network simulation using swc file
Posted: Tue Jul 12, 2016 8:33 pm
Hi,
I just started using NEURON, 2 days ago and I am supposed to do the following:
Create a network by downloading the swc file of a cell, making a copy of it and connecting these identical cells together. Then I should impose an external activity and make them do something such as spike!
I transformed swc file into a neuron template file as the following:
1- Tools -> Miscellaneous -> Import 3D
2- "choose a file" button, then select a file and click "Read"
3- export - CellBuilder
4- use the Biophysics tab, when "Specify Strategy" was checked, I chose all tap, and I checked Ra, cm to change there default values to the following:
Ra=160
cm=1
5- Use the management tab to export by selecting "Cell type", optionally entering a "Mycell" as class name and then selecting "Save hoc code in file", called "new.hoc"
then I wrote this python script to import this file to NEURON and make a copy of it and then connect these two cells as the following:
from neuron import h
h.load_file('new.hoc')
cell1 = h.Mycell()
cell2 = h.Mycell()
cell1.position(1,2,0)
cell2.position(1,1,0)
post_syn = h.Exp2Syn(0.5, sec=cell2.dend[0])
connection = cell1.connect2target(post_syn)
connection.weight[0] = 1
Then I imposed this current:
ic = h.IClamp(0.5, sec=cell1.soma)
ic.delay = 1
ic.dur = 1
ic.amp = 100
and ran the simulation. But when I plot the output voltage, I dont see anything happening. Could you please kindly help me understand where the problem is.
Thanks
Fahimeh
I just started using NEURON, 2 days ago and I am supposed to do the following:
Create a network by downloading the swc file of a cell, making a copy of it and connecting these identical cells together. Then I should impose an external activity and make them do something such as spike!
I transformed swc file into a neuron template file as the following:
1- Tools -> Miscellaneous -> Import 3D
2- "choose a file" button, then select a file and click "Read"
3- export - CellBuilder
4- use the Biophysics tab, when "Specify Strategy" was checked, I chose all tap, and I checked Ra, cm to change there default values to the following:
Ra=160
cm=1
5- Use the management tab to export by selecting "Cell type", optionally entering a "Mycell" as class name and then selecting "Save hoc code in file", called "new.hoc"
then I wrote this python script to import this file to NEURON and make a copy of it and then connect these two cells as the following:
from neuron import h
h.load_file('new.hoc')
cell1 = h.Mycell()
cell2 = h.Mycell()
cell1.position(1,2,0)
cell2.position(1,1,0)
post_syn = h.Exp2Syn(0.5, sec=cell2.dend[0])
connection = cell1.connect2target(post_syn)
connection.weight[0] = 1
Then I imposed this current:
ic = h.IClamp(0.5, sec=cell1.soma)
ic.delay = 1
ic.dur = 1
ic.amp = 100
and ran the simulation. But when I plot the output voltage, I dont see anything happening. Could you please kindly help me understand where the problem is.
Thanks
Fahimeh