/****** These lines are copied from ~/research/Neuron/shared/hoc/syn_params.hoc *******************/
//define these now, redefine when used
objref stimEsyndend[10], connEsyndend[10], Esyndend[10]
objref stimIsyndend[10], connIsyndend[10], Isyndend[10]
objref stimEsynsoma[1], connEsynsoma[1], Esynsoma[1]
objref stimIsynsoma[1], connIsynsoma[1], Isynsoma[1]
objref stimEsynprox[1], connEsynprox[1], Esynprox[1]
objref stimIsynprox[1], connIsynprox[1], Isynprox[1]
objref stimEsyndist[1], connEsyndist[1], Esyndist[1]
objref stimIsyndist[1], connIsyndist[1], Isyndist[1]
EXTHZ = 1 //Hz //10 //
INTHZ = 5.5 //Hz //65 //
NOISE = 1
ISI_EXC = 1000/INTHZ
ISI_INH = 1000/INTHZ
START_EXC = 50
START_INH = 50
//densities of AMPA, GABA are per 100um^2,
GABAaDENDDEN=1//10 //density of GABAa at dendrites
AMPADENDDEN=1//60 //density of AMPA at dendrites
TOTAL_GABAa_g=491.4 //nS
TOTAL_AMPA_g =5898 //nS
SEEDNUM = 1
SEED = 6514302
NSEG= 27
NSEG_SPINE=3
OFFSET=50 //start
ONSET=50 //end of applying events
NOISE=1
CURRINJ=0.03 // current injected
DT = 0.025
TSTOP = 1000 //
PLOTSMS=4
// These parameter values are modified from Traub, Contreras, et al. 2005:
// Single-column thalamocortical network model exhibiting gamma oscillations,
// sleep spindles and epileptogenic bursts. J Neurophysiol 93(4): 2194-2232,
// (2005). PMID: 15525801. See Appendix B, starting on page 2224.
//
// These are from superficial pyramid parameters reported in that reference.
// Note some alternative conductances reported for different connection types,
// e.g. pyramid->pyramid AMPA connections vs. stellate->pyramid connections.
// See Traub et al. to see which connections use which conductance values.
//
// values for PFC model from Amatrudo, Weaver et al (2012)
//
AMPA_tau1 = 0.15 //(ms), time constant for AMPA
AMPA_tau2 = 4 //(ms),
AMPA_Esyn = 0 //reversal potential
AMPA_g=0.00054 // change in conductance
//
// revised AMPA_g for V1 model (low gAMPA) from Amatrudo, Weaver et al (2012)
//
// AMPA_g=0.00017 // (uS) 1.0nS // change in conductance; other connections used 0.25 nS, 0.5 nS
GABAa_g=0.001 // 1.0nS // change in conductance; other connections used 0.05 nS, 0.1 nS
GABAa_Esyn = -81 //reversal potential for superficial pyramids; other neuron types in the model used -75 mV
GABAa_tau1 = 6.0 //
GABAa_tau2 = 6.0 //
/**** update, Jan 23 2012: Jennie found that the amplitude of PSCs for V1 cells are about HALF what they are for PFC.
Mean amplitude: 12.5 pA PFC; 6 pA V1
Rise times were approximately: PFC: 1.6 ms; 1.1 ms for V1
Half width: PFC 7 ms; 5 ms for V1
Decay Time: PFC 7 ms; 5 ms for V1.
So if we use the SAME synaptic parameters for both cells, the model and data differ substantially.
****/
START_EXC = 100
/*********************************************
input $o1 SectionList where synapses are needed
$o2 vector of synapse locations
$3 starting time of excitation
$4 timing between subsequent PSPs
*********************************************/
func AddSynapses() { local cnt, nSyn, DELAY, ST_EXC, stopTime
nSyn = $o2.size()
ST_EXC = $3
DELAY = $4
objref stimEsyndend[nSyn], connEsyndend[nSyn], Esyndend[nSyn]
cnt = 0
forsec $o1 {
Esyndend[cnt] = new Exp2Syn($o2.x[cnt])
Esyndend[cnt].tau1=AMPA_tau1 //--- ms decay time constatn
Esyndend[cnt].tau2=AMPA_tau2 //--- ms decay time constatn
Esyndend[cnt].e=AMPA_Esyn //-- mV reversal potential
stimEsyndend[cnt]= new NetStim($o2.x[cnt])
stimEsyndend[cnt].interval= 1e9
stimEsyndend[cnt].start= $3 + cnt*DELAY
stimEsyndend[cnt].noise=0
stimEsyndend[cnt].number=1
connEsyndend[cnt] = new NetCon(stimEsyndend[cnt],Esyndend[cnt],-55,0,AMPA_g)
cnt += 1
}
stopTime = START_EXC+(nSyn+2)*DELAY
printf("Added %d synapses, final time %d\n",nSyn,START_EXC + nSyn*DELAY)
return stopTime
}
objref sref
/*********************************************
input $1 total number of excitatory apical synapses
$2 total number of excitatory basal synapses
$3 starting time of excitation
$4 timing between subsequent PSPs
$o5 SectionList to which sections are added
$o6 vector of locations
*********************************************/
func AddExcSynapses_byNumber() { local cnt, nSyn, DELAY, ST_EXC, stopTime, SAspacing, totSA, SAcnt, numSec, cntSec, xloc
nASyn = $1
nBSyn = $2
nSyn = nASyn + nBSyn
ST_EXC = $3
DELAY = $4
objref stimEsyndend[nSyn], connEsyndend[nSyn], Esyndend[nSyn]
soma { distance(0) }
$o5 = new SectionList()
$o6 = new Vector()
// apical synapses first
if( nASyn > 0 ) {
totSA = 0
forsec apical {
for(x) {
totSA += area(x)
}
}
SAspacing = totSA / nASyn
printf("Spacing for apical EXC synapses: every %g = %g / %d microns ^ 2\n",SAspacing,totSA,nASyn)
SAcnt = 0
cnt = 0
/*** no excitatory synapses added to soma ***/
numSec = 0
forsec apical { numSec += 1 }
cntSec = 0
forsec apical {
cntSec += 1
for(x) {
SAcnt += area(x)
while( SAcnt >= SAspacing ) {
// add synapse here
sref = new SectionRef()
$o5.append()
$o6.append(x)
//printf("SynLoc[%d] %s(%g) Dist %g\tCutoff %g > %g, total %g out of %g\n",cnt,secname(),x,distance(x), SAcnt,SAspacing,SAcnt+cnt*SAspacing,totSA)
Esyndend[cnt] = new Exp2Syn(x)
Esyndend[cnt].tau1=AMPA_tau1 //--- ms decay time constatn
Esyndend[cnt].tau2=AMPA_tau2 //--- ms decay time constatn
Esyndend[cnt].e=AMPA_Esyn //-- mV reversal potential
stimEsyndend[cnt]= new NetStim(x)
stimEsyndend[cnt].interval= 1e9
stimEsyndend[cnt].start= $3 + cnt*DELAY
stimEsyndend[cnt].noise=0
stimEsyndend[cnt].number=1
connEsyndend[cnt] = new NetCon(stimEsyndend[cnt],Esyndend[cnt],-55,0,AMPA_g)
cnt += 1
SAcnt -= SAspacing
}
}
// if it's the end of the SectionList and we still have a synapse to add, put it here.
