I'm trying to template my multi-compartmental cell base on a previous .geo file ( https://senselab.med.yale.edu/ModelDB/S ... ctc200.geo). For this purpose, I tried to follow the tutorial here: http://www.anc.ed.ac.uk/school/neuron/t ... /tutC.html
Everything seems to work well if I just copy the sample programs and run them on my NEURON platform. But I got confused reading the following:
How does NEURON assign different Z coordinates to multiple neurons?Each time we create a new section and connect it to others, NEURON places the section in a 3-D space and assigns an X, Y and Z coordinate to each end of the section. When creating more than one neuron, as we have above, each neuron is given a different Z coordinate for all of its sections.
In their sample program, the soma was created as follows:
Code: Select all
create soma
soma {
nseg = 1
diam = 18.8
L = 18.8
Ra = 123.0
insert hh
gnabar_hh=0.25
gl_hh = .0001666
el_hh = -60.0
}
Code: Select all
nSThcells = 4
objectvar SThcells[nSThcells]
for i = 0, nSThcells-1 {
SThcells[i] = new SThcell()
}
This is the thing I tried for my 200-compartment neuron (by manipulating the z coordinates):
Code: Select all
access soma_tc
f=new File()
for counter=0,3 {
soma_tc[counter] {
nseg = 1
pt3dclear()
f.ropen("soma.dat")
for j = 1, 13 {
pt3dadd(f.scanvar(),f.scanvar(),f.scanvar()+counter*200,f.scanvar())
printf(" fscanvar=%d ", counter)
insert hh
gnabar_hh= 0.2
gl_hh = .0001666
el_hh = -60.0
insert pas
}
}
}
Code: Select all
13
-23.25 -7.35 -34.2 0
-21.9 -6.18 -31.05 14.959
-21 -5.8875 -30.4875 21.439
-20.1 -5.03862 -28.6974 24.974
-16.95 -4.48638 -27.5526 25.363
-16.05 -4.26426 -26.5824 26.719
-13.8 -3.05889 -24.0111 28.865
-9.75 -1.51125 -21.6675 28.311
-4.8 1.0875 -17.5662 25.297
-3.45 0.795 -15.435 23.776
-0.75 1.875 -11.4192 15.383
0.15 1.56 -10.53 10.826
1.5 3 -9 0
Code: Select all
nSThcells = 4 (n, the number of neurons you want for your network, in this case 4)
objectvar SThcells[nSThcells]
for i = 0, nSThcells-1 {
SThcells[i] = new SThcell()
}
Code: Select all
access soma_tc
//set parameters for soma_tc section
f=new File()
f.ropen("soma.dat")
soma_tc {
nseg = 1
pt3dclear()
for j = 1, 13 {
pt3dadd(f.scanvar(),f.scanvar(),f.scanvar(),f.scanvar())
}
}
I noticed people tried similar things before but failed ( http://www.neuron.yale.edu/phpBB/viewto ... =13&t=1826 ). So it's not possible to load a .geo file in a template?
Sorry for making such a long thread. My major questions are:
1. How does NEURON assign different spatial location, e.g., by using different z coordinates, to templated neurons?
2. Does that work if we have to specify the soma's coordinates?
3. Any easier way to template a 200-compartment neuron?
Please let me know if any of the above is unclear, and in case you would like to check on my codes.
I deeply appreciate your time and patience.
Ibuki.