neuron_morphology.features.branching.bifurcations

Module Contents

Functions

calculate_outer_bifs(morphology: Morphology, soma: Dict, node_types: Optional[List[int]]) → int	Counts the number of bifurcation points beyond the a sphere
num_outer_bifurcations(data: MorphologyLike, node_types: Optional[List[int]] = None) → int	Feature Extractor interface to calculate_outer_bifurcations. Returns
mean_bifurcation_angle_local(data: MorphologyLike, node_types: Optional[List[int]] = None) → float	Compute the average angle between child segments at
mean_bifurcation_angle_remote(data: MorphologyLike, node_types: Optional[List[int]] = None) → float	Compute the average angle between the next branch point or terminal

neuron_morphology.features.branching.bifurcations.calculate_outer_bifs(morphology: Morphology, soma: Dict, node_types: Optional[List[int]]) → int

Counts the number of bifurcation points beyond the a sphere with 1/2 the radius from the soma to the most distant point in the morphology, with that sphere centered at the soma.

Parameters:

morphology: Describes the structure of a neuron

soma: Must have keys “x”, “y”, and “z”, describing the position of this

morphology’s soma in

node_types: Restrict included nodes to these types. See

neuron_morphology.constants for avaiable node types.

Returns:

the number of bifurcations

neuron_morphology.features.branching.bifurcations.num_outer_bifurcations(data: MorphologyLike, node_types: Optional[List[int]] = None) → int

Feature Extractor interface to calculate_outer_bifurcations. Returns the number of bifurcations (branch points), excluding those too close to the root (threshold is 1/2 the max distance from the root to any node).

Parameters:

data : Holds a morphology object. No additional data is required

node_types : Restrict included nodes to these types. See

neuron_morphology.constants for avaiable node types.

neuron_morphology.features.branching.bifurcations.mean_bifurcation_angle_local(data: MorphologyLike, node_types: Optional[List[int]] = None) → float

Compute the average angle between child segments at bifurcations throughout the morphology. Trifurcations are ignored. Note: this introduces possible segmentation artifacts if trifurcations are due to large segment sizes.

Parameters:

data: The reconstruction whose max euclidean distance will be

calculated

node_types: restrict consideration to these types

Returns:

Scalar value

neuron_morphology.features.branching.bifurcations.mean_bifurcation_angle_remote(data: MorphologyLike, node_types: Optional[List[int]] = None) → float

Compute the average angle between the next branch point or terminal tip of child segments at each bifurcation. Trifurcations are ignored. Note: this introduces possible segmentation artifacts if trifurcations are due to large segment sizes.

Parameters:

data: The reconstruction whose max euclidean distance will be

calculated

node_types: restrict consideration to these types

Returns:

Scalar value, nan if no nodes