if( cnt < nASyn && cntSec == numSec ) {
//printf("---Added %d synapses, need a total of %d\n",cnt,nSyn)
while( cnt < nASyn ) {
xloc = 1
// add synapse here
sref = new SectionRef()
$o5.append()
$o6.append(xloc)
//printf("\t\tSynLoc[%d] %s(%g) Dist %g\n",cnt,secname(),xloc,distance(xloc))
Esyndend[cnt] = new Exp2Syn(xloc)
Esyndend[cnt].tau1=AMPA_tau1 //--- ms decay time constatn
Esyndend[cnt].tau2=AMPA_tau2 //--- ms decay time constatn
Esyndend[cnt].e=AMPA_Esyn //-- mV reversal potential
stimEsyndend[cnt]= new NetStim(xloc)
stimEsyndend[cnt].interval= 1e9
stimEsyndend[cnt].start= $3 + cnt*DELAY
stimEsyndend[cnt].noise=0
stimEsyndend[cnt].number=1
connEsyndend[cnt] = new NetCon(stimEsyndend[cnt],Esyndend[cnt],-55,0,AMPA_g)
cnt += 1
}
}
}
printf("Finished with apical dendrites, added %d synapses, %g SA till next synapse\n",cnt,SAcnt)
} else { printf("No apical synapses added.\n") }
// now basal synapses
if( nBSyn > 0 ) {
totSA = 0
forsec basal {
for(x) {
totSA += area(x)
}
}
SAspacing = totSA / nBSyn
printf("Spacing for basal EXC synapses: every %g = %g / %d microns ^ 2\n",SAspacing,totSA,nBSyn)
SAcnt = 0
// note: we do NOT reinitialize 'cnt' here.
numSec = 0
forsec basal { numSec += 1 }
cntSec = 0
forsec basal {
cntSec += 1
for(x) {
SAcnt += area(x)
while( SAcnt >= SAspacing ) {
// add synapse here
sref = new SectionRef()
$o5.append()
$o6.append(x)
//printf("SynLoc[%d] %s(%g) Dist %g\tCutoff %g > %g, total %g out of %g\n",cnt,secname(),x,distance(x), SAcnt,SAspacing,SAcnt+cnt*SAspacing,totSA)
Esyndend[cnt] = new Exp2Syn(x)
Esyndend[cnt].tau1=AMPA_tau1 //--- ms decay time constatn
Esyndend[cnt].tau2=AMPA_tau2 //--- ms decay time constatn
Esyndend[cnt].e=AMPA_Esyn //-- mV reversal potential
stimEsyndend[cnt]= new NetStim(x)
stimEsyndend[cnt].interval= 1e9
stimEsyndend[cnt].start= $3 + cnt*DELAY
stimEsyndend[cnt].noise=0
stimEsyndend[cnt].number=1
connEsyndend[cnt] = new NetCon(stimEsyndend[cnt],Esyndend[cnt],-55,0,AMPA_g)
cnt += 1
SAcnt -= SAspacing
}
}
// if it's the end of the SectionList and we still have a synapse to add, put it here.
if( cnt < nSyn && cntSec == numSec ) {
//printf("---Added %d synapses, need a total of %d\n",cnt,nSyn)
while( cnt < nSyn ) {
xloc = 1
// add synapse here
sref = new SectionRef()
$o5.append()
$o6.append(xloc)
//printf("\t\tSynLoc[%d] %s(%g) Dist %g\n",cnt,secname(),xloc,distance(xloc))
Esyndend[cnt] = new Exp2Syn(xloc)
Esyndend[cnt].tau1=AMPA_tau1 //--- ms decay time constatn
Esyndend[cnt].tau2=AMPA_tau2 //--- ms decay time constatn
Esyndend[cnt].e=AMPA_Esyn //-- mV reversal potential
stimEsyndend[cnt]= new NetStim(xloc)
stimEsyndend[cnt].interval= 1e9
stimEsyndend[cnt].start= $3 + cnt*DELAY
stimEsyndend[cnt].noise=0
stimEsyndend[cnt].number=1
connEsyndend[cnt] = new NetCon(stimEsyndend[cnt],Esyndend[cnt],-55,0,AMPA_g)
cnt += 1
}
}
}
printf("Finished with basal dendrites, added %d synapses, %g SA till next synapse\n",cnt,SAcnt)
} else { printf("No basal synapses added.\n") }
printf("Added %d excitatory synapses, final time %d\n",nSyn,START_EXC + nSyn*DELAY)
return nSyn
}
/*********************************************
input $1 total number of inhibitory synapses
$2 maximal distance from soma for dendritic inhib synapses
$3 starting time of excitation
$4 timing between subsequent PSPs
$o5 SectionList to which sections are added
$o6 vector of locations
$7 count of sections added
*********************************************/
func AddInhSynapses() { local cnt, nSyn, DELAY, ST_EXC, stopTime, SAspacing, totSA, SAcnt, numSec, cntSec, xloc
nSyn = $1
ST_EXC = $3
DELAY = $4
totSA = countSA($2)
SAspacing = totSA / nSyn
printf("Spacing for INH synapses: every %g = %g / %d microns ^ 2\n",SAspacing,totSA,nSyn)
objref stimIsyndend[nSyn], connIsyndend[nSyn], Isyndend[nSyn]
soma { distance(0) }
SAcnt = 0
cnt = 0
$o5 = new SectionList()
$o6 = new Vector()
forsec "soma" {
for(x) {
SAcnt += area(x)
while( SAcnt >= SAspacing ) {
sref = new SectionRef()
$o5.append()
$o6.append(x)
// add synapse here
//printf("SynLoc %s(%g)\tCutoff %g > %g, total %g out of %g\n",secname(),x,SAcnt,SAspacing,SAcnt+cnt*SAspacing,totSA)
Isyndend[cnt] = new Exp2Syn(x) // PICK UP HERE!!!!
