morph_stats: morphometric statistics extractionΒΆ

The morph_stats application extracts morphometrics from a set of neuron morpholigy files and produces a summary JSON output. 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_lehgths, 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