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