diff --git a/README.md b/README.md new file mode 100644 index 0000000000000000000000000000000000000000..cf46ebc34d1269b8265271f74fbc7894090cd2b6 --- /dev/null +++ b/README.md @@ -0,0 +1,99 @@ +--- +license: apache-2.0 +task_categories: + - image-segmentation +modality: + - CT +language: [] +tags: + - medical-imaging + - whole-body-CT + - anatomy-segmentation + - autopet + - multi-organ +pretty_name: DAP Atlas +size_categories: + - n<1K +--- + +# DAP Atlas — Dense Anatomical Prediction Atlas + +Whole-body CT dataset with **142 anatomical structures** segmented across 533 volumes. +The CT images come from the AutoPET FDG-PET-CT-Lesions cohort; the segmentation masks +were produced by Jaus et al. (2023) via knowledge aggregation across 14 source datasets, +nnU-Net pseudo-labelling, and post-processing using anatomical guidelines. + +## Dataset Summary + +| Field | Details | +|---|---| +| Modality | CT (whole-body) | +| Body Part | Full body | +| Subjects | 482 unique patients (533 CT volumes — some patients have multiple studies) | +| Labels | 142 anatomical structures + background + unknown_tissue (144 entries, gap at ID 11) | +| Volume Shape | typically 512×512×~390 (varies per study) | +| Spacing | ~0.8 × 0.8 × 2.5 mm | +| Total Size | ~55 GB | +| Mask License | Apache-2.0 | +| CT License | TCIA Restricted (free-use; TCIA fully public since 2025-07-07) | + +## Data Structure + +``` +DAP_Atlas/ +├── images/ +│ └── AutoPET__.nii.gz # 533 CT volumes +├── masks/ +│ └── AutoPET__.nii.gz # 533 mask volumes (paired by filename) +└── labels.json # ID → anatomical structure name +``` + +CT and mask filenames are identical — pair each `images/X.nii.gz` with `masks/X.nii.gz`. +Mask voxels are uint8 with values in {0, 1, ..., 144} (with a gap at 11). See `labels.json` +for the canonical ID → name mapping (sourced from Table 2 of the paper). + +## Splits + +The released dataset has no official train/val/test split. All 533 cases form a single +pool. Downstream papers carve their own subsets. + +## Notes + +- **Mask source:** the published 533 NIfTI files are the V1 expert-validated masks + (`Atlas_final_dataset_V1_533/`). The repo also distributes nnU-Net model weights + (Task901 / Task902) for inference on new CTs; those are not redistributed here. +- **Costa numbering** is reversed vs. TotalSegmentator (DAP `costa_1` = lowest rib). + See https://github.com/alexanderjaus/AtlasDataset/issues/7 for the mapping. +- **Sex-conditional labels** (prostate, uterus, etc.) appear only for matching sex. +- ID 11 is intentionally absent. + +## Citation + +```bibtex +@article{jaus2023towards, + title = {Towards Unifying Anatomy Segmentation: Automated Generation of a + Full-body CT Dataset via Knowledge Aggregation and Anatomical Guidelines}, + author = {Jaus, Alexander and Seibold, Constantin and Hermann, Kelsey and + Walter, Alexandra and Giske, Kristina and Haubold, Johannes and + Kleesiek, Jens and Stiefelhagen, Rainer}, + journal = {arXiv preprint arXiv:2307.13375}, + year = {2023} +} + +@article{gatidis2022whole, + title = {A whole-body FDG-PET/CT dataset with manually annotated tumor lesions}, + author = {Gatidis, Sergios and Hepp, Tobias and Früh, Marcel and others}, + journal = {Scientific Data}, + volume = {9}, + number = {1}, + pages = {601}, + year = {2022}, + doi = {10.1038/s41597-022-01718-3} +} +``` + +## Sources + +- Original masks: https://github.com/alexanderjaus/AtlasDataset +- AutoPET CTs (TCIA): https://www.cancerimagingarchive.net/collection/fdg-pet-ct-lesions/ +- Paper: https://arxiv.org/abs/2307.13375 diff --git a/images/AutoPET_0011f3deaf_10445.nii.gz b/images/AutoPET_0011f3deaf_10445.nii.gz new file mode 100644 index 0000000000000000000000000000000000000000..41ae24ee21fb4e36606cdfe21e9d245d75f69c5d --- /dev/null +++ b/images/AutoPET_0011f3deaf_10445.nii.