Calculate current flowing from one compartment to another

Anything that doesn't fit elsewhere.
Post Reply
pranit
Posts: 7
Joined: Mon Nov 22, 2010 4:23 pm

Calculate current flowing from one compartment to another

Post by pranit » Fri Apr 06, 2012 2:54 pm

Hi,
I am working on a multi-compartment model and need to find out the magnitude of current flowing from one compartment to another. I am having nseg = 1 for now for all compartments. I am using the formula ((Vsoma(0.5)-Vdend[0](0.5))/((2Rasoma*Lsoma/(pi * Dsoma^2))+(2Radend*Ldend/(pi * Ddend^2))) to plot the current. Is there an easier way to calculate this in neuron. I need to do that for all the compartments and so wanted to know if neuron has some default function/parameter which does this..


Thanks
--Pranit

ted
Site Admin
Posts: 5572
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

Re: Calculate current flowing from one compartment to anothe

Post by ted » Sat Apr 07, 2012 12:42 pm

NEURON calculates the time course of membrane potential at points in space that are called nodes. Each section has a node at its 0 and 1 ends, and at nseg evenly spaced internal locations that range from 0.5/nseg to (nseg-1+0.5)/nseg, where nseg is the section's discretization parameter.

NEURON has a function called ri() that is useful for what you want. ri(x) returns the resistance between the node at x and its parent. This procedure iterates over all nodes in the currently accessed section to report the axial current between each adjacent pair of nodes in the section.

Code: Select all

// for each node in current section that has x>0
//   report axial current that enters this node from its parent
proc seciax() { local vp, vthis
  print secname()
  for (x) {
    if (x==0) {
      vp = v(x)
    } else {
      vthis = v(x)
      print x, (vp-vthis)/ri(x)
      vp = vthis // prepare to deal with next node
    }
  }
}
All you have to do is iterate over all sections in your model cell and execute seciax() each time. This one-liner will do it:

Code: Select all

forall seciax()

pranit
Posts: 7
Joined: Mon Nov 22, 2010 4:23 pm

Re: Calculate current flowing from one compartment to anothe

Post by pranit » Tue Apr 10, 2012 5:30 pm

Thanks Ted. This was exactly what i was looking for.

Post Reply