print "\tAdded Exp2Syn"
Isyndend[cnt].tau1=GABAa_tau1 //--- ms decay time constatn
print "\tset tau1"
Isyndend[cnt].tau2=GABAa_tau2 //--- ms decay time constatn
print "\tset tau2"
Isyndend[cnt].e=GABAa_Esyn //-- mV reversal potential
print "\tset Esyn"
stimIsyndend[cnt]= new NetStim(x)
print "\tAdded NetStim"
stimIsyndend[cnt].interval= 1e9
stimIsyndend[cnt].start= $3 + cnt*DELAY
stimIsyndend[cnt].noise=0
stimIsyndend[cnt].number=1
print "\tset NetStim params"
connIsyndend[cnt] = new NetCon(stimIsyndend[cnt],Isyndend[cnt],-55,0,GABAa_g)
print "\tAdded NetCon"
cnt += 1
SAcnt -= SAspacing
}
}
}
printf("Finished with soma, added %d synapses, %g SA till next synapse\n",cnt,SAcnt)
numSec = 0
forsec dendritic { numSec += 1 }
cntSec = 0
forsec dendritic {
cntSec += 1
for(x) {
if( distance(x) > $2 ) continue
SAcnt += area(x)
while( SAcnt >= SAspacing ) {
// add synapse here
sref = new SectionRef()
$o5.append()
$o6.append(x)
//printf("SynLoc[%d] %s(%g) Dist %g\tCutoff %g > %g, total %g out of %g\n",cnt,secname(),x,distance(x), SAcnt,SAspacing,SAcnt+cnt*SAspacing,totSA)
Isyndend[cnt] = new Exp2Syn(x)
Isyndend[cnt].tau1=GABAa_tau1 //--- ms decay time constatn
Isyndend[cnt].tau2=GABAa_tau2 //--- ms decay time constatn
Isyndend[cnt].e=GABAa_Esyn //-- mV reversal potential
stimIsyndend[cnt]= new NetStim(x)
stimIsyndend[cnt].interval= 1e9
stimIsyndend[cnt].start= $3 + cnt*DELAY
stimIsyndend[cnt].noise=0
stimIsyndend[cnt].number=1
connIsyndend[cnt] = new NetCon(stimIsyndend[cnt],Isyndend[cnt],-55,0,GABAa_g)
cnt += 1
SAcnt -= SAspacing
}
}
// if it's the end of the SectionList and we still have a synapse to add, put it here.
if( cnt < nSyn && cntSec == numSec ) {
//printf("---Added %d synapses, need a total of %d\n",cnt,nSyn)
while( cnt < nSyn ) {
xloc = 1
// add synapse here
sref = new SectionRef()
$o5.append()
$o6.append(xloc)
//printf("\t\tSynLoc[%d] %s(%g) Dist %g\n",cnt,secname(),xloc,distance(xloc))
Isyndend[cnt] = new Exp2Syn(xloc)
Isyndend[cnt].tau1=GABAa_tau1 //--- ms decay time constatn
Isyndend[cnt].tau2=GABAa_tau2 //--- ms decay time constatn
Isyndend[cnt].e=GABAa_Esyn //-- mV reversal potential
stimIsyndend[cnt]= new NetStim(xloc)
stimIsyndend[cnt].interval= 1e9
stimIsyndend[cnt].start= $3 + cnt*DELAY
stimIsyndend[cnt].noise=0
stimIsyndend[cnt].number=1
connIsyndend[cnt] = new NetCon(stimIsyndend[cnt],Isyndend[cnt],-55,0,GABAa_g)
cnt += 1
}
}
}
printf("Finished with dendrites, added %d synapses, %g SA till next synapse\n",cnt,SAcnt)
stopTime = START_EXC+(nSyn+2)*DELAY
printf("Added %d inhibitory synapses, final time %d\n",nSyn,START_EXC + nSyn*DELAY)
$7 = cnt
return stopTime
}
/*********************************************
input $1 total number of inhibitory synapses
$2 maximal distance from soma for dendritic inhib synapses
$3 starting time of excitation
$4 timing between subsequent PSPs
$o5 SectionList to which sections are added
$o6 vector of locations
$7 count of sections added
$8 proportion of all synapses to distribute proximally
Distribute a proportion of the total number of inhibitory synapse close to
the soma. Then, distribute the rest uniformly across the whole soma and
dendrites.
