Proposal for morphologies

Morphology are used for two purposes: for simulation, and for access and plotting. For simulation, the geometry doesn't actually matter, only the electrical properties do. I propose to separate those two sets of properties.

Electrical properties

A morphology consists of a tree, each node being a branch. Each branch is a set of compartments. What we need to know for a simulation is:

• area of each compartment;
• resistance between two successive compartments;
• (half-)resistance at the end points.

I propose the following idea.

First, we only store the area and total resistance of each compartment. We then assume that potential and other variables are meant at electrical, and not geometrical, middle points. That is, at half-resistance. The geometrical meaning would depend on the implied geometry, but in practice it doesn't really matter. In this way we can readily deduce all required values (i.e. sum half-resistance of successive compartments).

Second, since the resistance depends on intracellular resistivity, which is only specified later, we instead calculated an effective length, that is, so that resistance is intracellular resistivity divided by effective length (for a cylinder, pi * d**2/4L).

The advantage here is that those values do not depend on the actual geometry of the compartment, so the simulation core does not need to know about it, and all geometrical aspects are confined into the Morphology module.

Thinking about diffusion

We need to keep in mind that we will want to also simulate diffusion at some point, which means we will want to know the volume of compartments. Let us have that also specified.

Geometrical properties

Those are used mostly for plotting and access (eg, access point at distance 10 um). Access also goes through the Morphology class.