//////////////////////////////////////////////////
// Instrumentation, i.e. stimulation and recording
//////////////////////////////////////////////////
// setup activity in EC stims
proc mkEC() {local i, necs localobj cstim, rs
EClist = new Vector()
necs = 0
print "Make EC input..."
for i=0, cells.count-1 {
gid = gidvec.x[i] // id of cell
if (gid >= iECL3180 && gid < iECL3180+nECL3180) { // appropriate target cell
// create cue stimulus
cstim = cells.object(i).stim
//cstim.number = ECL3180NUM
//cstim.start = ECL3180START
//cstim.interval = ECL3180INT
//cstim.noise = ECL3180NOISE
//cstim.burstint = ECL3180BINT
//cstim.burstlen = ECL3180BLEN
cstim.number = ECL3180NUM
cstim.start = ECL3180START
cstim.interval = ECL3180INT
cstim.noise = ECL3180NOISE
}
if (gid >= iECL3360 && gid < iECL3360+nECL3360) { // appropriate target cell
// create cue stimulus
cstim = cells.object(i).stim
rs = ranlist.object(i)
//cstim.number = ECL3360NUM
//cstim.start = ECL3360START
//cstim.interval = ECL3360INT
//cstim.noise = ECL3360NOISE
//cstim.burstint = ECL3360BINT
//cstim.burstlen = ECL3360BLEN
cstim.number = ECL3360NUM
cstim.start = ECL3360START
cstim.interval = ECL3360INT
cstim.noise = ECL3360NOISE
}
if (gid >= iECL2180 && gid < iECL2180+nECL2180) { // appropriate target cell
// create cue stimulus
cstim = cells.object(i).stim
//cstim.number = ECL2180NUM
//cstim.start = ECL2180START
//cstim.interval = ECL2180INT
//cstim.noise = ECL2180NOISE
//cstim.burstint = ECL2180BINT
//cstim.burstlen = ECL2180BLEN
cstim.number = ECL2180NUM
cstim.start = ECL2180START
cstim.interval = ECL2180INT
cstim.noise = ECL2180NOISE
}
if (gid >= iECL2360 && gid < iECL2360+nECL2360) { // appropriate target cell
// create cue stimulus
cstim = cells.object(i).stim
rs = ranlist.object(i)
//cstim.number = ECL2360NUM
//cstim.start = ECL2360START
//cstim.interval = ECL2360INT
//cstim.noise = ECL2360NOISE
//cstim.burstint = ECL2360BINT
//cstim.burstlen = ECL2360BLEN
cstim.number = ECL2360NUM
cstim.start = ECL2360START
cstim.interval = ECL2360INT
cstim.noise = ECL2360NOISE
// Use the gid-specific random generator so random streams are
// independent of where and how many stims there are.
cstim.noiseFromRandom(rs.r)
rs.r.normal(0, 1)
rs.start()
EClist.append(i)
necs += 1
}
}
}
objref cue, fp
// setup activity pattern in input cue stims
proc mkcueECL2180() {local i, j, ncue localobj cstim, target, rs
print "Make cue (ECL2180) input..."
cuelistECL2180 = new Vector()
// open patterns file
fp = new File($s1)
fp.ropen()
cue = new Vector(nECL2180)
cue.scanf(fp, $2, $4) // read pattern
// cue.printf()
fp.close()
ncue = 0
// find active cells in pattern
for i=0, cue.size()-1 {
//if (!pc.gid_exists(i+iECL2180)) { continue }
if (ncue <= SPATT*$3) { // fraction of active cells in cue
if (cue.x[i] == 1) {
print "Cue cell ", i
//cstim = pc.gid2cell(i+iECL2180)
cstim = cells.object(i+iECL2180).stim
for j=0, cells.count-1 {
if (gidvec.x[j] == i+iECL2180) {break} // find cell index
}
rs = ranlist.object(j)
// create cue stimulus
//cstim.number = ECL2180NUM
//cstim.start = ECL2180START
//cstim.interval = ECL2180INT
//cstim.noise = ECL2180NOISE
//cstim.burstint = ECL2180BINT
//cstim.burstlen = ECL2180BLEN
cstim.number = ECL2180NUM
cstim.start = ECL2180START
cstim.interval = ECL2180INT
cstim.noise = ECL2180NOISE
// Use the gid-specific random generator so random streams are
// independent of where and how many stims there are.
