├── .binder ├── postBuild └── runtime.txt ├── .codecov.yml ├── .coveragerc ├── .gitattributes ├── .github └── workflows │ ├── mirror-ebrains.yml │ ├── publish-sdist.yml │ └── run-tox.yml ├── .gitignore ├── .gitlab-ci.yml ├── .readthedocs.yml ├── .zenodo.json ├── AUTHORS.md ├── CHANGELOG.rst ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── asv.conf.json ├── doc └── source │ ├── api.rst │ ├── changelog.rst │ ├── cli.rst │ ├── conf.py │ ├── definitions.rst │ ├── developer.rst │ ├── documentation.rst │ ├── examples.rst │ ├── features.rst │ ├── heterogeneous.rst │ ├── images │ ├── heterogeneous_neurite.png │ ├── heterogeneous_neuron.png │ ├── spherical_coordinates.svg │ └── spherical_coordinates.tex │ ├── index.rst │ ├── install.rst │ ├── license.rst │ ├── logo │ └── NeuroM.jpg │ ├── migration.rst │ ├── morph_check.rst │ ├── morph_stats.rst │ ├── quickstart.rst │ ├── spherical_coordinates.rst │ ├── tutorial.rst │ └── validation.rst ├── examples ├── boxplot.py ├── density_plot.py ├── end_to_end_distance.py ├── extract_distribution.py ├── features_graph_table.py ├── get_features.py ├── histogram.py ├── iteration_analysis.py ├── nl_fst_compat.py ├── plot_somas.py ├── radius_of_gyration.py ├── section_ids.py └── soma_radius_fit.py ├── neurom ├── __init__.py ├── apps │ ├── __init__.py │ ├── annotate.py │ ├── cli.py │ ├── config │ │ ├── morph_check.yaml │ │ └── morph_stats.yaml │ ├── morph_check.py │ └── morph_stats.py ├── check │ ├── __init__.py │ ├── morphology_checks.py │ ├── morphtree.py │ └── runner.py ├── core │ ├── __init__.py │ ├── dataformat.py │ ├── morphology.py │ ├── population.py │ ├── soma.py │ └── types.py ├── exceptions.py ├── features │ ├── __init__.py │ ├── bifurcation.py │ ├── morphology.py │ ├── neurite.py │ ├── population.py │ └── section.py ├── geom │ ├── __init__.py │ └── transform.py ├── io │ ├── __init__.py │ └── utils.py ├── morphmath.py ├── stats.py ├── utils.py └── view │ ├── __init__.py │ ├── dendrogram.py │ ├── matplotlib_impl.py │ ├── matplotlib_utils.py │ └── plotly_impl.py ├── pylintrc ├── pyproject.toml ├── setup.py ├── tests ├── __init__.py ├── apps │ ├── __init__.py │ ├── test_annotate.py │ ├── test_cli.py │ ├── test_config.py │ └── test_morph_stats.py ├── check │ ├── __init__.py │ ├── test_check.py │ ├── test_morphology_checks.py │ ├── test_morphtree.py │ └── test_runner.py ├── conftest.py ├── core │ ├── __init__.py │ ├── test_dataformat.py │ ├── test_iter.py │ ├── test_neurite.py │ ├── test_neuron.py │ ├── test_population.py │ ├── test_section.py │ ├── test_soma.py │ └── test_types.py ├── data │ ├── README.md │ ├── dataset │ │ └── point_neuron_feature_values.json │ ├── extracted-stats.csv │ ├── h5 │ │ ├── v1 │ │ │ ├── Neuron.h5 │ │ │ ├── Neuron_2_branch.h5 │ │ │ ├── big_neuron.h5 │ │ │ ├── bio_neuron-000.h5 │ │ │ ├── bio_neuron-001.h5 │ │ │ ├── deep_neuron.h5 │ │ │ └── ordering │ │ │ │ ├── sample.h5 │ │ │ │ └── sample_mixed_tree_sections.h5 │ │ └── v2 │ │ │ └── Neuron.h5 │ ├── mixed │ │ ├── expected_morphology_features.json │ │ ├── expected_neurite_features.json │ │ ├── expected_population_features.json │ │ └── mixed.h5 │ ├── neurolucida │ │ ├── axon-sprout-from-dendrite.asc │ │ ├── bio_neuron-000.asc │ │ ├── bio_neuron-001.asc │ │ ├── broken-spine.asc │ │ ├── multifurcation.asc │ │ ├── not_too_complex.asc │ │ ├── sample.asc │ │ └── spine.asc │ ├── neuromorpho │ │ └── README.md │ ├── swc │ │ ├── Neuron-flat.swc │ │ ├── Neuron-monotonic.swc │ │ ├── Neuron.swc │ │ ├── Neuron_3_random_walker_branches.swc │ │ ├── Neuron_disconnected_components.swc │ │ ├── Neuron_missing_ids.swc │ │ ├── Neuron_missing_parents.swc │ │ ├── Neuron_no_missing_ids_no_zero_segs.swc │ │ ├── Neuron_small_radius.swc │ │ ├── Neuron_zero_length_sections.swc │ │ ├── Neuron_zero_length_segments.swc │ │ ├── Neuron_zero_radius.swc │ │ ├── Single_apical.swc │ │ ├── Single_apical_no_soma.swc │ │ ├── Single_axon.swc │ │ ├── Single_basal.swc │ │ ├── Soma_origin.swc │ │ ├── Soma_translated_1.swc │ │ ├── Soma_translated_2.swc │ │ ├── custom_type.swc │ │ ├── dangling_axon.swc │ │ ├── dangling_dendrite.swc │ │ ├── empty_segments.swc │ │ ├── fat_end.swc │ │ ├── heterogeneous_morphology.swc │ │ ├── multiple_somata.swc │ │ ├── narrow_start.swc │ │ ├── no-axon.swc │ │ ├── non_increasing_trunk_off_1_16pt.swc │ │ ├── ordering │ │ │ ├── reversed_NRN_neurite_order.swc │ │ │ ├── sample.swc │ │ │ ├── sample_disordered.swc │ │ │ └── sample_mixed_tree_sections.swc │ │ ├── point_soma.swc │ │ ├── point_soma_single_neurite.swc │ │ ├── point_soma_single_neurite2.swc │ │ ├── random_trunk_off_0_16pt.swc │ │ ├── repeated_id.swc │ │ ├── root_node_jump.swc │ │ ├── sequential_trunk_off_0_16pt.swc │ │ ├── sequential_trunk_off_1_16pt.swc │ │ ├── sequential_trunk_off_42_16pt.swc │ │ ├── simple-different-section-types.swc │ │ ├── simple-different-soma.swc │ │ ├── simple.swc │ │ ├── simple_reversed.swc │ │ ├── simple_trunk.swc │ │ ├── soma │ │ │ ├── bifurcating_soma.swc │ │ │ └── three_pt_soma.swc │ │ ├── soma_with_neurite_parent.swc │ │ ├── soma_zero_radius.swc │ │ ├── split_soma_two_neurites.swc │ │ ├── strahler.swc │ │ ├── test_morph.swc │ │ ├── undefined_type.swc │ │ └── z_jump.swc │ ├── unsupported_extension.fake │ └── valid_set │ │ ├── Neuron.swc │ │ ├── Neuron_2_branch_h5v1.h5 │ │ ├── Neuron_h5v1.h5 │ │ ├── Neuron_slice.h5 │ │ └── README.md ├── features │ ├── __init__.py │ ├── test_bifurcation.py │ ├── test_features.py │ ├── test_get_features.py │ ├── test_morphology.py │ ├── test_neurite.py │ ├── test_population.py │ └── test_section.py ├── geom │ ├── __init__.py │ ├── test_geom.py │ └── test_transform.py ├── io │ ├── __init__.py │ ├── test_io_utils.py │ ├── test_neurolucida.py │ └── test_swc_reader.py ├── test_examples.py ├── test_import.py ├── test_mixed.py ├── test_morphmath.py ├── test_stats.py ├── test_utils.py └── view │ ├── __init__.py │ ├── conftest.py │ ├── test_dendrogram.py │ ├── test_matplotlib_impl.py │ ├── test_matplotlib_utils.py │ └── test_plotly_impl.py ├── 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