├── .gitignore ├── README.md ├── data_test ├── Task01_BrainTumour │ ├── imagesTr │ │ ├── BRATS_002_100.jpg │ │ ├── BRATS_002_101.jpg │ │ ├── BRATS_002_102.jpg │ │ ├── BRATS_002_103.jpg │ │ ├── BRATS_002_104.jpg │ │ ├── BRATS_002_105.jpg │ │ ├── BRATS_002_106.jpg │ │ ├── BRATS_002_107.jpg │ │ ├── BRATS_002_108.jpg │ │ └── BRATS_002_109.jpg │ └── labelsTr_npz │ │ ├── BRATS_002_100.npz │ │ ├── BRATS_002_101.npz │ │ ├── BRATS_002_102.npz │ │ ├── BRATS_002_103.npz │ │ ├── BRATS_002_104.npz │ │ ├── BRATS_002_105.npz │ │ ├── BRATS_002_106.npz │ │ ├── BRATS_002_107.npz │ │ ├── BRATS_002_108.npz │ │ └── BRATS_002_109.npz ├── Task06_Lung │ ├── imagesTr │ │ ├── lung_004_280.jpg │ │ ├── lung_004_281.jpg │ │ ├── lung_004_282.jpg │ │ ├── lung_004_283.jpg │ │ ├── lung_004_284.jpg │ │ ├── lung_004_285.jpg │ │ ├── lung_004_286.jpg │ │ ├── lung_004_287.jpg │ │ ├── lung_004_288.jpg │ │ └── lung_004_289.jpg │ └── labelsTr_npz │ │ ├── lung_004_280.npz │ │ ├── lung_004_281.npz │ │ ├── lung_004_282.npz │ │ ├── lung_004_283.npz │ │ ├── lung_004_284.npz │ │ ├── lung_004_285.npz │ │ ├── lung_004_286.npz │ │ ├── lung_004_287.npz │ │ ├── lung_004_288.npz │ │ └── lung_004_289.npz └── Task07_Pancreas │ ├── imagesTr │ ├── pancreas_001_90.jpg │ ├── pancreas_001_91.jpg │ ├── pancreas_001_92.jpg │ ├── pancreas_001_93.jpg │ ├── pancreas_001_94.jpg │ ├── pancreas_001_95.jpg │ ├── pancreas_001_96.jpg │ ├── pancreas_001_97.jpg │ ├── pancreas_001_98.jpg │ └── pancreas_001_99.jpg │ └── labelsTr_npz │ ├── pancreas_001_90.npz │ ├── pancreas_001_91.npz │ ├── pancreas_001_92.npz │ ├── pancreas_001_93.npz │ ├── pancreas_001_94.npz │ ├── pancreas_001_95.npz │ ├── pancreas_001_96.npz │ ├── pancreas_001_97.npz │ ├── pancreas_001_98.npz │ └── pancreas_001_99.npz ├── medseg ├── __init__.py ├── datagen.py ├── engine.py ├── models │ ├── DenseNet3D.py │ ├── DilatedDenseNet.py │ ├── UNet2D.py │ └── __init__.py └── utils.py ├── misc ├── save_resized_volumes.ipynb ├── save_resized_volumes.py └── slice_data.py ├── notebooks └── data_exploration.ipynb ├── output ├── debug │ ├── debug.yaml │ └── logs │ │ ├── accuracy.png │ │ ├── log.csv │ │ └── loss.png └── debug_segment │ ├── debug_segment.yaml │ ├── logs │ ├── accuracy.png │ ├── log.csv │ └── loss.png │ └── outputs │ ├── Task01_BrainTumour │ ├── BRATS_002_100.jpg │ ├── BRATS_002_101.jpg │ ├── BRATS_002_102.jpg │ ├── BRATS_002_103.jpg │ ├── BRATS_002_104.jpg │ ├── BRATS_002_105.jpg │ ├── BRATS_002_106.jpg │ ├── BRATS_002_107.jpg │ ├── BRATS_002_108.jpg │ └── BRATS_002_109.jpg │ ├── Task06_Lung │ ├── lung_001_100.jpg │ ├── lung_001_101.jpg │ ├── lung_001_102.jpg │ ├── lung_001_103.jpg │ ├── lung_001_104.jpg │ ├── lung_001_105.jpg │ ├── lung_001_106.jpg │ ├── lung_001_107.jpg │ ├── lung_001_108.jpg │ ├── lung_001_109.jpg │ ├── lung_001_266.jpg │ ├── lung_001_272.jpg │ ├── lung_001_299.jpg │ ├── lung_003_149.jpg │ ├── lung_003_161.jpg │ ├── lung_003_175.jpg │ ├── lung_003_18.jpg │ ├── lung_003_24.jpg │ ├── lung_004_11.jpg │ ├── lung_004_280.jpg │ ├── lung_004_281.jpg │ ├── lung_004_282.jpg │ ├── lung_004_283.jpg │ ├── lung_004_284.jpg │ ├── lung_004_285.jpg │ ├── lung_004_286.jpg │ ├── lung_004_287.jpg │ ├── lung_004_288.jpg │ ├── lung_004_289.jpg │ ├── lung_004_323.jpg │ └── lung_004_337.jpg │ └── Task07_Pancreas │ ├── pancreas_001_0.jpg │ ├── pancreas_001_1.jpg │ ├── pancreas_001_2.jpg │ ├── pancreas_001_3.jpg │ ├── pancreas_001_4.jpg │ ├── pancreas_001_5.jpg │ ├── pancreas_001_6.jpg │ ├── pancreas_001_7.jpg │ ├── pancreas_001_8.jpg │ ├── pancreas_001_9.jpg │ ├── pancreas_001_90.jpg │ ├── pancreas_001_91.jpg │ ├── pancreas_001_92.jpg │ ├── pancreas_001_93.jpg │ ├── pancreas_001_94.jpg │ ├── pancreas_001_95.jpg │ ├── pancreas_001_96.jpg │ ├── pancreas_001_97.jpg │ ├── pancreas_001_98.jpg │ └── pancreas_001_99.jpg └── scripts ├── classify.ipynb ├── classify.py ├── configs ├── config_classify.yaml ├── config_segment_densenet.yaml └── config_segment_unet.yaml ├── segment.ipynb ├── segment.py └── test_segment.ipynb /.gitignore: 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