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. What matters mostly for access is the distance parameter. Specifically, we need to know the distance (along the branch, not Euclidian distance) of end points of compartments to the origin of the branch. This is also somehow independent of what specific geometry is implied. It is directly implied by the length parameter (cumulative sum) and therefore length should be understood as length along the branch, not Euclidian distance.

In summary, coordinates should be decoupled from other parameters (length, area etc). The question what the coordinates should refer to in terms of geometry, but that is mostly meaningful for plotting purposes. I would suggest that the coordinates correspond to those of the electrical midpoint, as defined previously, because it corresponds to where the values of V etc are taken. Depending on the geometry, end points can be calculated directly from the other geometrico-electrical parameters.