cstim.noiseFromRandom(rs.r)
rs.r.normal(0, 1)
rs.start()
cuelistECL2180.append(i)
ncue += 1
}
}
}
//print " cue size ", ncue
}
// setup activity pattern in input cue stims
proc mkcueECL2360() {local i, j, ncue localobj cstim, target, rs
print "Make cue (ECL2360) input..."
cuelistECL2360 = new Vector()
// open patterns file
fp = new File($s1)
fp.ropen()
cue = new Vector(nECL2360)
cue.scanf(fp, $2, $4) // read pattern
// cue.printf()
fp.close()
ncue = 0
// find active cells in pattern
for i=0, cue.size()-1 {
//if (!pc.gid_exists(i+iECL2360)) { continue }
if (ncue <= SPATT*$3) { // fraction of active cells in cue
if (cue.x[i] == 1) {
print "Cue cell ", i
//cstim = pc.gid2cell(i+iECL2360)
cstim = cells.object(i+iECL2360).stim
for j=0, cells.count-1 {
if (gidvec.x[j] == i+iECL2360) {break} // find cell index
}
rs = ranlist.object(j)
// create cue stimulus
//cstim.number = ECL2360NUM
//cstim.start = ECL2360START
//cstim.interval = ECL2360INT
//cstim.noise = ECL2360NOISE
//cstim.burstint = ECL2360BINT
//cstim.burstlen = ECL2360BLEN
cstim.number = ECL2360NUM
cstim.start = ECL2360START
cstim.interval = ECL2360INT
cstim.noise = ECL2360NOISE
// Use the gid-specific random generator so random streams are
// independent of where and how many stims there are.
cstim.noiseFromRandom(rs.r)
rs.r.normal(0, 1)
rs.start()
cuelistECL2360.append(i)
ncue += 1
}
}
}
//print " cue size ", ncue
}
// setup activity pattern in input cue stims
proc mkcueECL3180() {local i, j, ncue localobj cstim, target, rs
print "Make cue (ECL3180) input..."
cuelistECL3180 = new Vector()
// open patterns file
fp = new File($s1)
fp.ropen()
cue = new Vector(nECL3180)
cue.scanf(fp, $2, $4) // read pattern
// cue.printf()
fp.close()
ncue = 0
// find active cells in pattern
for i=0, cue.size()-1 {
//if (!pc.gid_exists(i+iECL3180)) { continue }
if (ncue <= SPATT*$3) { // fraction of active cells in cue
if (cue.x[i] == 1) {
print "Cue cell ", i
//cstim = pc.gid2cell(i+iECL3180)
cstim = cells.object(i+iECL3180).stim
for j=0, cells.count-1 {
if (gidvec.x[j] == i+iECL3180) {break} // find cell index
}
rs = ranlist.object(j)
// create cue stimulus
//cstim.number = ECL3180NUM
//cstim.start = ECL3180START
//cstim.interval = ECL3180INT
//cstim.noise = ECL3180NOISE
//cstim.burstint = ECL3180BINT
//cstim.burstlen = ECL3180BLEN
cstim.number = ECL3180NUM
cstim.start = ECL3180START
cstim.interval = ECL3180INT
cstim.noise = ECL3180NOISE
// Use the gid-specific random generator so random streams are
// independent of where and how many stims there are.
cstim.noiseFromRandom(rs.r)
rs.r.normal(0, 1)
rs.start()
cuelistECL3180.append(i)
ncue += 1
}
}
}
//print " cue size ", ncue
}
// setup activity pattern in input cue stims
proc mkcueECL3360() {local i, j, ncue localobj cstim, target, rs
print "Make cue (ECL3360) input..."
cuelistECL3360 = new Vector()
// open patterns file
fp = new File($s1)
fp.ropen()
cue = new Vector(nECL3360)
cue.scanf(fp, $2, $4) // read pattern
// cue.printf()
fp.close()
ncue = 0
// find active cells in pattern
for i=0, cue.size()-1 {
//if (!pc.gid_exists(i+iECL3360)) { continue }
if (ncue <= SPATT*$3) { // fraction of active cells in cue
if (cue.x[i] == 1) {
print "Cue cell ", i
//cstim = pc.gid2cell(i+iECL3360)
cstim = cells.object(i+iECL3360).stim
for j=0, cells.count-1 {
if (gidvec.x[j] == i+iECL3360) {break} // find cell index
}
rs = ranlist.object(j)
// create cue stimulus
//cstim.number = ECL3360NUM
//cstim.start = ECL3360START
//cstim.interval = ECL3360INT
//cstim.noise = ECL3360NOISE
//cstim.burstint = ECL3360BINT
//cstim.burstlen = ECL3360BLEN
cstim.number = ECL3360NUM
cstim.start = ECL3360START
cstim.interval = ECL3360INT
cstim.noise = ECL3360NOISE
// Use the gid-specific random generator so random streams are
// independent of where and how many stims there are.
