neurom.fst.get¶
-
neurom.fst.
get
(feature, obj, **kwargs)[source]¶ Obtain a feature from a set of morphology objects
Parameters: - feature (string) – feature to extract
- obj – a neuron, population or neurite tree
- **kwargs – parameters to forward to underlying worker functions
Returns: features as a 1D or 2D numpy array.
- Features:
- Neurite features (neurite, neuron, neuron population):
- local_bifurcation_angles:
Get a list of local bifurcation angles in a collection of neurites
- neurite_lengths:
Get the path length per neurite in a collection
- neurite_volume_density:
Get the volume density per neurite
The volume density is defined as the ratio of the neurite volume and the volume of the neurite’s enclosung convex hull
- neurite_volumes:
Get the volume per neurite in a collection
- number_of_bifurcations:
number of bifurcation points in a collection of neurites
- number_of_forking_points:
number of forking points in a collection of neurites
- number_of_neurites:
Number of neurites in a collection of neurites
- number_of_sections:
Number of sections in a collection of neurites
- number_of_sections_per_neurite:
Get the number of sections per neurite in a collection of neurites
- number_of_segments:
Number of sections in a collection of neurites
- number_of_terminations:
number of leaves points in a collection of neurites
- partition:
Partition at bifurcation points of a collection of neurites
- partition_asymmetry:
Partition asymmetry at bifurcation points of a collection of neurites
- principal_direction_extents:
Principal direction extent of neurites in neurons
- remote_bifurcation_angles:
Get a list of remote bifurcation angles in a collection of neurites
- section_areas:
section areas in a collection of neurites
- section_bif_branch_orders:
Bifurcation section branch orders in a collection of neurites
- section_bif_lengths:
Bifurcation section lengths in a collection of neurites
- section_branch_orders:
section branch orders in a collection of neurites
- section_lengths:
section lengths in a collection of neurites
- section_path_distances:
Path lengths of a collection of neurites
- section_radial_distances:
Remote bifurcation angles in a collection of neurites
- section_term_branch_orders:
Termination section branch orders in a collection of neurites
- section_term_lengths:
Termination section lengths in a collection of neurites
- section_tortuosity:
section tortuosities in a collection of neurites
- section_volumes:
section volumes in a collection of neurites
- segment_lengths:
Lengths of the segments in a collection of neurites
- segment_meander_angles:
Inter-segment opening angles in a section
- segment_midpoints:
Return a list of segment mid-points in a collection of neurites
- segment_radial_distances:
Lengths of the segments in a collection of neurites
- segment_radii:
arithmetic mean of the radii of the points in segments in a collection of neurites
- segment_taper_rates:
taper rates of the segments in a collection of neurites
The taper rate is defined as the absolute radii differences divided by length of the section
- segment_volumes:
Volumes of the segments in a collection of neurites
- terminal_path_lengths_per_neurite:
Get the path lengths to each terminal point per neurite in a collection
- total_length:
Get the total length of all sections in the group of neurons or neurites
- total_length_per_neurite:
Get the path length per neurite in a collection
- Neuron features (neuron, neuron population):
- soma_radii:
Get the radii of the somata of a population of neurons
- Note:
If a single neuron is passed, a single element list with the radius of its soma member is returned.
- soma_surface_areas:
Get the surface areas of the somata in a population of neurons
- Note:
The surface area is calculated by assuming the soma is spherical.
- Note:
If a single neuron is passed, a single element list with the surface area of its soma member is returned.
- trunk_origin_azimuths:
Get a list of all the trunk origin azimuths of a neuron or population
The azimuth is defined as Angle between x-axis and the vector defined by (initial tree point - soma center) on the x-z plane.
The range of the azimuth angle [-pi, pi] radians
- trunk_origin_elevations:
Get a list of all the trunk origin elevations of a neuron or population
The elevation is defined as the angle between x-axis and the vector defined by (initial tree point - soma center) on the x-y half-plane.
The range of the elevation angle [-pi/2, pi/2] radians
- trunk_origin_radii:
radii of the trunk sections of neurites in a neuron
- trunk_section_lengths:
list of lengths of trunk sections of neurites in a neuron