### Modeling branching off of a soma compartment

Posted:

**Sat Jun 25, 2011 12:30 am**I'm a bit new to computational neuroscience and I'm having some trouble understanding how branching (especially off the soma) is modeled in compartmental models.

Is there a standard way (or set of ways) to model multiple (more than two) compartmental connections to a soma?

For example, in the Traub, et al. 1991 model of the CA3 neuron, the apical and basal dendrites are modeled by a simplified single apical cable on one side of the soma and a single basal cable on the other side of the soma. How might I go about attaching an axon (or, for example, splitting the basal dendrites into multiple branches off the soma)? Is the typical method to simply connect the soma to each adjacent compartment through some resistance (if so, is this resistance calculated differently from other axial resistances)?

Also, I would imagine that, in an appropriately complex model, currents through the soma would be affected by the relative positions of each connected compartment and the 3D shape of the soma itself. For example, if the axon and basal dendrites are on the bottom of a pyramidal cell, and the apical dendrite is at the top, then I would imagine that currents would be conducted slightly faster and over slightly less resistance between the axon and the basal dendrites than between the axon and the apical dendrite, or the apical dendrite and the basal dendrites (not sure about the faster part). Is this accurate, and if so is it beyond the scope of compartmental modeling (and would this be due to the assumption of a single dimension, x)?

A related question - is there a definitive paper on modeling compartmental branching explicitly (i.e. without a 3/2 power rule or other such simplification), including equations for calculating axial current, and perhaps some discussion of relations to morphology? It seems like there are multiple methods in use for modeling branches (typically dendritic branches), but I can't seem to find any material actually discussing a method in detail. Right now I'm using a sort of "Y" branch method, which is what I think both NEURON and GENESIS use (basically, the point where Vm is calculated at the center of each compartment is connected to two axial resistors on each side, and in a Y branch, 3 resistors from 3 compartments are connected at a central point [the middle of the Y-shape], and the current entering a compartment from the Y branch is calculated by solving the equivalent electrical circuit).

Thank you for your time.

[Also, is this the best place to ask this kind of question?]

Is there a standard way (or set of ways) to model multiple (more than two) compartmental connections to a soma?

For example, in the Traub, et al. 1991 model of the CA3 neuron, the apical and basal dendrites are modeled by a simplified single apical cable on one side of the soma and a single basal cable on the other side of the soma. How might I go about attaching an axon (or, for example, splitting the basal dendrites into multiple branches off the soma)? Is the typical method to simply connect the soma to each adjacent compartment through some resistance (if so, is this resistance calculated differently from other axial resistances)?

Also, I would imagine that, in an appropriately complex model, currents through the soma would be affected by the relative positions of each connected compartment and the 3D shape of the soma itself. For example, if the axon and basal dendrites are on the bottom of a pyramidal cell, and the apical dendrite is at the top, then I would imagine that currents would be conducted slightly faster and over slightly less resistance between the axon and the basal dendrites than between the axon and the apical dendrite, or the apical dendrite and the basal dendrites (not sure about the faster part). Is this accurate, and if so is it beyond the scope of compartmental modeling (and would this be due to the assumption of a single dimension, x)?

A related question - is there a definitive paper on modeling compartmental branching explicitly (i.e. without a 3/2 power rule or other such simplification), including equations for calculating axial current, and perhaps some discussion of relations to morphology? It seems like there are multiple methods in use for modeling branches (typically dendritic branches), but I can't seem to find any material actually discussing a method in detail. Right now I'm using a sort of "Y" branch method, which is what I think both NEURON and GENESIS use (basically, the point where Vm is calculated at the center of each compartment is connected to two axial resistors on each side, and in a Y branch, 3 resistors from 3 compartments are connected at a central point [the middle of the Y-shape], and the current entering a compartment from the Y branch is calculated by solving the equivalent electrical circuit).

Thank you for your time.

[Also, is this the best place to ask this kind of question?]