neurom.features.bifurcationfunc

Bifurcation point functions.

Functions

bifurcation_partition

Calculate the partition at a bifurcation point.

diameter_power_relation

Calculate the diameter power relation at a bifurcation point.

local_bifurcation_angle

Return the opening angle between two out-going sections in a bifurcation point.

partition_asymmetry

Calculate the partition asymmetry at a bifurcation point.

partition_pair

Calculate the partition pairs at a bifurcation point.

remote_bifurcation_angle

Return the opening angle between two out-going sections in a bifurcation point.

sibling_ratio

Calculate the sibling ratio of a bifurcation point.

class neurom.features.bifurcationfunc.COLS[source]

Bases: object

Column labels for internal data representation.

exception neurom.features.bifurcationfunc.NeuroMError[source]

Bases: Exception

Base class for NeuroM errors.

neurom.features.bifurcationfunc.bifurcation_partition(bif_point)[source]

Calculate the partition at a bifurcation point.

We first ensure that the input point has only two children.

The number of nodes in each child tree is counted. The partition is defined as the ratio of the largest number to the smallest number.

neurom.features.bifurcationfunc.diameter_power_relation(bif_point, method='first')[source]

Calculate the diameter power relation at a bifurcation point.

The diameter power relation is defined in https://www.ncbi.nlm.nih.gov/pubmed/18568015

This quantity gives an indication of how far the branching is from the Rall ratio

diameter_power_relation==1 means perfect Rall ratio

neurom.features.bifurcationfunc.local_bifurcation_angle(bif_point)[source]

Return the opening angle between two out-going sections in a bifurcation point.

We first ensure that the input point has only two children.

The bifurcation angle is defined as the angle between the first non-zero length segments of a bifurcation point.

neurom.features.bifurcationfunc.partition_asymmetry(bif_point, uylings=False)[source]

Calculate the partition asymmetry at a bifurcation point.

By default partition asymmetry is defined as in https://www.ncbi.nlm.nih.gov/pubmed/18568015. However if uylings=True is set then https://jvanpelt.nl/papers/Uylings_Network_13_2002_397-414.pdf is used.

The number of nodes in each child tree is counted. The partition is defined as the ratio of the absolute difference and the sum of the number of bifurcations in the two child subtrees at each branch point.

neurom.features.bifurcationfunc.partition_pair(bif_point)[source]

Calculate the partition pairs at a bifurcation point.

The number of nodes in each child tree is counted. The partition pairs is the number of bifurcations in the two child subtrees at each branch point.

neurom.features.bifurcationfunc.remote_bifurcation_angle(bif_point)[source]

Return the opening angle between two out-going sections in a bifurcation point.

We first ensure that the input point has only two children.

The angle is defined as between the bifurcation point and the last points in the out-going sections.

neurom.features.bifurcationfunc.section_mean_radius(section)[source]

Compute the mean radius of a section weighted by segment lengths.

neurom.features.bifurcationfunc.sibling_ratio(bif_point, method='first')[source]

Calculate the sibling ratio of a bifurcation point.

The sibling ratio is the ratio between the diameters of the smallest and the largest child. It is a real number between 0 and 1. Method argument allows one to consider mean diameters along the child section instead of diameter of the first point.