### Many poisson inputs to one cell

Posted:

**Thu Mar 03, 2016 2:53 am**Hello! I have been using NEURON for a few months now and these forums have been a huge help. I am stuck on something new and I have not seen any other threads that address this.

I have created a simple cell model (axon, soma, and small dendrite tree) and would like to create some inputs on the tree that obey Poisson statistics. In my current code, I create a NetStim source and connect it to the cell at some place with NetConn. This works just fine for one input, but I would like to do many inputs at the same time, at many different places in the tree. Right now my code places two identically constructed inputs, but the spike trains do not overlap in time. My code is attached:

Observe the output file: t_s2 looks fine, but t_s1 is supposed to have 10 values (times that the input from stim1 occurred). I only ever get 2 values for t_s1, and it looks like maybe the spike trains never overlap despite having set them starting at t=spikeonset=10. Thus, my question is 2-part:

1) How do I get both artificial cells to run spike trains at the same time? or Why is my second connection seemingly overriding the first?

2) Suppose I want 1000 artificial cells to input in this fashion. How do I set this up without hardcoding for 1000 NetStims and 1000 NetConns?

Thank you in advance!

-jordan

I have created a simple cell model (axon, soma, and small dendrite tree) and would like to create some inputs on the tree that obey Poisson statistics. In my current code, I create a NetStim source and connect it to the cell at some place with NetConn. This works just fine for one input, but I would like to do many inputs at the same time, at many different places in the tree. Right now my code places two identically constructed inputs, but the spike trains do not overlap in time. My code is attached:

