neurom stats: morphometric statistics extraction

The neurom stats application extracts morphometrics from a set of 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 morphology features.

An example usage:

neurom stats path/to/morph/file_or_dir --config path/to/config --output path/to/output/file

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

neurom stats --help

The functionality can be best explained by looking at a sample configuration file that is supposed to go under --config option:

Config

Short format (prior version 3.0.0)

An example config:

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

neurite_type:
    - AXON
    - APICAL_DENDRITE
    - BASAL_DENDRITE
    - ALL

neuron:
    soma_radius:
        - 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 morphology, e.g. the soma radius, the trunk radii, etc.

Each category sub-item (section_lengths, soma_radius, etc) corresponds to a neurom.get() feature, and each one of its sub-items corresponds to a statistic aggregating function, 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. It applies only to neurite features. A sample output using the above configuration:

{
  "some/path/morph.swc":{
    "mean_soma_radius":0.17071067811865476,
    "axon":{
      "sum_section_lengths":207.87975220908129,
      "max_section_lengths":11.018460736176685,
      "max_section_branch_orders":10,
      "sum_section_volumes":276.73857657289523
    },
    "all":{
      "sum_section_lengths":840.68521442251949,
      "max_section_lengths":11.758281556059444,
      "max_section_branch_orders":10,
      "sum_section_volumes":1104.9077419665782
    },
    "apical_dendrite":{
      "sum_section_lengths":214.37304577550353,
      "max_section_lengths":11.758281556059444,
      "max_section_branch_orders":10,
      "sum_section_volumes":271.9412385728449
    },
    "basal_dendrite":{
      "sum_section_lengths":418.43241643793476,
      "max_section_lengths":11.652508126101711,
      "max_section_branch_orders":10,
      "sum_section_volumes":556.22792682083821
    }
  }
}

Kwargs format (starting version 3.0.0)

The new format:

• requires to use morphology instead of neuron key in the config.

• requires to use sum instead of total statistic aggregating function.

• allows to specify features arguments.

For example, partition_asymmetry feature has additional arguments like method and variant (see neurom.features.neurite.partition_asymmetries()). Before it wasn’t possible to set them. Here is how you can set them now:

neurite:
    partition_asymmetry:
        kwargs:
           variant: 'length'
           method: 'petilla'
        modes:
           - max
           - sum

Instead of statistic aggregating functions right after a feature name, config expects kwargs and modes properties. The former sets the feature arguments. The latter sets the statistic aggregating function. This allows to set neurite_type directly on the feature, and overwrites global setting of neurite types via neurite_type global config field. For example:

neurite:
    section_lengths:
        kwargs:
           neurite_type: APICAL_DENDRITE
        modes:
           - max
           - sum

So the example config from Short format (prior version 3.0.0) looks:

neurite:
    section_lengths:
        modes:
           - max
           - sum
    section_volumes:
        modes:
           - sum
    section_branch_orders:
        modes:
           - max

neurite_type:
    - AXON
    - APICAL_DENDRITE
    - BASAL_DENDRITE
    - ALL

morphology:
    soma_radius:
        modes:
           - mean

List of features format (starting version 3.2.0)

The kwargs entry was converted into a list to allow running the same feature with different arguments. The partition_asymmetry feature in the example above can be specified multiple times with different arguments as follows:

neurite:
  partition_asymmetry:
    kwargs:
    - method: petilla
      variant: length
    - method: uylings
      variant: branch-order
    modes:
    - max
    - sum

To allow differentiation between the feature multiples, the keys and values of the kwargs are appended at the end of the feature name:

partition_asymmetry__variant:length__method:petilla
partition_asymmetry__variant:branch-order__method:uylings

The example config from Short format (prior version 3.0.0) becomes:

neurite:
  section_branch_orders:
    kwargs:
    - {}
    modes:
    - max
  section_lengths:
    kwargs:
    - {}
    modes:
    - max
    - sum
  section_volumes:
    kwargs:
    - {}
    modes:
    - sum
morphology:
  soma_radius:
    kwargs:
    - {}
    modes:
    - mean
neurite_type:
- AXON
- APICAL_DENDRITE
- BASAL_DENDRITE
- ALL

Features

All available features for --config are documented in neurom.features.morphology, neurom.features.neurite, neurom.features.population.