].delay = 0
}
}
}
}
// adds the microcircuit connections
// $o1 conVec - where 0 (no connection), 1 (one way), rcpWeightFactor (reciprocated)
proc insertMCcons(){local sitenum,syni,ii,jj localobj TconVec,sl
strdef cmd2,treename
TconVec = $o1
for(ii=0;ii<TconVec.size();ii+=1){
if(TconVec.x[ii]!=0){
for(jj=0;jj<contactsNumE;jj+=1){
if (rd1.repick()<pA){
treename = "apic"
} else {
treename = "dend"
}
sl = locateSites(treename,rd1.repick()*getLongestBranch(treename))
sitenum = int((sl.count()-1)*rd1.repick())
siteVec[0] = sl.o[sitenum].x[0]
siteVec[1] = sl.o[sitenum].x[1]
sprint(cmd2,"access %s[siteVec[0]]",treename)
execute(cmd2,this)
sprint(cmd2,"%s[siteVec[0]] sref = new SectionRef()",treename)
execute(cmd2,this)
sref {
synlist.append(new ProbAMPANMDA2(siteVec[1]))
syni = synlist.count()-1 //synapse index
rList.append(new Random(int(1000000*rd1.repick())))
rList.o[syni].negexp(1)
synlist.o[syni].setRNG(rList.o[syni])
synlist.o[syni].tau_r_AMPA = 0.3
synlist.o[syni].tau_d_AMPA = 3
synlist.o[syni].tau_r_NMDA = 2
synlist.o[syni].tau_d_NMDA = 65
synlist.o[syni].e = 0
synlist.o[syni].Dep = 0
synlist.o[syni].Fac = 0
synlist.o[syni].Use = 0.25
synlist.o[syni].u0 = 0
synlist.o[syni].gmax = TconVec.x[ii] * EsynConductance
}
}
}
}
}
//$o1 list of event time vectors
proc setpretrains(){local i,j,k,indsum localobj preTrainThis,preTrainIndicesThis,sortedIndicesThis
for (i=0;i<syngroupIndexList.count();i+=1) { //The two loops can be combined as syngroupIndexList[0-14] only contain exc. and syngroupIndexList[15-29] only contain inh. syngroup indices
preTrainThis = new Vector()
preTrainIndicesThis = new Vector()
for (j=0;j<syngroupIndexList.o[i].size();j+=1) {
k = syngroupIndexList.o[i].x[j]
preTrainThis.append($o1.o[k])
preTrainIndicesThis.append(new Vector($o1.o[k].size(),j))
}
sortedIndicesThis = new Vector()
sortedIndicesThis = preTrainThis.sortindex()
preTrainList.append(preTrainThis.index(sortedIndicesThis))
preTrainIndexList.append(preTrainIndicesThis.index(sortedIndicesThis))
sortedIndicesThis.resize(0)
}
}
proc queuePreTrains(){
fih = new FInitializeHandler("initPreSynTrain()",this)
}
// sets presynaptic spike events
proc initPreSynTrain(){local syni,ti
for(syni=0;syni<preTrainList.count();syni+=1){
for(ti=0;ti<preTrainList.o[syni].size();ti+=1){
preconlist.o[syni].event(preTrainList.o[syni].x[ti])
}
synlist.o[syni].setVec2(preTrainIndexList.o[syni])
//synlist.o[syni].printVec2()
preTrainList.o[syni].resize(0)
preTrainIndexList.o[syni].resize(0)
}
preTrainList.remove_all()
preTrainIndexList.remove_all()
}
endtemplate TTC