Adding extracellular stimulation and defining neuron topology

Anything that doesn't fit elsewhere.
Post Reply
leanne
Posts: 5
Joined: Wed Oct 18, 2017 5:15 am

Adding extracellular stimulation and defining neuron topology

Post by leanne » Mon Nov 06, 2017 6:45 am

Hi,

I'm a new user to neuron and I'm currently trying to implement extracellular stimulation using files from the extracellular_stim_and_rec method written bij Ted (only the files needed for stimulation, not recording). I'm implementing this mechanism in a double cable model that I adapted form McIntyre et al (Modeling the Excitability of Mammalian Nerve Fibers: Influence of Afterpotentials on the Recovery Cycle, https://senselab.med.yale.edu/modeldb/s ... model=3810), where the internode is divided into different segments (mysa, flut and stin).

In a later stage, I would like to add a branching architecture to the model, but now I am first trying to make a straight cable using the pt3dadd() mechanism.

Here is part of the hoc code that I am using to construct the neuron (axon_myelinated.hoc):

create node[nr_nodes], MYSA[nr_mysa], FLUT[nr_flut], STIN[nr_stin]

proc initialize(){
for i=0,nr_nodes-1 {
node{
nseg = 1
diam = node_diameter // um
L = node_length // um
Ra = rho_a // ohm*cm
pt3dclear()
pt3dadd(0,0,0,diam)
pt3dadd(L,0,0,diam)
cm = c_node // uF/cm2
insert axnode
insert extracellular
xraxial=rax_ex_node xg=1e10 xc=0 // S/cm2 (conductance), uF/cm2 (capacitance)
xraxial[1]=1e+09 xg[1]=1e+09 xc[1]=0 e_extracellular=0
insert xtra
}
}
for i=0, nr_mysa-1 {
MYSA{
nseg = 1
diam = fiber_diameter // um
L = mysa_length // um
Ra = rho_a*(1/(mysa_diameter/fiber_diameter)^2) // ohm*cm
pt3dclear()
pt3dadd(0,0,0,diam)
pt3dadd(L,0,0,diam)
cm = c_internode*mysa_diameter/fiber_diameter // uF/cm2
insert pas
g_pas = g_mysa*mysa_diameter/fiber_diameter // S/cm2
e_pas = -80 // mV
insert extracellular
xraxial=rax_myelin_mysa xg=g_myelin/(myelin_lemella*2)
xc=c_myelin/(myelin_lemella*2) // waarom 2?
xraxial[1]=1e+09 xg[1]=1e+09 xc[1]=0 e_extracellular=0
insert xtra
}
}
for i=0, nr_flut-1 {
FLUT{
nseg = 1
diam = fiber_diameter // um
L = flut_length // um
Ra = rho_a*(1/(flut_diameter/fiber_diameter)^2) // ohm*cm
pt3dclear()
pt3dadd(0,0,0,diam)
pt3dadd(L,0,0,diam)
cm = c_internode*flut_diameter/fiber_diameter // uF/cm2
insert pas
g_pas = g_flut*flut_diameter/fiber_diameter // S/cm2
e_pas = -80 // mV
insert extracellular
xraxial=rax_myelin_flut xg=g_myelin/(myelin_lemella*2)
xc=c_myelin/(myelin_lemella*2)
xraxial[1]=1e+09 xg[1]=1e+09 xc[1]=0 e_extracellular=0
insert xtra
}
}
for i=0, nr_stin-1 {
STIN{
nseg = 1
diam = fiber_diameter // um
L = stin_length // um
Ra = rho_a*(1/(stin_diameter/fiber_diameter)^2) // ohm*cm
pt3dclear()
pt3dadd(0,0,0,diam)
pt3dadd(L,0,0,diam)
cm = c_internode*stin_diameter/fiber_diameter // uF/cm2
insert pas
g_pas = g_stin*stin_diameter/fiber_diameter // S/cm2
e_pas = -80 // mV
insert extracellular
xraxial=rax_myelin_stin xg=g_myelin/(myelin_lemella*2)
xc=c_myelin/(myelin_lemella*2)
xraxial[1]=1e+09 xg[1]=1e+09 xc[1]=0 e_extracellular=0
insert xtra
}
}
for i=0, nr_nodes-2 {
connect MYSA[2*i](0), node(1)
connect FLUT[2*i](0), MYSA[2*i](1)
connect STIN(0), FLUT[2*i](1)
connect FLUT[2*i+1](0), STIN(1)
connect MYSA[2*i+1](0), FLUT[2*i+1](1)
connect node[i+1](0), MYSA[2*i+1](1)
}

finitialize(v_init)
fcurrent()
}
initialize()

Furthermore, I added

load_file("axon_myelinated.hoc")
define_shape()

to initxstim.hoc.

I have two questions:

1. Did I correctly define xraxial... and xraxial[1]... etc. for the myelin sheeth and the extracellular space?
2. I am having some trouble defining the topology. I tried to place every segment at (0,0,0) to (L, 0, 0) and then connect them later, such that each end would be added to the previous segment. However, a segmentation violation showed up and the geometry does not look as it should (it seems as if all single elements start at zero, looking at the shape plot, but I'm not sure). Setpointers is called after constructing the neuron (in initxstim). Any ideas what could cause the error?

Many thanks in advance for any help!

ted
Site Admin
Posts: 5376
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

Re: Adding extracellular stimulation and defining neuron topology

Post by ted » Mon Nov 06, 2017 4:45 pm

1. Did I correctly define xraxial... and xraxial[1]... etc. for the myelin sheeth and the extracellular space?
2. I am having some trouble defining the topology
Are you saying you can't just look at all this code and tell where there might be a problem? That's strange; neither can I, especially since it involves other code that I can't see. Well, maybe I could, but it would be artificially difficult. If you zip up the hoc, ses, and mod files that are needed to execute your code, and email that to me
ted dot carnevale at yale dot edu
it'll be easier for me to figure out what's wrong.

Post Reply