// ALLOCATE VGAT+ SYNAPSES AS BEING OTHER TYPES OF SYNAPSES (e.g., SST+, NPY+)
// This function flags the given SectionRef synapses as being part of the given
// genotype.
//
// $o1: SectionRef instance. The section to implement the flagging.
// $o2: Vector instance. Contains the scaling rule to implement. If the
// density is uniform across the branch (e.g., 0.1 synapses/um2), then
// simply supply as
// foo = new Vector(1); foo.x[0] = 0.1; $o1 = foo
// Conversely, if
// there is spatial variation across the branch (say, 0.1 synapses/um2 in the
// first third, 0.2 synapses/um2 in the second third, and 0.3 synapses/um2
// in the final third), then, supply as
// foo = new Vector(3) ; foo.x[0] = 0.1, foo.x[1] = 0.2;
// foo.x[2] = 0.3 ; $o1 = foo
// $s3: strdef instance. The genotype to flag.
//
// The number of synapses added is returned.
func flagVgatInhibition() {local nDiv,iii,kk,numToConvert localobj theSa,tempToConvert
nDiv = $o2.size()
theSa = new Vector(nDiv) // track SA; eventually overwrite to # of synapses
// identify number of synapses to flag.
for(x,0){
theSa.x[int(x_eff(x)*nDiv)] = theSa.x[int(x_eff(x)*nDiv)] + area(x)
}
theSa.mul($o2) // multiple SA by density.
theSa.floor()
// flag corresponding synapses
for iii=1,nDiv{
numToConvert = theSa.x[iii-1]
tempToConvert = synIndSubset(curSec,numToConvert,-1,(iii-1)/nDiv,iii/nDiv)
for kk=1,tempToConvert.size(){
if(abs(strcmp($s3,"sst"))<0.0001){
synGABA[tempToConvert.x[kk-1]].sst = 1
synGABArect[tempToConvert.x[kk-1]].sst = 1
synGABAB[tempToConvert.x[kk-1]].sst = 1
}
if(abs(strcmp($s3,"npy"))<0.0001){
synGABA[tempToConvert.x[kk-1]].npy = 1
synGABArect[tempToConvert.x[kk-1]].npy = 1
synGABAB[tempToConvert.x[kk-1]].npy = 1
}
if(abs(strcmp($s3,"pv"))<0.0001){
synGABA[tempToConvert.x[kk-1]].pv = 1
synGABArect[tempToConvert.x[kk-1]].pv = 1
synGABAB[tempToConvert.x[kk-1]].pv = 1
}
}
}
return theSa.sum()
}
// DEFINE OBJECTS AND PARAMETERS FOR FLAGGING SYNAPSES
// SST.
objref denSstTuftTerm,denSstTuftPar
denSstTuftTerm = new Vector(3)
denSstTuftTerm.x[0] = 0.0575
denSstTuftTerm.x[1] = 0.0675
denSstTuftTerm.x[2] = 0.1075
denSstTuftPar = new Vector(3)
denSstTuftPar.x[0] = 0.045
denSstTuftPar.x[1] = 0.055
denSstTuftPar.x[2] = 0.05
// NPY.
objref denNpyObl,denNpyOblTemp
denNpyObl = new Vector(3)
denNpyObl.x[0] = 0.022 //0.022
denNpyObl.x[1] = 0.02 // 0.014
denNpyObl.x[2] = 0.01
denNpyOblTemp = new Vector(denNpyObl.size())
denNpyOblBase = 0//0.025 // base amount to be added everywhere after scaling
objref denNpyTrunk,denNpyTrunkTemp
denNpyTrunk = new Vector(1)
denNpyTrunk.x[0] = 0.0425
denNpyTrunkTemp = new Vector(denNpyTrunk.size())
objref denNpySoma
denNpySoma = new Vector(1)
denNpySoma.x[0] = 0 // =0, as do not want somatic inhibition
objref denNpyBasalPrim,denNpyBasalSec,denNpyBasalTerm
denNpyBasalPrim = new Vector(1)
denNpyBasalPrim.x[0] = 0.04
denNpyBasalSec = new Vector(1)
denNpyBasalSec.x[0] = 0.05
denNpyBasalTerm = new Vector(1)
denNpyBasalTerm.x[0] = 0.020
// PV.
objref denPvObl
denPvObl = new Vector(1)
denPvObl.x[0] = 0.008 // changed from 0.004 per Erik's request, 022415, to have ~15 synapses
objref denPvSoma
denPvSoma = new Vector(1)
denPvSoma.x[0] = 0.032
objref denPvBasalPrim,denPvBasalSec,denPvBasalTerm
denPvBasalPrim = new Vector(1)
denPvBasalPrim.x[0] = 0.05
denPvBasalSec = new Vector(1)
denPvBasalSec.x[0] = 0.02
denPvBasalTerm = new Vector(1)
denPvBasalTerm.x[0] = 0.001
// ADD IN SYNAPSES.
