neuron_morphology.features.size

Module Contents

Functions

total_length(data: MorphologyLike, node_types: Optional[List[int]] = None) → float Calculate the total length across all compartments in a reconstruction
total_surface_area(data: MorphologyLike, node_types: Optional[List[int]] = None) → float Calculates the sum of lateral surface areas across all comparments
total_volume(data: MorphologyLike, node_types: Optional[List[int]] = None) → float Calculates the sum of volumes across all comparments (linked pairs of
mean_diameter(data: MorphologyLike, node_types: Optional[List[int]] = None) → float Calculates the mean diameter of all nodes
parent_daughter_ratio_visitor(node: Dict[str, Any], morphology: Morphology, counters: Dict[str, Union[int, float]], node_types: Optional[List[int]] = None) Calculates for a single node the ratio of the node’s parent’s radius to
mean_parent_daughter_ratio(data: MorphologyLike, node_types: Optional[List[int]] = None) → float Calculate the average ratio of parent radii to child radii across a
max_euclidean_distance(data: MorphologyLike, node_types: Optional[List[int]] = None) → float Calculate the furthest distance, in 3-space, of a compartment’s end from
neuron_morphology.features.size.total_length(data: MorphologyLike, node_types: Optional[List[int]] = None) → float

Calculate the total length across all compartments in a reconstruction

Parameters:
data : the input reconstruction
node_types : if provided, restrict the calculation to compartments

involving these types
Returns:
The sum of segment lengths across all segments in the reconstruction

Notes

Excludes compartments where the parent is:
  1. the soma
  2. a root of the reconstruction

The logic here is that the soma root is likely to substantially overlap any of its compartments, while non-root soma nodes will be closer to the soma surface.

neuron_morphology.features.size.total_surface_area(data: MorphologyLike, node_types: Optional[List[int]] = None) → float

Calculates the sum of lateral surface areas across all comparments (linked pairs of nodes) in a reconstruction. This approximates the total surface area of the reconstruction. See Morphology.get_compartment_surface_area for details.

Parameters:
data : The reconstruction whose surface area will be computed
node_types : restrict the calculation to compartments involving these node

types
Returns:
The sum of compartment lateral surface areas across this reconstruction
neuron_morphology.features.size.total_volume(data: MorphologyLike, node_types: Optional[List[int]] = None) → float

Calculates the sum of volumes across all comparments (linked pairs of nodes) in a reconstruction. This approximates the total volume of the reconstruction. See Morphology.get_compartment_volume for details.

Parameters:
data : The reconstruction whose volume will be computed
node_types : restrict the calculation to compartments involving these node

types
Returns:
The sum of compartment volumes across this reconstruction
neuron_morphology.features.size.mean_diameter(data: MorphologyLike, node_types: Optional[List[int]] = None) → float

Calculates the mean diameter of all nodes

Parameters:
morphology : The reconstruction whose mean diameter
node_types : restrict the calculation to compartments involving these node

types
Returns:
The average diameter across selected nodes
neuron_morphology.features.size.parent_daughter_ratio_visitor(node: Dict[str, Any], morphology: Morphology, counters: Dict[str, Union[int, float]], node_types: Optional[List[int]] = None)

Calculates for a single node the ratio of the node’s parent’s radius to the node’s radius. Stores these values in a provided dictionary.

Parameters:
node : The node under consideration
morphology : The reconstruction to which this node belongs
counters : a dictionary used for storing running ratio totals and counts.
node_types : skip nodes not of one of these types

Notes

see mean_parent_daughter_ratio for usage

neuron_morphology.features.size.mean_parent_daughter_ratio(data: MorphologyLike, node_types: Optional[List[int]] = None) → float

Calculate the average ratio of parent radii to child radii across a reconstruction.

Parameters:
data : The reconstruction whose mean parent daugther ratio will be computed
node_types : restrict the calculation to compartments involving these node

types

Notes

Note that this function differs from the L-measure parent daughter ratio, which calculates the ratio of the child node size to the parent. Note also that both the parent and child must be in node_types in order for a compartment to be included in the calculation

neuron_morphology.features.size.max_euclidean_distance(data: MorphologyLike, node_types: Optional[List[int]] = None) → float

Calculate the furthest distance, in 3-space, of a compartment’s end from the soma. This is equivalent to the distance to the furthest SWC node.

Parameters:
data: The reconstruction whose max euclidean distance will be

calculated

node_types: restrict consideration to these types
Returns:
The distance between the soma and the farthest-from-soma node in this
morphology.