morph_stats: morphometric statistics extraction

The morph_stats application extracts morphometrics from a set of neuron morphology files and produces a summary in JSON or CSV format. It may obtain any of the morphometrics available in the neurom.get() function, and is highly configurable, allowing the user to get raw or summary statistics from a large set of neurite and neuron features.

The functionality can be best explained by looking at a sample configuration file:

neurite:
    section_lengths:
        - max
        - total
    section_volumes:
        - total
    section_branch_orders:
        - max

neurite_type:
    - AXON
    - APICAL_DENDRITE
    - BASAL_DENDRITE
    - ALL

neuron:
    soma_radii:
        - mean

Here, there are two feature categories,

1. neurite: these are morphometrics obtained from neurites, e.g. branch orders, section lengths, bifurcation angles, path lengths.
2. neuron: these are morphometrics that can be applied to a whole neuron, e.g. the soma radius, the trunk radii, etc.

Each category sub-item (section_lengths, soma_radii, etc) corresponds to a neurom.get() feature, and each one of its sub-items corresponds to a statistic, e.g.

• raw: array of raw values
• max, min, mean, median, std: self-explanatory.
• total: sum of the raw values

An additional field neurite_type specifies the neurite types into which the morphometrics are to be split. This is a sample output using the above configuration:

{
  "some/path/morph.swc":{
    "mean_soma_radius":0.17071067811865476,
    "axon":{
      "total_section_length":207.87975220908129,
      "max_section_length":11.018460736176685,
      "max_section_branch_order":10,
      "total_section_volume":276.73857657289523
    },
    "all":{
      "total_section_length":840.68521442251949,
      "max_section_length":11.758281556059444,
      "max_section_branch_order":10,
      "total_section_volume":1104.9077419665782
    },
    "apical_dendrite":{
      "total_section_length":214.37304577550353,
      "max_section_length":11.758281556059444,
      "max_section_branch_order":10,
      "total_section_volume":271.9412385728449
    },
    "basal_dendrite":{
      "total_section_length":418.43241643793476,
      "max_section_length":11.652508126101711,
      "max_section_branch_order":10,
      "total_section_volume":556.22792682083821
    }
  }
}

For more information on the application and available options, invoke it with the --help or -h option.

morph_stats --help

Features

$ morph_stats -l

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