connect to soma(0)

[anjan]

We want to connect apical dendrites to one end of the soma, and basal dendrites to the other end (please, see code below). However, connecting to soma(0) gives the problem that ri(x) of dend(0) is infinite. This does somehow not effect voltage recording at that site, but does it effect the calculation of intracellular resistivity? Are there any other effects of this high ri(x) known?

Code: Select all

///////// -- morphology -- /////////
create soma, dend, apic
soma {  L = 10  diam = 10  nseg = 3}
dend {  L = 50  diam = 2  nseg = 11}
apic {  L = 100  diam = 4  nseg = 15}
access soma

connect dend(0), soma(0)
connect apic(0), soma(1)

///////// -- end morphology -- /////////

forall {
    insert pas
    e_pas = 0
}

forall {
	Ra = 100
	g_pas = 0.0001
	cm = 1.0
}

soma distance(0,0.5)
forall { for (x) print secname(), x, distance(x), diam(x), ri(x) }

[ted]

There is no problem. This is as it should be.

Referring to the Programmer's Reference, ri(x) returns "the resistance (in megohms) between the center of the segment containing x and its parent segment. . . . If there is no parent the "infinite" resistance returned is 1e30."
http://www.neuron.yale.edu/neuron/stati ... ry.html#ri

For the purpose of determining what is the "parent" it is helpful to think of a model cell as a directed graph in the shape of a tree. The tree's nodes are the nodes of the sections, i.e. the 0 and 1 ends of the sections and the internal nodes of the sections (the nodes that lie at segment centers).

The root section of the tree is the section to which all other sections are connected. The root node of the tree is the node at the 0 end of the root section. This node has no parent node, i.e. there is no node that is conceptually "upstream" from the root node. Every other node in the tree has a parent.

Consider the model cell specified by

Code: Select all

create soma, dend
connect dend(0), soma(0)

The root section is soma, so the root node is soma(0).
The statement

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soma print ri(0)

returns 1e+30 because this node has no parent.

Connecting the 0 end of dend to the root node of the tree means that dend(0) also has no parent (there is no node that is conceptually upstream from dend(0)). This is why

Code: Select all

dend print ri(0)

also returns 1e+30.

[anjan]

Thank you for your fast reply.
I would like to ask 2 further questions:

(1) When I do the following:

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objref sRef
dend sRef = new SectionRef()
sRef.has_parent()

This gives me 1, i.e. dend has a parent.
Why does it then give me 1e+30 for ri(0)?

(2) If it is true that soma(0) and dend(0) have a ri(x) of 1e+30, does this effect in any way the recording of voltage or intracellular current at that connection? Would it be better to connect dend(0) to soma(0.1) instead of soma(0)?

Best,
Anja.

[ted]

Code: Select all

objref sRef
dend sRef = new SectionRef()
sRef.has_parent()

This gives me 1, i.e. dend has a parent.
Why does it then give me 1e+30 for ri(0)?

Another good question.

has_parent() only tells you whether a section is, or is not, the root section. See
http://www.neuron.yale.edu/neuron/stati ... has_parent

has_trueparent() tells whether the parent node is, or is not, the root node. See
http://www.neuron.yale.edu/neuron/stati ... trueparent

In the typically terse style employed by the Programmer's Reference, "parent" is generally (always?) used to refer to the parent section. When parent node is intended, the term "parent node" is used.

(2) If it is true that soma(0) and dend(0) have a ri(x) of 1e+30, does this effect [affect] in any way the recording of voltage or intracellular current at that connection? Would it be better to connect dend(0) to soma(0.1) instead of soma(0)?

No and no. ri merely reports the axial resistance between a node and its parent node. The system equations that are solved by NEURON are correct regardless of how one specifies the model's topology.

[anjan]

No and no. ri merely reports the axial resistance between a node and its parent node. The system equations that are solved by NEURON are correct regardless of how one specifies the model's topology.

This is good news. Thank you very much.

Anja.

[ted]

Thanks for using NEURON!