cstim.noiseFromRandom(rs.r)
rs.r.normal(0, 1)
rs.start()
cuelistECL3360.append(i)
ncue += 1
}
}
}
//print " cue size ", ncue
}
// remove activity pattern in input cue stims
proc erasecue() {local i, j localobj cstim
for i=0, cuelist.size()-1 {
//if (!pc.gid_exists(i+iCA3)) { continue }
//cstim = pc.gid2cell(i+iCA3)
cstim = cells.object(cuelist.x[i]+iCA3).stim
cstim.number = 0
}
}
mkcueECL2180(FDGPATT, CPATT, CFRAC, NPATT) // cue from already stored pattern
//mkcueECL2180(FDGSTORE, CPATT, CFRAC, NSTORE) // cue from new pattern
mkcueECL2360(FDGPATT, CPATT, CFRAC, NPATT) // cue from already stored pattern
//mkcueECL2360(FDGSTORE, CPATT, CFRAC, NSTORE) // cue from new pattern
//mkcueECL3180(FCA1PATT, CPATT, CFRAC, NPATT) // cue from already stored pattern
////mkcueECL3180(FCA1STORE, CPATT, CFRAC, NSTORE) // cue from new pattern
//mkcueECL3360(FCA1PATT, CPATT, CFRAC, NPATT) // cue from already stored pattern
////mkcueECL3360(FCA1STORE, CPATT, CFRAC, NSTORE) // cue from new pattern
mkEC()
//mkECL2()
//mkECL3()
// Spike recording
objref tvec, idvec // will be Vectors that record all spike times (tvec)
// and the corresponding id numbers of the cells that spiked (idvec)
proc spikerecord() {local i localobj nc, nil
print "Record spikes..."
tvec = new Vector()
idvec = new Vector()
for i=0, cells.count-1 {
nc = cells.object(i).connect2target(nil)
nc.record(tvec, idvec, i)
// the Vector will continue to record spike times
// even after the NetCon has been destroyed
}
}
spikerecord()
// Record cell voltage traces
objref vDGGC, vDGBC, vDGMC, vDGHC // Vectors that record voltages from DG-GC, DG-MC, DG-BC, DG-HC
objref vCA3PC, vCA3AAC, vCA3BC, vCA3OLM // Vectors that record voltages from CA3-PC, CA3-AAC, CA3-BC, CA3-OLM
objref vCA1PC, vCA1AAC, vCA1BC, vCA1BSC, vCA1OLM // Vectors that record voltages from CA1-PC, CA1-AAC, CA1-BC, CA1-BSC, CA1-OLM
proc vrecord() {local i, gid
print "Record example voltage traces..."