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:727c24288e9ea51378393c96afbc32548a58ddeb3046d33b13641c8b1a6bff18 +size 112854803 diff --git a/images/AutoPET_01140d52d8_56839.nii.gz b/images/AutoPET_01140d52d8_56839.nii.gz new file mode 100644 index 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Total: 144 entries. Excluding background (0) and unknown_tissue (1) gives 142 anatomical structures.", + "0": "background", + "1": "unknown_tissue", + "2": "muscles", + "3": "fat", + "4": "abdominal_tissue", + "5": "mediastinal_tissue", + "6": "esophagus", + "7": "stomach", + "8": "small_bowel", + "9": "duodenum", + "10": "colon", + "12": "gallbladder", + "13": "liver", + "14": "pancreas", + "15": "kidney_left", + "16": "kidney_right", + "17": "bladder", + "18": "gonads", + "19": "prostate", + "20": "uterocervix", + "21": "uterus", + "22": "breast_left", + "23": "breast_right", + "24": "spinal_canal", + "25": "brain", + "26": "spleen", + "27": "adrenal_gland_left", + "28": "adrenal_gland_right", + "29": "thyroid_left", + "30": "thyroid_right", + "31": "thymus", + "32": "gluteus_maximus_left", + "33": "gluteus_maximus_right", + "34": "gluteus_medius_left", + "35": "gluteus_medius_right", + "36": "gluteus_minimus_left", + "37": "gluteus_minimus_right", + "38": "iliopsoas_left", + "39": "iliopsoas_right", + "40": "autochthon_left", + "41": "autochthon_right", + "42": "skin", + "43": "vertebrae_C1", + "44": "vertebrae_C2", + "45": "vertebrae_C3", + "46": "vertebrae_C4", + "47": "vertebrae_C5", + "48": "vertebrae_C6", + "49": "vertebrae_C7", + "50": "vertebrae_T1", + "51": "vertebrae_T2", + "52": "vertebrae_T3", + "53": "vertebrae_T4", + "54": "vertebrae_T5", + "55": "vertebrae_T6", + "56": "vertebrae_T7", + "57": "vertebrae_T8", + "58": "vertebrae_T9", + "59": "vertebrae_T10", + "60": "vertebrae_T11", + "61": "vertebrae_T12", + "62": "vertebrae_L1", + "63": "vertebrae_L2", + "64": "vertebrae_L3", + "65": "vertebrae_L4", + "66": "vertebrae_L5", + "67": "costa_1_left", + "68": "costa_1_right", + "69": "costa_2_left", + "70": "costa_2_right", + "71": "costa_3_left", + "72": "costa_3_right", + "73": "costa_4_left", + "74": "costa_4_right", + "75": "costa_5_left", + "76": "costa_5_right", + "77": "costa_6_left", + "78": "costa_6_right", + "79": "costa_7_left", + "80": "costa_7_right", + "81": "costa_8_left", + "82": "costa_8_right", + "83": "costa_9_left", + "84": "costa_9_right", + "85": "costa_10_left", + "86": "costa_10_right", + "87": "costa_11_left", + "88": "costa_11_right", + "89": "costa_12_left", + "90": "costa_12_right", + "91": "rib_cartilage", + "92": "sternum_corpus", + "93": "clavicula_left", + "94": "clavicula_right", + "95": "scapula_left", + "96": "scapula_right", + "97": "humerus_left", + "98": "humerus_right", + "99": "skull", + "100": "hip_left", + "101": "hip_right", + "102": "sacrum", + "103": "femur_left", + "104": "femur_right", + "105": "heart", + "106": "heart_atrium_left", + "107": "heart_tissue", + "108": "heart_atrium_right", + "109": "heart_myocardium", + "110": "heart_ventricle_left", + "111": "heart_ventricle_right", + "112": "iliac_artery_left", + "113": "iliac_artery_right", + "114": "aorta", + "115": "iliac_vena_left", + "116": "iliac_vena_right", + "117": "inferior_vena_cava", + "118": "portal_vein_and_splenic_vein", + "119": "celiac_trunk", + "120": "lung_lower_lobe_left", + "121": "lung_upper_lobe_left", + "122": "lung_lower_lobe_right", + "123": "lung_middle_lobe_right", + "124": "lung_upper_lobe_right", + "125": "bronchus", + "126": "trachea", + "127": "pulmonary_artery", + "128": "cheek_left", + "129": "cheek_right", + "130": "eyeball_left", + "131": "eyeball_right", + "132": "nasal_cavity", + "133": "artery_common_carotid_right", + "134": "artery_common_carotid_left", + "135": "sternum_manubrium", + "136": "artery_internal_carotid_right", + "137": "artery_internal_carotid_left", + "138": "internal_jugular_vein_right", + "139": "internal_jugular_vein_left", + "140": "artery_brachiocephalic", + "141": "vein_brachiocephalic_right", + "142": "vein_brachiocephalic_left", + "143": "artery_subclavian_right", + "144": "artery_subclavian_left" +}