*********************************************/
func AddInhSynapses_ProxAndUni() { local cnt, nSyn, DELAY, ST_EXC, stopTime, SAspacing, totSA, prxSA, SAcnt, numSec, cntSec, xloc, nClose, nFar
nSyn = $1
ST_EXC = $3
DELAY = $4
nClose = int(nSyn * $8 + 0.5 )
nFar = nSyn - nClose
objref stimIsyndend[nSyn], connIsyndend[nSyn], Isyndend[nSyn]
$o5 = new SectionList()
$o6 = new Vector()
soma { distance(0) }
numSec = 0
forsec dendritic { numSec += 1 }
/**** STEP 1: distribute a proportion the synapses on the soma & proximal dendrites. ****/
prxSA = countSA($2)
SAspacing = prxSA / nClose
printf("Spacing for proximal INH synapses: every %g = %g / %d microns ^ 2\n",SAspacing,prxSA,nClose)
SAcnt = 0
cnt = 0
forsec "soma" {
for(x) {
SAcnt += area(x)
while( SAcnt >= SAspacing ) {
sref = new SectionRef()
$o5.append()
$o6.append(x)
// add synapse here
//printf("SOMA: SynLoc %s(%g)\tCutoff %g > %g, total %g out of %g\n",secname(),x,SAcnt,SAspacing,SAcnt+cnt*SAspacing,totSA)
Isyndend[cnt] = new Exp2Syn(x)
Isyndend[cnt].tau1=GABAa_tau1 //--- ms decay time constatn
Isyndend[cnt].tau2=GABAa_tau2 //--- ms decay time constatn
Isyndend[cnt].e=GABAa_Esyn //-- mV reversal potential
stimIsyndend[cnt]= new NetStim(x)
stimIsyndend[cnt].interval= 1e9
stimIsyndend[cnt].start= $3 + cnt*DELAY
stimIsyndend[cnt].noise=0
stimIsyndend[cnt].number=1
connIsyndend[cnt] = new NetCon(stimIsyndend[cnt],Isyndend[cnt],-55,0,GABAa_g)
cnt += 1
SAcnt -= SAspacing
}
}
}
printf("Finished with soma, added %d synapses, %g SA till next synapse\n",cnt,SAcnt)
cntSec = 0
forsec dendritic {
cntSec += 1
for(x) {
if( distance(x) > $2 ) continue
SAcnt += area(x)
while( SAcnt >= SAspacing ) {
// add synapse here
sref = new SectionRef()
$o5.append()
$o6.append(x)
//printf("PROX: SynLoc[%d] %s(%g) Dist %g\tCutoff %g > %g, total %g out of %g\n",cnt,secname(),x,distance(x), SAcnt,SAspacing,SAcnt+cnt*SAspacing,totSA)
Isyndend[cnt] = new Exp2Syn(x)
Isyndend[cnt].tau1=GABAa_tau1 //--- ms decay time constatn
Isyndend[cnt].tau2=GABAa_tau2 //--- ms decay time constatn
Isyndend[cnt].e=GABAa_Esyn //-- mV reversal potential
stimIsyndend[cnt]= new NetStim(x)
stimIsyndend[cnt].interval= 1e9
stimIsyndend[cnt].start= $3 + cnt*DELAY
stimIsyndend[cnt].noise=0
stimIsyndend[cnt].number=1
connIsyndend[cnt] = new NetCon(stimIsyndend[cnt],Isyndend[cnt],-55,0,GABAa_g)
cnt += 1
SAcnt -= SAspacing
}
}
}
printf("Finished with proximal dendrites, added %d synapses, %g SA till next synapse\n",cnt,SAcnt)
/**** STEP 2: distribute remaining synapses througout medial and distal dendrites. ****/
if( nFar > 0 ) {
totSA = countSA(1e9)
SAspacing = (totSA - prxSA ) / nFar
printf("Spacing for distal INH synapses: every %g = %g / %d microns ^ 2\n",SAspacing,(totSA-prxSA),nFar)
SAcnt = 0
cntSec = 0
forsec dendritic {
cntSec += 1
for(x) {
if( distance(x) <= $2 ) continue
SAcnt += area(x)
while( SAcnt >= SAspacing ) {
// add synapse here
sref = new SectionRef()
$o5.append()
$o6.append(x)
//printf("DISTAL: SynLoc[%d] %s(%g) Dist %g\tCutoff %g > %g, total %g out of %g\n",cnt,secname(),x,distance(x), SAcnt,SAspacing,SAcnt+cnt*SAspacing,(totSA-prxSA))
Isyndend[cnt] = new Exp2Syn(x)
Isyndend[cnt].tau1=GABAa_tau1 //--- ms decay time constatn
Isyndend[cnt].tau2=GABAa_tau2 //--- ms decay time constatn
Isyndend[cnt].e=GABAa_Esyn //-- mV reversal potential
stimIsyndend[cnt]= new NetStim(x)
stimIsyndend[cnt].interval= 1e9
stimIsyndend[cnt].start= $3 + cnt*DELAY
stimIsyndend[cnt].noise=0
stimIsyndend[cnt].number=1
connIsyndend[cnt] = new NetCon(stimIsyndend[cnt],Isyndend[cnt],-55,0,GABAa_g)
cnt += 1
SAcnt -= SAspacing
}
}
// if it's the end of the SectionList and we still have a synapse to add, put it here.
if( cnt < nSyn && cntSec == numSec ) {
//printf("---Added %d synapses, need a total of %d\n",cnt,nSyn)
while( cnt < nSyn ) {
xloc = 1
// add synapse here
sref = new SectionRef()
$o5.append()
$o6.append(xloc)
//printf("\t\tSynLoc[%d] END %s(%g) Dist %g\n",cnt,secname(),xloc,distance(xloc))
Isyndend[cnt] = new Exp2Syn(xloc)
Isyndend[cnt].tau1=GABAa_tau1 //--- ms decay time constatn
Isyndend[cnt].tau2=GABAa_tau2 //--- ms decay time constatn
Isyndend[cnt].e=GABAa_Esyn //-- mV reversal potential
stimIsyndend[cnt]= new NetStim(xloc)
stimIsyndend[cnt].interval= 1e9
stimIsyndend[cnt].start= $3 + cnt*DELAY
stimIsyndend[cnt].noise=0
stimIsyndend[cnt].number=1
connIsyndend[cnt] = new NetCon(stimIsyndend[cnt],Isyndend[cnt],-55,0,GABAa_g)
cnt += 1
}
}
}
printf("Finished with dendrites, added %d synapses, %g SA till next synapse\n",cnt,SAcnt)
}
stopTime = START_EXC+(nSyn+2)*DELAY
printf("Added %d inhibitory synapses, final time %d\n",nSyn,START_EXC + nSyn*DELAY)
$7 = cnt
return stopTime
}
/*********************************************
input $1 base density of inhibitory synapses
$2 maximal distance from soma for dendritic inhib synapses
$3 starting time of excitation
$4 timing between subsequent PSPs
$o5 SectionList to which sections are added
$o6 vector of locations
$7 count of sections added
$8 inhib synapse density on proximal spines
$9 inhib synapse density on distal spines
Specify a baseline density of inhibitory synapse throughout dendrites, and
extra density terms to represent inhib synapses that would have been on
dendritic spines. Distribute these uniformly in their respective regions.