for i=0, cells.count-1 { // loop over possible target cells
gid = gidvec.x[i] // id of cell
if (gid==iDGGC+32) {
vDGGC = new Vector()
vDGGC.record(&cells.object(i).soma.v(0.5))
}
if (gid==iDGMC) {
vDGMC = new Vector()
vDGMC.record(&cells.object(i).soma.v(0.5))
}
if (gid==iDGBC) {
vDGBC = new Vector()
vDGBC.record(&cells.object(i).soma.v(0.5))
}
if (gid==iDGHC) {
vDGHC = new Vector()
vDGHC.record(&cells.object(i).soma.v(0.5))
}
if (gid==iCA3PC+1) {
vCA3PC = new Vector()
vCA3PC.record(&cells.object(i).soma.v(0.5))
}
if (gid==iCA3AAC) {
vCA3AAC = new Vector()
vCA3AAC.record(&cells.object(i).soma.v(0.5))
}
if (gid==iCA3BC) {
vCA3BC = new Vector()
vCA3BC.record(&cells.object(i).soma.v(0.5))
}
if (gid==iCA3OLM) {
vCA3OLM = new Vector()
vCA3OLM.record(&cells.object(i).soma.v(0.5))
}
if (gid==iCA1PC+8) {
vCA1PC = new Vector()
vCA1PC.record(&cells.object(i).soma.v(0.5))
}
if (gid==iCA1AAC) {
vCA1AAC = new Vector()
vCA1AAC.record(&cells.object(i).soma.v(0.5))
}
if (gid==iCA1BC) {
vCA1BC = new Vector()
vCA1BC.record(&cells.object(i).soma.v(0.5))
}
if (gid==iCA1BSC) {
vCA1BSC = new Vector()
vCA1BSC.record(&cells.object(i).soma.v(0.5))
}
// if (gid==iCA1OLM) {
// vCA1OLM = new Vector()
// vCA1OLM.record(&cells.object(i).soma.v(0.5))
// }
}
}
vrecord()
// Record CA1 pyramidal cell voltage traces
objref vCA1PC_soma, vCA1PC_lm_thick, vCA1PC_radTprox, vCA1PC_radTdist, vCA1PC_radTmed
proc vCA1PCrecord() {local i, gid
print "Record example voltage traces..."
for i=0, cells.count-1 { // loop over possible target cells
gid = gidvec.x[i] // id of cell
if (gid==iCA1PC+8) {
vCA1PC_soma = new Vector()
vCA1PC_soma.record(&cells.object(i).soma.v(0.5))
vCA1PC_lm_thick = new Vector()
vCA1PC_lm_thick.record(&cells.object(i).lm_thick1.v(0.5))
vCA1PC_radTprox = new Vector()
vCA1PC_radTprox.record(&cells.object(i).radTprox.v(0.5))
vCA1PC_radTmed = new Vector()
vCA1PC_radTmed.record(&cells.object(i).radTmed.v(0.5))
vCA1PC_radTdist = new Vector()
vCA1PC_radTdist.record(&cells.object(i).radTdist.v(0.5))
}
}
}
vCA1PCrecord()
////////////////////////////
// Simulation control
////////////////////////////
strdef fstem
fstem = "Results/Results_DG_CA3_CA1_w_inhibition"
tstop = SIMDUR
celsius = 34
//run()
////////////////////////////
// Report simulation results
////////////////////////////
objref fo
strdef fno
proc spikeout() { local i
printf("\ntime\t cell\n") // print header once
sprint(fno,"%s_spt.dat", fstem)
fo = new File(fno)
fo.wopen()
for i=0, tvec.size-1 {
printf("%g\t %d\n", tvec.x[i], idvec.x[i])
fo.printf("%g\t %d\n", tvec.x[i], idvec.x[i])
}
fo.close()
}
proc vout() { local i, j, gid
for j=0, cells.count-1 { // loop over possible target cells
gid = gidvec.x[j] // id of cell
// if (gid==iDGGC) {
if (gid==iDGGC+32) {
sprint(fno,"%s_DGGC.dat", fstem)
fo = new File(fno)
fo.wopen()
for i=0, vDGGC.size-1 {
fo.printf("%g\n", vDGGC.x[i])
}
fo.close()
}
if (gid==iDGMC) {
sprint(fno,"%s_DGMC.dat", fstem)
fo = new File(fno)
fo.wopen()
for i=0, vDGMC.size-1 {
fo.printf("%g\n", vDGMC.x[i])
}
fo.close()
}
if (gid==iDGBC) {
sprint(fno,"%s_DGBC.dat", fstem)
