├── .github └── workflows │ ├── python-package.yml │ └── python-publish.yml ├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── README.md ├── airway ├── __init__.py ├── analysis │ ├── __init__.py │ ├── analyze_tree.py │ ├── create_color_masks.py │ ├── data_quality_evaluation.py │ ├── metadata.py │ └── plot_connected_lobes_status.py ├── classification │ ├── __init__.py │ ├── angle_analysis.py │ ├── clustering.py │ ├── lobe_validation.py │ ├── segment_validation.py │ └── split_classification.py ├── cli │ ├── __init__.py │ ├── base.py │ ├── cli.py │ ├── config.py │ ├── run_example.py │ ├── stages.py │ ├── tutorial.py │ └── visualization.py ├── configs │ ├── __init__.py │ ├── array_encoding.yaml │ ├── classification.yaml │ ├── example_defaults.yaml │ └── stage_configs.yaml ├── data_generation │ ├── __init__.py │ └── create_dummy_bronchus.py ├── example_data │ └── model.npz ├── image_processing │ ├── __init__.py │ ├── generate_bronchus_coords.py │ ├── remove_all_0_layers.py │ └── save_images_as_npz.py ├── jupyter_kmeans │ └── kmeans-airway.ipynb ├── obj_generation │ ├── __init__.py │ ├── gen_obj.py │ └── gen_split_obj.py ├── tree_extraction │ ├── __init__.py │ ├── bfs_distance_method.py │ ├── compose_tree.py │ ├── create_tree.py │ ├── post_processing.py │ └── separate_lobes.py ├── util │ ├── __init__.py │ ├── color.py │ ├── config_parsers.py │ ├── const.py │ ├── helper_functions.py │ ├── parsing.py │ └── util.py └── visualization │ ├── __init__.py │ ├── analyse_dist_to_coords.py │ ├── blender │ ├── __init__.py │ ├── render_with_blender.py │ └── run_blender.py │ ├── create_website.py │ ├── cytoscape │ ├── __init__.py │ ├── airway-gml.xml │ ├── airway-style-graphml.xml │ └── cytoscape-automation.py │ ├── generate_2d_tree.py │ ├── plot_dist_animation.py │ ├── plot_dist_to_first_split.py │ ├── plot_isometric.py │ ├── plot_lobes.py │ ├── plot_splits.py │ └── website │ ├── bin │ └── obj-simplify │ ├── fullscreen-bronchus.html │ ├── index.html │ ├── js │ ├── jsmodeler.ext.three.js │ ├── jsmodeler.js │ ├── online3dembedder.js │ └── three.min.js │ ├── split_type.png │ ├── style.css │ └── template.html ├── airway_cli.py ├── media ├── images │ ├── 3183090-tree.png │ ├── AnnotatedLung.png │ ├── AnnotatedLung2.png │ ├── bronchus-classification.png │ ├── bronchus0.png │ ├── bronchus_left_and_right_colored.png │ ├── bronchus_left_and_right_colored2.png │ ├── connection-status.png │ ├── distance-to-top.png │ ├── front-to-back-heatmap.png │ ├── left_upper_lobe0.png │ ├── lobe-2-3183090.graphml.png │ ├── lobe-3-3183090.graphml.png │ ├── lobe-4-3183090.graphml.png │ ├── lobe-5-3183090.graphml.png │ ├── lobe-6-3183090.graphml.png │ ├── lobe-visualization.png │ ├── lobe-visualization2.png │ ├── lungs-and-tree.png │ ├── pixel-count-per-distance.png │ ├── right-to-left-heatmap.png │ ├── top-to-bottom-heatmap.png │ ├── tree-only.png │ └── tree-with-annotations.png └── videos │ └── lung-bronchus.mp4 ├── requirements.txt ├── scripts └── 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