*********************************************/
func AddInhSynapses_ProxDist_byDensity() { local cnt, nSyn, DELAY, ST_EXC, stopTime, Lspacing, totSA, prxSA, Lcnt, numSec, cntSec, xloc, nClose, nFar, baseDens, prxSpDens, dstSpDens, totL, prxL, dstL, lastX
baseDens = $1
ST_EXC = $3
DELAY = $4
prxL = find_totLen($2)
totL = find_totLen(1e9)
dstL = totL - prxL
prxSpDens = $8
dstSpDens = $9
nClose = int(prxL * (baseDens + prxSpDens) + 0.5 )
nFar = int(dstL * (baseDens + dstSpDens) + 0.5 )
nSyn = nClose + nFar
printf("Inh syn density: %g base/t%g prox Spines/t%g dist Spines\n",baseDens,prxSpDens,dstSpDens)
printf("Want a total of %d synapses: %d close and %d far from soma.\n",nSyn,nClose,nFar)
objref stimIsyndend[nSyn], connIsyndend[nSyn], Isyndend[nSyn]
$o5 = new SectionList()
$o6 = new Vector()
soma { distance(0) }
numSec = 0
forsec dendritic { numSec += 1 }
/**** STEP 1: distribute a proportion the synapses on the soma & proximal dendrites. ****/
Lspacing = prxL / nClose
printf("Spacing for proximal INH synapses: every %g = %g / %d microns of length\n",Lspacing,prxL,nClose)
Lcnt = 0
cnt = 0
forsec "soma" {
for(x) {
if( x==0 || x == 1 ) continue
Lcnt += L / nseg
while( Lcnt >= Lspacing ) {
sref = new SectionRef()
$o5.append()
$o6.append(x)
// add synapse here
//printf("SOMA: SynLoc %s(%g)\tCutoff %g > %g, total %g out of %g\n",secname(),x,Lcnt,Lspacing,Lcnt+cnt*Lspacing,totL)
Isyndend[cnt] = new Exp2Syn(x)
Isyndend[cnt].tau1=GABAa_tau1 //--- ms decay time constatn
Isyndend[cnt].tau2=GABAa_tau2 //--- ms decay time constatn
Isyndend[cnt].e=GABAa_Esyn //-- mV reversal potential
stimIsyndend[cnt]= new NetStim(x)
stimIsyndend[cnt].interval= 1e9
stimIsyndend[cnt].start= $3 + cnt*DELAY
stimIsyndend[cnt].noise=0
stimIsyndend[cnt].number=1
connIsyndend[cnt] = new NetCon(stimIsyndend[cnt],Isyndend[cnt],-55,0,GABAa_g)
cnt += 1
Lcnt -= Lspacing
}
}
}
printf("Finished with soma, added %d synapses, %g L till next synapse\n",cnt,Lcnt)
cntSec = 0
forsec dendritic {
cntSec += 1
for(x) {
if( distance(x) > $2 ) { continue }
//if( distance(x) > $2 ) { printf("---- Skip %s\t",secname() ) continue }
if( x==0 || x==1 ) continue
Lcnt += L / nseg
//printf("\n\t+++\t%s(%g) L add %g -> Lcnt %g\n",secname(),x,L/nseg,Lcnt)
while( Lcnt >= Lspacing ) {
if( cnt > nClose ) { printf("\ttrying to add synapse %d\n",cnt) }
// add synapse here
sref = new SectionRef()
$o5.append()
$o6.append(x)
//printf("PROX: SynLoc[%d] %s(%g) Dist %g\tCutoff %g > %g, total %g out of %g\n",cnt,secname(),x,distance(x), Lcnt,Lspacing,Lcnt+cnt*Lspacing,prxL)
Isyndend[cnt] = new Exp2Syn(x)
Isyndend[cnt].tau1=GABAa_tau1 //--- ms decay time constatn
Isyndend[cnt].tau2=GABAa_tau2 //--- ms decay time constatn
Isyndend[cnt].e=GABAa_Esyn //-- mV reversal potential
stimIsyndend[cnt]= new NetStim(x)
stimIsyndend[cnt].interval= 1e9
stimIsyndend[cnt].start= $3 + cnt*DELAY
stimIsyndend[cnt].noise=0
stimIsyndend[cnt].number=1
connIsyndend[cnt] = new NetCon(stimIsyndend[cnt],Isyndend[cnt],-55,0,GABAa_g)
cnt += 1
Lcnt -= Lspacing
}
}
}
printf("Finished with proximal dendrites, added %d synapses, %g length till next synapse\n",cnt,Lcnt)
/**** STEP 2: distribute remaining synapses througout medial and distal dendrites. ****/
//Lcnt = 0
if( nFar > 0 ) { // continue here.