fo = new File(fno)
fo.wopen()
for i=0, vDGBC.size-1 {
fo.printf("%g\n", vDGBC.x[i])
}
fo.close()
}
if (gid==iDGHC) {
sprint(fno,"%s_DGHC.dat", fstem)
fo = new File(fno)
fo.wopen()
for i=0, vDGHC.size-1 {
fo.printf("%g\n", vDGHC.x[i])
}
fo.close()
}
if (gid==iCA3PC+1) {
sprint(fno,"%s_CA3PC.dat", fstem)
fo = new File(fno)
fo.wopen()
for i=0, vCA3PC.size-1 {
fo.printf("%g\n", vCA3PC.x[i])
}
fo.close()
}
if (gid==iCA3AAC) {
sprint(fno,"%s_CA3AAC.dat", fstem)
fo = new File(fno)
fo.wopen()
for i=0, vCA3AAC.size-1 {
fo.printf("%g\n", vCA3AAC.x[i])
}
fo.close()
}
if (gid==iCA3BC) {
sprint(fno,"%s_CA3BC.dat", fstem)
fo = new File(fno)
fo.wopen()
for i=0, vCA3BC.size-1 {
fo.printf("%g\n", vCA3BC.x[i])
}
fo.close()
}
if (gid==iCA3OLM) {
sprint(fno,"%s_CA3OLM.dat", fstem)
fo = new File(fno)
fo.wopen()
for i=0, vCA3OLM.size-1 {
fo.printf("%g\n", vCA3OLM.x[i])
}
fo.close()
}
if (gid==iCA1PC+8) {
sprint(fno,"%s_CA1PC.dat", fstem)
fo = new File(fno)
fo.wopen()
for i=0, vCA1PC.size-1 {
fo.printf("%g\n", vCA1PC.x[i])
}
fo.close()
}
if (gid==iCA1AAC) {
sprint(fno,"%s_CA1AAC.dat", fstem)
fo = new File(fno)
fo.wopen()
for i=0, vCA1AAC.size-1 {
fo.printf("%g\n", vCA1AAC.x[i])
}
fo.close()
}
if (gid==iCA1BC) {
sprint(fno,"%s_CA1BC.dat", fstem)
fo = new File(fno)
fo.wopen()
for i=0, vCA1BC.size-1 {
fo.printf("%g\n", vCA1BC.x[i])
}
fo.close()
}
if (gid==iCA1BSC) {
sprint(fno,"%s_CA1BSC.dat", fstem)
fo = new File(fno)
fo.wopen()
for i=0, vCA1BSC.size-1 {
fo.printf("%g\n", vCA1BSC.x[i])
}
fo.close()
}
// if (gid==iCA1OLM) {
// sprint(fno,"%s_CA1OLM.dat", fstem)
// fo = new File(fno)
// fo.wopen()
// for i=0, vCA1OLM.size-1 {
// fo.printf("%g\n", vCA1OLM.x[i])
// }
// fo.close()
// }
}
}
proc vCA1PCout() { local i, j, gid
for j=0, cells.count-1 { // loop over possible target cells
gid = gidvec.x[j] // id of cell
if (gid==iCA1PC+8) {
sprint(fno,"%s_CA1PCsoma.dat", fstem)
fo = new File(fno)
fo.wopen()
for i=0, vCA1PC_soma.size-1 {
fo.printf("%g\n", vCA1PC_soma.x[i])
}
fo.close()
sprint(fno,"%s_CA1PCradTprox.dat", fstem)
fo = new File(fno)
fo.wopen()
for i=0, vCA1PC_radTprox.size-1 {
fo.printf("%g\n", vCA1PC_radTprox.x[i])
}
fo.close()
sprint(fno,"%s_CA1PCradTmed.dat", fstem)
fo = new File(fno)
fo.wopen()
for i=0, vCA1PC_radTmed.size-1 {
fo.printf("%g\n", vCA1PC_radTmed.x[i])
}
fo.close()
sprint(fno,"%s_CA1PCradTdist.dat", fstem)
fo = new File(fno)
fo.wopen()
for i=0, vCA1PC_radTdist.size-1 {
fo.printf("%g\n", vCA1PC_radTdist.x[i])
}
fo.close()
sprint(fno,"%s_CA1PClmthick.dat", fstem)
fo = new File(fno)
fo.wopen()
for i=0, vCA1PC_lm_thick.size-1 {
fo.printf("%g\n", vCA1PC_lm_thick.x[i])
}
fo.close()
}
}
}
// produce raster plot of spiking activity
objref gs
proc spikeplot() { local i
gs = new Graph()
gs.size(0, tstop, -1, ntot)
for i=0, tvec.size-1 {
gs.mark(tvec.x[i], idvec.x[i], "|", 8)
}
gs.flush()
}
// panel for simulation results
proc xspikeres() {
xpanel("Spike results")
xbutton("Write voltages out", "vout()")
xbutton("Write CA1 PC voltages out", "vCA1PCout()")
xbutton("Write spikes out", "spikeout()")
xbutton("Plot", "spikeplot()")
xpanel()
}
xspikeres()
