morph_check: the morphology checker

The morph_check application performs checks on reconstructed morphologies from data contained in morphology files, and so may be used as a morphology validaiton of sorts.

The tests are grouped in two categories:

1. Structural tests. These apply to the structure of the data and are a good indicator as to whether a neuron object or any of its sub-components can actually be reconstructed. Failure in some of these may make further tests fail.
2. Neuron tests. These are applied to properties of reconstructed neurons and their constituent soma and neurites, and can be thought of as “quality” checks.

It is very likely that a failure in the structural tests will make the neuron tests fail. Furthermore, inability to build a soma typically results in an inability to build neurites. Failure to build a soma or neurites results in an early faulure for a given morphology file.

The application may be invoked with a YAML configuration file specifying which checks to perform. The structure of the configuration file reflects the test categories mentioned above. Here is an example configuration:

checks:
    structural_checks:
        - is_single_tree
        - has_soma_points
        - has_valid_soma
        - has_valid_neurites
    neuron_checks:
        - has_basal_dendrite
        - has_axon
        - has_all_nonzero_segment_lengths
        - has_all_nonzero_section_lengths
        - has_all_nonzero_neurite_radii
        - has_nonzero_soma_radius

options :
    has_nonzero_soma_radius         : 0.0
    has_all_nonzero_neurite_radii   : 0.007
    has_all_nonzero_segment_lengths : 0.01
    has_all_nonzero_section_lengths : 0.01

As can be seen, the configuration file is split into two sections checks, and options. Each of the checks sub-items corresponds to a sub-module of neurom.check, namely structural_checks and neuron_checks. And each of their sub-items corresponds to a function in that sub-module. This illustrates the possible checks that may be applied by morph_check.

The application also produces a summary json file, which can be useful when processing more than one file:

{
    "files": {
        "test_data/swc/Neuron.swc": {
            "Is single tree": true,
            "Has soma points": true,
            "No missing parents": true,
            "Has sequential ids": true,
            "Has increasing ids": true,
            "Has valid soma": true,
            "Has valid neurites": true,
            "Has basal dendrite": true,
            "Has axon": true,
            "Has apical dendrite": true,
            "Has all nonzero segment lengths": true,
            "Has all nonzero section lengths": true,
            "Has all nonzero neurite radii": true,
            "Has nonzero soma radius": true,
            "ALL": true
        }
    },
    "STATUS": "PASS"
}

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

morph_check --help