Releases: lassoan/SlicerMONAIAuto3DSeg
3D Slicer MONAI Auto3DSeg models
Testing hardware: Intel(R) Core(TM) i9-10900X CPU @ 3.70GHz, 64 GB RAM, NVIDIA GeForce RTX 3090 24GB
Abdominal organs TS2 - quick (v2.0.0)
Low-resolution (3mm) for quick preview. Trained on class_map_part_organs of TotalSegmentatorV2 dataset. Input image is abdominal, chest, or whole body CT.
Processing time: 30 sec on GPU, 55 sec on CPU
Segment names: Left Adrenal gland, Right Adrenal gland, Colon, Duodenum, Esophagus, Gallbladder, Left Kidney, Right Kidney, Liver, Left Lower lobe of lung, Right Lower lobe of lung, Middle lobe of right lung, Left Upper lobe of lung, Right Upper lobe of lung, Pancreas, Small Intestine, Spleen, Stomach, Trachea, Urinary bladder, Cyst in Left Kidney, Cyst in Right Kidney, Prostate
Abdominal organs TS2 (v2.0.0)
Trained on class_map_part_organs of TotalSegmentatorV2 dataset. Input image is abdominal, chest, or whole body CT.
Processing time: 30 sec on GPU, 3 min on CPU
Segment names: Left Adrenal gland, Right Adrenal gland, Colon, Duodenum, Esophagus, Gallbladder, Left Kidney, Right Kidney, Liver, Left Lower lobe of lung, Right Lower lobe of lung, Middle lobe of right lung, Left Upper lobe of lung, Right Upper lobe of lung, Pancreas, Small Intestine, Spleen, Stomach, Trachea, Urinary bladder, Cyst in Left Kidney, Cyst in Right Kidney, Prostate
Body TS2 (v2.0.0)
Trained on TotalSegmentatorV2 dataset. Input image is abdominal, chest, or whole body CT.
Processing time: 25 sec on GPU, 6 min on CPU
Segment names: Trunk, Limb
Body TS2 - quick (v2.0.0)
Low-resolution (3mm) for quick preview. Trained on TotalSegmentatorV2 dataset. Input image is abdominal, chest, or whole body CT.
Processing time: 20 sec on GPU, 50 sec on CPU
Segment names: Trunk, Limb
Vertebrae TS2 - quick (v2.0.0)
Low-resolution (3mm) for quick preview. Trained on class_map_part_vertebrae of TotalSegmentatorV2 dataset. Input image is abdominal, chest, or whole body CT.
Processing time: 20 sec on GPU, 55 sec on CPU
Segment names: Sacrum, C1 vertebra, C2 vertebra, C3 vertebra, C4 vertebra, C5 vertebra, C6 vertebra, C7 vertebra, L1 vertebra, L2 vertebra, L3 vertebra, L4 vertebra, L5 vertebra, T1 vertebra, T2 vertebra, T3 vertebra, T4 vertebra, T5 vertebra, T6 vertebra, T7 vertebra, T8 vertebra, T9 vertebra, T10 vertebra, T11 vertebra, T12 vertebra
Vertebrae TS2 (v2.0.0)
Trained on class_map_part_vertebrae of TotalSegmentatorV2 dataset. Input image is abdominal, chest, or whole body CT.
Processing time: 25 sec on GPU, 7 min on CPU
Segment names: Sacrum, C1 vertebra, C2 vertebra, C3 vertebra, C4 vertebra, C5 vertebra, C6 vertebra, C7 vertebra, L1 vertebra, L2 vertebra, L3 vertebra, L4 vertebra, L5 vertebra, T1 vertebra, T2 vertebra, T3 vertebra, T4 vertebra, T5 vertebra, T6 vertebra, T7 vertebra, T8 vertebra, T9 vertebra, T10 vertebra, T11 vertebra, T12 vertebra
Mediastinal anatomy TS2 (v2.0.1)
Trained on TotalSegmentatorV2 dataset. Input image is abdominal, chest, or whole body CT.
Processing time: 30 sec on GPU, 7 min on CPU
Segment names: Aorta, Esophagus, Inferior vena cava, Left Lower lobe of lung, Right Lower lobe of lung, Middle lobe of right lung, Left Upper lobe of lung, Right Upper lobe of lung, Pulmonary artery, Trachea, Heart, Pulmonary vein, Brachiocephalic artery, Right Subclavian artery, Left Subclavian artery, Right Common carotid artery, Left Common carotid artery, Left Brachiocephalic vein, Right Brachiocephalic vein, Left Entire atrial appendage, Superior Vena cava, Blood vessel in Lung
Mediastinal anatomy TS2 - quick (v2.0.0)
Low-resolution (3mm) for quick preview. Trained on TotalSegmentatorV2 dataset. Input image is abdominal, chest, or whole body CT.