Code: Select all

```
proc celldef() { //builds cell
topol()
subsets()
geom()
biophys()
geom_nseg()
}
create soma, axon, dend[6] // create cell pieces
proc topol() { local i //connect cell
connect axon(0), soma(0)
for i = 0, 1 connect dend[i](0), soma(1)
for i = 2, 3 connect dend[i](0), dend(1)
for i = 4, 5 connect dend[i](0), dend[1](1)
basic_shape()
}
proc shape3d_1() { // make cell in 3d
soma {pt3dclear()
pt3dadd(0, 0, 0, 1)
pt3dadd(15, 0, 0, 1)
}
axon {pt3dclear()
pt3dadd(0, 0, 0, 1)
pt3dadd(-179, 0, 0, 1)
}
dend {pt3dclear()
pt3dadd(15, 0, 0, 1)
pt3dadd(60, -134, 0, 1)
}
dend[1] {pt3dclear()
pt3dadd(15, 0, 0, 1)
pt3dadd(45, 15, 0, 1)
}
dend[2] {pt3dclear()
pt3dadd(60, -134, 0, 1)
pt3dadd(90, -134, 0, 1)
}
dend[3] {pt3dclear()
pt3dadd(60, -134, 0, 1)
pt3dadd(60, -15, 0, 1)
}
dend[4] {pt3dclear()
pt3dadd(45, 15, 0, 1)
pt3dadd(75, 15, 0, 1)
}
dend[5] {pt3dclear()
pt3dadd(45, 15, 0, 1)
pt3dadd(45, 135, 0, 1)
}
}
proc basic_shape() { // does shape3d_1
shape3d_1()
}
objref all // need for subsets
proc subsets() { local i // make subsets
objref all
all = new SectionList()
soma all.append()
axon all.append()
for i=0, 5 dend[i] all.append()
}
proc geom() {
forsec all { }
dend { }
}
proc geom_nseg() {
forsec all { nseg = 11 }
}
proc biophys() { // biophys parameters
soma {
insert pas
g_pas = 0.001
e_pas = -70
}
axon {
insert pas
g_pas = 0.001
e_pas = -70
}
dend[0] {
insert pas
g_pas = 0.001
e_pas = -70
}
dend[1] {
insert pas
g_pas = 0.001
e_pas = -70
}
dend[2] {
insert pas
g_pas = 0.001
e_pas = -70
}
dend[3] {
insert pas
g_pas = 0.001
e_pas = -70
}
dend[4] {
insert pas
g_pas = 0.001
e_pas = -70
}
dend[5] {
insert pas
g_pas = 0.001
e_pas = -70
}
}
proc setdendnseg(){ local i //make all dends have # of segments
dendnseg=$1
for i=0,5{
dend[i].nseg=$1
}
ncomp=dendnseg*6 // 6 dendrites
}
celldef() // builds cell
setdendnseg(11)
//simulation time
tstop = 200
tlength=tstop/dt
objectvar source1,source2, syn1, syn2, conn1,conn2 // initialize object variables
objref rect, vsoma, ts1, ts2 //initialize values to record
rect = new Vector()
vsoma = new Vector()
ts1 = new Vector()
ts2 = new Vector()
nspikes = 10 //number of spikes
spikeint = 20 //spike interval
spikeonset = 10 //spike onset
// place stim1
proc places1(){
s1dend=$1 //s1 dendrite
s1comp=$2 //s1 compartment
s1coord=s1comp/dendnseg //s1 coordinate
source1 = new NetStim(0.5) //create source 1
source1.interval = spikeint
source1.number = nspikes
source1.start = spikeonset
source1.noise = 1 //set to 1 for Poisson mode
dend[s1dend] syn1 = new Exp2Syn(s1coord) //exp2 style input
syn1.tau1 = .1 //rise time
syn1.tau2 = .2 //decay time
syn1.e = 0 //rev potential
thresh1 = 10
delay1 = 0.1
weight1 = 0.1
conn1 = new NetCon(source1, syn1, thresh1, delay1, weight1)
}
//place stim2
proc places2(){
s2dend=$1 //s2 dendrite
s2comp=$2 //s2 compartment
s2coord=s2comp/dendnseg //s2 coordinate
source2 = new NetStim(0.5)
source2.interval = spikeint
source2.number = nspikes
source2.start = spikeonset
source2.noise = 1
dend[s2dend] syn2 = new Exp2Syn(s2coord)
syn2.tau1 = .1 //rise time
syn2.tau2 = .2 //decay time
syn2.e = 0 //rev potential
thresh2 = 10
delay2 = 0.1
weight2 = 0.1
conn2 = new NetCon(source2, syn2, thresh2, delay2, weight2)
}
places1(5,5)
places2(5,5)
proc getrect(){
rect.record(&t)
init()
run()
rect.play_remove()
}
proc getv(){
source1.number = nspikes
source2.number = nspikes
vsoma.record(&soma.v(0.5))
conn1.record(ts1)
conn2.record(ts2)
init()
run()
vsoma.play_remove()
ts1.play_remove()
ts2.play_remove()
}
getrect()
getv()
//output data
objref savdata
strdef filename
proc exportdata(){ local p
sprint(filename,"simplecell_pas_pois_%g_%1.2g_%g_%1.2g.csv",s1dend,s1comp,s2dend,s2comp)
savdata = new File(filename)
savdata.wopen(filename)
savdata.printf("s1dend, s1comp, s2dend, s2comp\n")
savdata.printf("%g,%g,%g,%g\n",s1dend, s1comp, s2dend, s2comp)
savdata.printf("t , vsoma , t_s1 , t_s2\n")
ts1 = ts1.resize(rect.size())
ts2 = ts2.resize(rect.size())
for p=0,(rect.size()-1) {
savdata.printf("%g , %g , %g , %g\n", rect.x(p), vsoma.x(p), ts1.x(p), ts2.x(p))
}
}
exportdata()
```

1) How do I get both artificial cells to run spike trains at the same time? or Why is my second connection seemingly overriding the first?

2) Suppose I want 1000 artificial cells to input in this fashion. How do I set this up without hardcoding for 1000 NetStims and 1000 NetConns?

Thank you in advance!

-jordan