NeuroM morphology definitions¶

These are NeuroM specific working definitions of various components of neuron morpholigies.

Point¶

A point is a vector of numbers [X, Y, Z, R, TYPE, ID, PID] where the components are

X, Y, Z: Cartesian coordinates of position
R: Radius
TYPE: One of the NeuroM valid point types
ID: Unique identifier of the point.
PID: ID of the parent of the point.

Typically only the first four or five components are of interest to morphology analysis. The rest are used to construct the soma and hierarchical tree structures of the neuron, and to check its semantic validity.

Note

For most of what follows, it suffices to consider a point as a vector of [X, Y, Z, R, TYPE]. The remaining components ID and PID can be considered book-keeping.

Todo

Point types may need to be restricted to align SWC with H5. This is dependent on future H5 specs.

Segment¶

A segment consists of two consecutive points belonging to the same neurite and section.

Section¶

A section is a series of two or more points whose first and last element are any of the following combinations:

root node, forking point
forking point, forking point
forking point, end point
root node, end point

The first point of a section is a duplicate of the last point of its parent section, unless the latter is a soma section.

Soma¶

A soma can be represented by one, three or more points. The soma is classified based on the number of points it contains thus:

Type A: 1 point defining the center and radius.
Type B: 3 points. Only the centers of the points are considered. The first point defines the center. The radius is extimated from the mean distance between the center and the two remaining points.
Type C: More than three points. Only the centers of the points are considered. The first point defines the center. The radius is estimated from the mean distance between the center and the remaining points.

Todo

Expand list if and when specifications require new types of soma.

The soma interface exports a center and radius. These can be calculated in different ways, but the default is to use the center and radius for type A and the mean center and radius for types B and C.

Todo

In the future, type B may be interpreted as 3 points on an ellipse. In this case, the points would have to be non-collinear. Currently there is no such restriction.

Neurite tree¶

There are two alternative representations of a neurite tree. A neurite may consist of a tree structure with either a points or a section in each vertex or node. The different representations are accessible via the ezy and fst modules respectively.

The tree structure implies the following:

A node can only have one parent.
A node can have an arbitrary number of children.
No loops are present in the structure.

Different type of points are allowed in the same tree as long as same conventions are followed

Todo

The conventions governing the types of points in a neurite tree need to be well defined

In NeuroM neurite trees are implemented using the recursive structure neurom.core.tree.Tree, with each node holding a reference to either a single morphology point, or an array of points representing a section<section-label>.

Neuron¶

A neuron structure consists of a single soma and a collection of trees.

The trees that are expected to be present depend on the type of cell:

Interneuron (IN): basal dendrite, axon
Pyramidal cell (PC): basal dendrite, apical dendrite, axon