Lspacing = dstL / nFar
printf("Spacing for distal INH synapses: every %g = %g / %d microns of length\n",Lspacing,dstL,nFar)
//Lcnt = 0
cntSec = 0
forsec dendritic {
cntSec += 1
for(x) {
if( x==0 || x==1 ) continue
if( distance(x) <= $2 ) continue
Lcnt += L / nseg
while( Lcnt >= Lspacing && cnt < nSyn ) {
// add synapse here
sref = new SectionRef()
$o5.append()
$o6.append(x)
//printf("DISTAL: SynLoc[%d] %s(%g) Dist %g\tCutoff %g > %g, total %g out of %g\n",cnt,secname(),x,distance(x), Lcnt,Lspacing,Lcnt+cnt*Lspacing,dstL)
Isyndend[cnt] = new Exp2Syn(x)
Isyndend[cnt].tau1=GABAa_tau1 //--- ms decay time constatn
Isyndend[cnt].tau2=GABAa_tau2 //--- ms decay time constatn
Isyndend[cnt].e=GABAa_Esyn //-- mV reversal potential
stimIsyndend[cnt]= new NetStim(x)
stimIsyndend[cnt].interval= 1e9
stimIsyndend[cnt].start= $3 + cnt*DELAY
stimIsyndend[cnt].noise=0
stimIsyndend[cnt].number=1
connIsyndend[cnt] = new NetCon(stimIsyndend[cnt],Isyndend[cnt],-55,0,GABAa_g)
cnt += 1
Lcnt -= Lspacing
}
}
// if it's the end of the SectionList and we still have a synapse to add, put it here.
if( cnt < nSyn && cntSec == numSec ) {
//printf("---Added %d synapses, need a total of %d\n",cnt,nSyn)
while( cnt < nSyn ) {
xloc = 1
// add synapse here
sref = new SectionRef()
$o5.append()
$o6.append(xloc)
//printf("\t\tSynLoc[%d] END %s(%g) Dist %g\n",cnt,secname(),xloc,distance(xloc))
Isyndend[cnt] = new Exp2Syn(xloc)
Isyndend[cnt].tau1=GABAa_tau1 //--- ms decay time constatn
Isyndend[cnt].tau2=GABAa_tau2 //--- ms decay time constatn
Isyndend[cnt].e=GABAa_Esyn //-- mV reversal potential
stimIsyndend[cnt]= new NetStim(xloc)
stimIsyndend[cnt].interval= 1e9
stimIsyndend[cnt].start= $3 + cnt*DELAY
stimIsyndend[cnt].noise=0
stimIsyndend[cnt].number=1
connIsyndend[cnt] = new NetCon(stimIsyndend[cnt],Isyndend[cnt],-55,0,GABAa_g)
cnt += 1
}
}
}
printf("Finished with dendrites, added %d synapses, %g length till next synapse\n",cnt,Lcnt)
}
stopTime = START_EXC+(nSyn+2)*DELAY
printf("Added %d inhibitory synapses, final time %d\n",nSyn,START_EXC + nSyn*DELAY)
$7 = cnt
return nSyn
//return stopTime
}
/*********************************************
input $1 base density of inhibitory synapses
$2 maximal distance from soma for dendritic inhib synapses
$3 starting time of excitation
$4 timing between subsequent PSPs
$o5 SectionList to which sections are added
$o6 vector of locations
$7 count of sections added
$8 inhib synapse density on proximal spines
$9 inhib synapse density on distal spines
$10 if 0, do only apical; if 1, do only basal; else do both.
Specify a baseline density of inhibitory synapse throughout dendrites, and
extra density terms to represent inhib synapses that would have been on
dendritic spines. Distribute these uniformly in their respective regions.
*********************************************/
func AddInhSynapses_ProxDist_byDensityAB() { local cnt, nSyn, DELAY, ST_EXC, stopTime, Lspacing, totSA, prxSA, Lcnt, numSec, cntSec, xloc, nClose, nFar, baseDens, prxSpDens, dstSpDens, totL, prxL, dstL, lastX
baseDens = $1
ST_EXC = $3
DELAY = $4
if( $10 == 0 ) {
prxL = find_totApicLen($2)
totL = find_totApicLen(1e9)
} else {
if( $10 == 1 ) {
prxL = find_totBasLen($2)
totL = find_totBasLen(1e9)
} else {
prxL = find_totLen($2)
totL = find_totLen(1e9)
}
}
dstL = totL - prxL
prxSpDens = $8
dstSpDens = $9
nClose = int(prxL * (baseDens + prxSpDens) + 0.5 )
nFar = int(dstL * (baseDens + dstSpDens) + 0.5 )
nSyn = nClose + nFar
printf("Inh syn density: %g base/t%g prox Spines/t%g dist Spines\n",baseDens,prxSpDens,dstSpDens)
printf("Want a total of %d synapses: %d close and %d far from soma.\n",nSyn,nClose,nFar)
objref stimIsyndend[nSyn], connIsyndend[nSyn], Isyndend[nSyn]
$o5 = new SectionList()
$o6 = new Vector()
soma { distance(0) }
numSec = 0
if( $10 == 0 ) { forsec apical { numSec += 1 }
} else {
if( $10 ==1 ) { forsec basal { numSec += 1 }
} else {
forsec dendritic { numSec += 1 }
}
}
/**** STEP 1: distribute a proportion the synapses on the soma & proximal dendrites. ****/
Lspacing = prxL / nClose
printf("Spacing for proximal INH synapses: every %g = %g / %d microns of length\n",Lspacing,prxL,nClose)
Lcnt = 0
cnt = 0
/**** this section is the same regardless of whether we consider apical or basal only, or all dendrites ****/
forsec "soma" {
for(x) {
if( x==0 || x == 1 ) continue
Lcnt += L / nseg
while( Lcnt >= Lspacing ) {
sref = new SectionRef()
$o5.append()
$o6.append(x)
// add synapse here
//printf("SOMA: SynLoc %s(%g)\tCutoff %g > %g, total %g out of %g\n",secname(),x,Lcnt,Lspacing,Lcnt+cnt*Lspacing,totL)
Isyndend[cnt] = new Exp2Syn(x)
Isyndend[cnt].tau1=GABAa_tau1 //--- ms decay time constatn