Processing time: 20 sec on GPU, 50 sec on CPU
Segment names: Aorta, Esophagus, Inferior vena cava, Left Lower lobe of lung, Right Lower lobe of lung, Middle lobe of right lung, Left Upper lobe of lung, Right Upper lobe of lung, Trachea, Heart, Pulmonary vein, Brachiocephalic artery, Right Subclavian artery, Left Subclavian artery, Right Common carotid artery, Left Common carotid artery, Left Brachiocephalic vein, Right Brachiocephalic vein, Left Entire atrial appendage, Superior Vena cava
Whole body segmentation TS1 (v1.0.0)
Segment 104 structures (abdominal organs, bones, vessels) on CT images. Trained on TotalSegmentatorV1 dataset.
Processing time: 45 sec on GPU, 4 min on CPU
Segment names: Left Adrenal gland, Right Adrenal gland, Aorta, Left Deep muscle of back, Right Deep muscle of back, Brain, Left Clavicle, Right Clavicle, Colon, Duodenum, Esophagus, Face, Left Femur, Right Femur, Gallbladder, Left Gluteus maximus muscle, Right Gluteus maximus muscle, Left Gluteus medius muscle, Right Gluteus medius muscle, Left Gluteus minius muscle, Right Gluteus minius muscle, Left atrium, Right atrium, Myocardium, Left ventricle of heart, Right ventricle of heart, Left Hip, Right Hip, Left Humerus, Right Humerus, Left Common iliac artery, Right Common iliac artery, Left Common iliac vein, Right Common iliac vein, Left Iliopsoas muscle, Right Iliopsoas muscle, Inferior vena cava, Left Kidney, Right Kidney, Liver, Left Lower lobe of lung, Right Lower lobe of lung, Middle lobe of right lung, Left Upper lobe of lung, Right Upper lobe of lung, Pancreas, Portal vein and splenic vein, Pulmonary artery, Left First rib, Left Second rib, Left Third rib, Left Fourth rib, Left Fifth rib, Left Sixth rib, Left Seventh rib, Left Eighth rib, Left Ninth rib, Left Tenth rib, Left Eleventh rib, Left Twelfth rib, Right First rib, Right Second rib, Right Third rib, Right Fourth rib, Right Fifth rib, Right Sixth rib, Right Seventh rib, Right Eighth rib, Right Ninth rib, Right Tenth rib, Right Eleventh rib, Right Twelfth rib, Sacrum, Left Scapula, Right Scapula, Small Intestine, Spleen, Stomach, Trachea, Urinary bladder, C1 vertebra, C2 vertebra, C3 vertebra, C4 vertebra, C5 vertebra, C6 vertebra, C7 vertebra, L1 vertebra, L2 vertebra, L3 vertebra, L4 vertebra, L5 vertebra, T1 vertebra, T2 vertebra, T3 vertebra, T4 vertebra, T5 vertebra, T6 vertebra, T7 vertebra, T8 vertebra, T9 vertebra, T10 vertebra, T11 vertebra, T12 vertebra
Whole body segmentation TS1 - quick (v1.0.0)
Segment 104 structures (abdominal organs, bones, vessels) on CT images. Trained on TotalSegmentatorV1 dataset.
Processing time: 35 sec on GPU, 1 min on CPU
Segment names: Left Adrenal gland, Right Adrenal gland, Aorta, Left Deep muscle of back, Right Deep muscle of back, Brain, Left Clavicle, Right Clavicle, Colon, Duodenum, Esophagus, Face, Left Femur, Right Femur, Gallbladder, Left Gluteus maximus muscle, Right Gluteus maximus muscle, Left Gluteus medius muscle, Right Gluteus medius muscle, Left Gluteus minius muscle, Right Gluteus minius muscle, Left atrium, Right atrium, Myocardium, Left ventricle of heart, Right ventricle of heart, Left Hip, Right Hip, Left Humerus, Right Humerus, Left Common iliac artery, Right Common iliac artery, Left Common iliac vein, Right Common iliac vein, Left Iliopsoas muscle, Right Iliopsoas muscle, Inferior vena cava, Left Kidney, Right Kidney, Liver, Left Lower lobe of lung, Right Lower lobe of lung, Middle lobe of right lung, Left Upper lobe of lung, Right Upper lobe of lung, Pancreas, Portal vein and splenic vein, Pulmonary artery, Left First rib, Left Second rib, Left Third rib, Left Fourth rib, Left Fifth rib, Left Sixth rib, Left Seventh rib, Left Eighth rib, Left Ninth rib, Left Tenth rib, Left Eleventh rib, Left Twelfth rib, Right First rib, Right Second rib, Right Thir...
TestingData
Release that contains testing data sets as release assets.
Source:
ProstateX-...: ProstateX data set on TCIAmsd-prostate-...: Medical Segmentation Decathlon data set - Task05 ProstateBRATS-...:Brain Tumor Segmentation - BRATS 2023ICH-ADAPT2-...: Sample image from ICH ADAPT II trial for intracranial hemorrhage