// Flag genotypes according to the above defined rules. Wrapped in a proc call
// so that can be re-called as needed, which will redraw synapses from the
// distributions (stochasticity present in the synIndSubset() call in
// flagVgatInhibition() ).
proc seedGenotypes(){local ii,mm,theX
// Clear previous identities.
for ii=0,totVgatAt-1{
synGABA[ii].sst = 0
synGABArect[ii].sst = 0
synGABAB[ii].sst = 0
synGABA[ii].npy = 0
synGABArect[ii].npy = 0
synGABAB[ii].npy = 0
synGABA[ii].pv = 0
synGABArect[ii].pv = 0
synGABAB[ii].pv = 0
}
// SST /////////////////////////////////////////////////////////////////
// Add SST synapses to tuft.
totSstTuft = 0
forsec tuftList {
curSec = new SectionRef()
if(isTerm_id){
numFlagged = flagVgatInhibition(curSec,denSstTuftTerm,"sst")
}else{
numFlagged = flagVgatInhibition(curSec,denSstTuftPar,"sst")
}
totSstTuft += numFlagged
}
print "The total number of SST synapses in tuft is ",totSstTuft
// NPY /////////////////////////////////////////////////////////////////
// Add synapses to oblique.
totNpyObl = 0
forsec obliqueList {
curSec = new SectionRef()
theOblDist = mainbif_dists
scaleFact = (200-theOblDist)/66
if(scaleFact<0){scaleFact=0}
denNpyOblTemp.copy(denNpyObl)
denNpyOblTemp.add(denNpyOblBase)
denNpyOblTemp.mul(scaleFact)
numFlagged = flagVgatInhibition(curSec,denNpyOblTemp,"npy")
totNpyObl+=numFlagged
}
print "The total number of NPY synapses in obliques is ",totNpyObl
// Add in synapses to trunk.
totNpyTrunk = 0
soma.sec {distance()}
forsec primList {
curSec = new SectionRef()
theDist = distance(0.5)
scaleFact = scaleFact = 1-theDist/250
if(scaleFact<0){scaleFact=0}
denNpyTrunkTemp.copy(denNpyTrunk)
denNpyTrunkTemp.mul(scaleFact)
numFlagged = flagVgatInhibition(curSec,denNpyTrunkTemp,"npy")
totNpyTrunk += numFlagged
}
// print "The total number of NPY synapses in trunk is ",totNpyTrunk
// Add synapses to soma.
totNpySoma=0
soma.sec {
curSec = new SectionRef()
numFlagged = flagVgatInhibition(curSec,denNpySoma,"npy")
totNpySoma+=numFlagged
}
print "The total number of NPY synapses at soma is ",totNpySoma
// Add synapses to basals.
totNpyBasal = 0
forsec basalList {
curSec = new SectionRef()
if(isTerm_id){
numFlagged = flagVgatInhibition(curSec,denNpyBasalTerm,"npy")
}else{
if(abs(brOrd_id-1)<0.001){
numFlagged = flagVgatInhibition(curSec,denNpyBasalPrim,"npy")
}else{
if(abs(brOrd_id-2)<0.001){
numFlagged = flagVgatInhibition(curSec,denNpyBasalSec,"npy")
}else{
numFlagged = flagVgatInhibition(curSec,denNpyBasalSec,"npy") // keep as 2ary for right now...
}
}
}
totNpyBasal += numFlagged
}
print "The total number of NPY synapses in basal is ",totNpyBasal
// PV //////////////////////////////////////////////////////////////////
// Add synapses to oblique.
totPvObl = 0
forsec obliqueList {
curSec = new SectionRef()
numFlagged = flagVgatInhibition(curSec,denPvObl,"pv")
totPvObl+=numFlagged
}
print "The total number of PV synapses in obliques is ",totPvObl
// Add synapses to soma.
totPvSoma=0
soma.sec {
curSec = new SectionRef()
numFlagged = flagVgatInhibition(curSec,denPvSoma,"pv")
totPvSoma+=numFlagged
}
print "The total number of PV synapses at soma is ",totPvSoma
// Add synapses to basals.
totPvBasal = 0
forsec basalList {
curSec = new SectionRef()
if(isTerm_id){
numFlagged = flagVgatInhibition(curSec,denPvBasalTerm,"pv")
}else{
if(abs(brOrd_id-1)<0.001){
numFlagged = flagVgatInhibition(curSec,denPvBasalPrim,"pv")
}else{
if(abs(brOrd_id-2)<0.001){
numFlagged = flagVgatInhibition(curSec,denPvBasalSec,"pv")
}else{
numFlagged = flagVgatInhibition(curSec,denPvBasalSec,"pv") // keep as 2ary for right now...
}
}
}
totPvBasal += numFlagged
}
print "The total number of PV synapses in basal is ",totPvBasal
// Update values storing number of each genotype at each synapse.
forall {
for (x,0) {
sstAt_syns(x)=0
npyAt_syns(x)=0
pvAt_syns(x)=0
}
}
for mm=1,totVgatAt{
synGABA[mm-1].get_loc() {
theX = synGABA[mm-1].get_loc()
if(synGABA[mm-1].sst==1){
sstAt_syns(theX) = sstAt_syns(theX)+1
}
if(synGABA[mm-1].npy==1){
npyAt_syns(theX) = npyAt_syns(theX)+1
}
if(synGABA[mm-1].pv==1){
pvAt_syns(theX) = pvAt_syns(theX)+1
}
pop_section()
}
pop_section()
}
}
seedGenotypes() // add in inhibition