Isyndend[cnt].tau2=GABAa_tau2 //--- ms decay time constatn
Isyndend[cnt].e=GABAa_Esyn //-- mV reversal potential
stimIsyndend[cnt]= new NetStim(x)
stimIsyndend[cnt].interval= 1e9
stimIsyndend[cnt].start= $3 + cnt*DELAY
stimIsyndend[cnt].noise=0
stimIsyndend[cnt].number=1
connIsyndend[cnt] = new NetCon(stimIsyndend[cnt],Isyndend[cnt],-55,0,GABAa_g)
cnt += 1
Lcnt -= Lspacing
}
}
}
printf("Finished with soma, added %d synapses, %g L till next synapse\n",cnt,Lcnt)
cntSec = 0
if( $10 != 1 ) {
forsec apical {
cntSec += 1
for(x) {
if( distance(x) > $2 ) { continue }
if( x==0 || x==1 ) continue
Lcnt += L / nseg
while( Lcnt >= Lspacing ) {
if( cnt > nClose ) { printf("\ttrying to add synapse %d\n",cnt) }
// add synapse here
sref = new SectionRef()
$o5.append()
$o6.append(x)
Isyndend[cnt] = new Exp2Syn(x)
Isyndend[cnt].tau1=GABAa_tau1 //--- ms decay time constatn
Isyndend[cnt].tau2=GABAa_tau2 //--- ms decay time constatn
Isyndend[cnt].e=GABAa_Esyn //-- mV reversal potential
stimIsyndend[cnt]= new NetStim(x)
stimIsyndend[cnt].interval= 1e9
stimIsyndend[cnt].start= $3 + cnt*DELAY
stimIsyndend[cnt].noise=0
stimIsyndend[cnt].number=1
connIsyndend[cnt] = new NetCon(stimIsyndend[cnt],Isyndend[cnt],-55,0,GABAa_g)
cnt += 1
Lcnt -= Lspacing
}
}
}
}
if( $10 != 0 ) {
forsec basal {
cntSec += 1
for(x) {
if( distance(x) > $2 ) { continue }
if( x==0 || x==1 ) continue
Lcnt += L / nseg
while( Lcnt >= Lspacing ) {
if( cnt > nClose ) { printf("\ttrying to add synapse %d\n",cnt) }
// add synapse here
sref = new SectionRef()
$o5.append()
$o6.append(x)
Isyndend[cnt] = new Exp2Syn(x)
Isyndend[cnt].tau1=GABAa_tau1 //--- ms decay time constatn
Isyndend[cnt].tau2=GABAa_tau2 //--- ms decay time constatn
Isyndend[cnt].e=GABAa_Esyn //-- mV reversal potential
stimIsyndend[cnt]= new NetStim(x)
stimIsyndend[cnt].interval= 1e9
stimIsyndend[cnt].start= $3 + cnt*DELAY
stimIsyndend[cnt].noise=0
stimIsyndend[cnt].number=1
connIsyndend[cnt] = new NetCon(stimIsyndend[cnt],Isyndend[cnt],-55,0,GABAa_g)
cnt += 1
Lcnt -= Lspacing
}
}
}
}
printf("Finished with proximal dendrites, added %d synapses, %g length till next synapse\n",cnt,Lcnt)
/**** STEP 2: distribute remaining synapses througout medial and distal dendrites. ****/
if( nFar > 0 ) { // continue here.
Lspacing = dstL / nFar
printf("Spacing for distal INH synapses: every %g = %g / %d microns of length\n",Lspacing,dstL,nFar)
cntSec = 0
if( $10 == 0 ) {
forsec apical {
cntSec += 1
for(x) {
if( x==0 || x==1 ) continue
if( distance(x) <= $2 ) continue
Lcnt += L / nseg
while( Lcnt >= Lspacing && cnt < nSyn ) {
// add synapse here
sref = new SectionRef()
$o5.append()
$o6.append(x)
Isyndend[cnt] = new Exp2Syn(x)
Isyndend[cnt].tau1=GABAa_tau1 //--- ms decay time constatn
Isyndend[cnt].tau2=GABAa_tau2 //--- ms decay time constatn
Isyndend[cnt].e=GABAa_Esyn //-- mV reversal potential
stimIsyndend[cnt]= new NetStim(x)
stimIsyndend[cnt].interval= 1e9
stimIsyndend[cnt].start= $3 + cnt*DELAY
stimIsyndend[cnt].noise=0
stimIsyndend[cnt].number=1
connIsyndend[cnt] = new NetCon(stimIsyndend[cnt],Isyndend[cnt],-55,0,GABAa_g)
cnt += 1
Lcnt -= Lspacing
}
}
// if it's the end of the SectionList and we still have a synapse to add, put it here.
if( cnt < nSyn && cntSec == numSec ) {
while( cnt < nSyn ) {
xloc = 1
// add synapse here
sref = new SectionRef()
$o5.append()
$o6.append(xloc)
Isyndend[cnt] = new Exp2Syn(xloc)
Isyndend[cnt].tau1=GABAa_tau1 //--- ms decay time constatn
Isyndend[cnt].tau2=GABAa_tau2 //--- ms decay time constatn
Isyndend[cnt].e=GABAa_Esyn //-- mV reversal potential
stimIsyndend[cnt]= new NetStim(xloc)
stimIsyndend[cnt].interval= 1e9
stimIsyndend[cnt].start= $3 + cnt*DELAY
stimIsyndend[cnt].noise=0
stimIsyndend[cnt].number=1
connIsyndend[cnt] = new NetCon(stimIsyndend[cnt],Isyndend[cnt],-55,0,GABAa_g)
cnt += 1
}
}
}
}
if( $10 == 1 ) {
forsec basal {
cntSec += 1
for(x) {
if( x==0 || x==1 ) continue
if( distance(x) <= $2 ) continue
Lcnt += L / nseg
while( Lcnt >= Lspacing && cnt < nSyn ) {
// add synapse here
sref = new SectionRef()
$o5.append()
$o6.append(x)
Isyndend[cnt] = new Exp2Syn(x)
Isyndend[cnt].tau1=GABAa_tau1 //--- ms decay time constatn
Isyndend[cnt].tau2=GABAa_tau2 //--- ms decay time constatn
Isyndend[cnt].e=GABAa_Esyn //-- mV reversal potential
stimIsyndend[cnt]= new NetStim(x)
stimIsyndend[cnt].interval= 1e9
stimIsyndend[cnt].start= $3 + cnt*DELAY
stimIsyndend[cnt].noise=0
stimIsyndend[cnt].number=1
connIsyndend[cnt] = new NetCon(stimIsyndend[cnt],Isyndend[cnt],-55,0,GABAa_g)
cnt += 1
Lcnt -= Lspacing
}
}
// if it's the end of the SectionList and we still have a synapse to add, put it here.
