neuron_morphology.features.soma

Module Contents

Functions

calculate_soma_surface(data: Data) → float	Approximates the surface area of the soma. Morphologies with only
calculate_relative_soma_depth(data: Data) → float	Calculate the soma depth relative to pia/wm
calculate_soma_features(data: Data)	Calculate the soma features
calculate_stem_exit_and_distance(data: Data, node_types: Optional[List[int]], z_scale=3.0)	Returns the relative radial position (stem_exit) on the soma where the

neuron_morphology.features.soma.calculate_soma_surface(data: Data) → float

Approximates the surface area of the soma. Morphologies with only a single soma node are supported.

Parameters:

data: Data Object containing a morphology

Returns:

Scalar value

neuron_morphology.features.soma.calculate_relative_soma_depth(data: Data) → float

Calculate the soma depth relative to pia/wm

Parameters:

data: Data Object containing a morphology

Returns:

Scalar value

neuron_morphology.features.soma.calculate_soma_features(data: Data)

Calculate the soma features

Parameters:

data: Data Object containing a morphology

Returns:

soma_features

neuron_morphology.features.soma.calculate_stem_exit_and_distance(data: Data, node_types: Optional[List[int]], z_scale=3.0)

Returns the relative radial position (stem_exit) on the soma where the tree holding the tree connects to the soma. 0 is on the bottom, 1 on the top, and 0.5 out a side. Also returns the distance (stem_distance) between the tree root and the soma surface.

Parameters:

data: Data Object containing a morphology

soma: dict

soma node

node_types: list (AXON, BASAL_DENDRITE, APICAL_DENDRITE)

Type to restrict search to

Returns:

(float, float):

First value is relative position (height, on [0,1]) of a

tree on soma. Second value is distance of the root from soma