if( cnt < nSyn && cntSec == numSec ) {
while( cnt < nSyn ) {
xloc = 1
// add synapse here
sref = new SectionRef()
$o5.append()
$o6.append(xloc)
Isyndend[cnt] = new Exp2Syn(xloc)
Isyndend[cnt].tau1=GABAa_tau1 //--- ms decay time constatn
Isyndend[cnt].tau2=GABAa_tau2 //--- ms decay time constatn
Isyndend[cnt].e=GABAa_Esyn //-- mV reversal potential
stimIsyndend[cnt]= new NetStim(xloc)
stimIsyndend[cnt].interval= 1e9
stimIsyndend[cnt].start= $3 + cnt*DELAY
stimIsyndend[cnt].noise=0
stimIsyndend[cnt].number=1
connIsyndend[cnt] = new NetCon(stimIsyndend[cnt],Isyndend[cnt],-55,0,GABAa_g)
cnt += 1
}
}
}
}
if( ($10 != 0 ) && ($10 != 1) ) {
forsec dendritic {
cntSec += 1
for(x) {
if( x==0 || x==1 ) continue
if( distance(x) <= $2 ) continue
Lcnt += L / nseg
while( Lcnt >= Lspacing && cnt < nSyn ) {
// add synapse here
sref = new SectionRef()
$o5.append()
$o6.append(x)
Isyndend[cnt] = new Exp2Syn(x)
Isyndend[cnt].tau1=GABAa_tau1 //--- ms decay time constatn
Isyndend[cnt].tau2=GABAa_tau2 //--- ms decay time constatn
Isyndend[cnt].e=GABAa_Esyn //-- mV reversal potential
stimIsyndend[cnt]= new NetStim(x)
stimIsyndend[cnt].interval= 1e9
stimIsyndend[cnt].start= $3 + cnt*DELAY
stimIsyndend[cnt].noise=0
stimIsyndend[cnt].number=1
connIsyndend[cnt] = new NetCon(stimIsyndend[cnt],Isyndend[cnt],-55,0,GABAa_g)
cnt += 1
Lcnt -= Lspacing
}
}
// if it's the end of the SectionList and we still have a synapse to add, put it here.
if( cnt < nSyn && cntSec == numSec ) {
while( cnt < nSyn ) {
xloc = 1
// add synapse here
sref = new SectionRef()
$o5.append()
$o6.append(xloc)
Isyndend[cnt] = new Exp2Syn(xloc)
Isyndend[cnt].tau1=GABAa_tau1 //--- ms decay time constatn
Isyndend[cnt].tau2=GABAa_tau2 //--- ms decay time constatn
Isyndend[cnt].e=GABAa_Esyn //-- mV reversal potential
stimIsyndend[cnt]= new NetStim(xloc)
stimIsyndend[cnt].interval= 1e9
stimIsyndend[cnt].start= $3 + cnt*DELAY
stimIsyndend[cnt].noise=0
stimIsyndend[cnt].number=1
connIsyndend[cnt] = new NetCon(stimIsyndend[cnt],Isyndend[cnt],-55,0,GABAa_g)
cnt += 1
}
}
}
}
printf("Finished with dendrites, added %d synapses, %g length till next synapse\n",cnt,Lcnt)
}
stopTime = START_EXC+(nSyn+2)*DELAY
printf("Added %d inhibitory synapses, final time %d\n",nSyn,START_EXC + nSyn*DELAY)
$7 = cnt
return nSyn
}
proc SynapsesOff() { local i
for i = 0, $1-1 {
stimEsyndend[i].start = 1e9
}
}
proc SynapseOn() {
stimEsyndend[$1].start = $2
}
/********
input $1 value of gAMPA
$2 number of synapses
********/
proc adjust_gAMPA() { local i
for i = 0, $2-1 {
connEsyndend[i].weight = $1
}
}
/********
input $1 value of gAMPA
$2 number of synapses
********/
proc adjust_gGABA() { local i
for i = 0, $2-1 {
connIsyndend[i].weight = $1
}
}
/********
input $1 value of tau1 for Exp2Syn
$2 number of synapses
********/
proc adjust_tau1() { local i
for i = 0, $2-1 {
Esyndend[i].tau1 = $1
}
}
/********
input $1 value of tau1 for Exp2Syn
$2 number of synapses
********/
proc adjust_tau2() { local i
for i = 0, $2-1 {
Esyndend[i].tau2 = $1
}
}
/********
input $1 value of tau1 for Exp2Syn
$2 number of synapses
********/
proc adjust_Itau1() { local i
for i = 0, $2-1 {
Isyndend[i].tau1 = $1
}
}
/********
input $1 value of tau1 for Exp2Syn
$2 number of synapses
********/
proc adjust_Itau2() { local i
for i = 0, $2-1 {
Isyndend[i].tau2 = $1
}
}
/******************
input $1 max distance to count, or -1 if full dendrites only should be counted
******************/
func countSA() { local sa
sa = 0
if( $1 >= 0 ) { forsec "soma" for(x) sa += area(x) }
forsec dendritic {
for(x) {
if( $1< 0 || distance(x) <= $1 ) {
//printf("%s\t%g\t%g\t%g\n",secname(), x, distance(x), area(x) )
sa += area(x)
}
}
}
return sa
}
