TotalSegmentator CT dataset v2.0.1: 1 228 CT volumes with 117 anatomical structures¶
pl.load("totalsegmentator_ct") loads this dataset. 1 228 CT examinations from the University Hospital Basel with 117 structures segmented (organs, vessels, bones, muscles) as one binary mask per structure - the data behind the TotalSegmentator model. Read subject by subject out of the 23.6 GB zip on Zenodo (HTTP Range: the 144 905-entry central directory costs 14 MB once, a CT a few MB). meta.csv at the archive root gives age, gender, institute and split.
import pardesline as pl
ds = pl.load("totalsegmentator_ct")
print(ds.describe()) # roles, frames, units, labels, licence, citation
s = ds[0]
obj = s.ct # fetched now, cached under ~/.cache/pardesline/datasets/totalsegmentator_ct
Provenance and licence¶
| Source | remote archive read by HTTP Range: https://zenodo.org/records/10047292/files/Totalsegmentator_dataset_v201.zip |
| Scheme | archive |
| Size of the whole source | 23.0 GB |
| Licence | CC-BY-4.0 |
| Commercial use | allowed by the licence |
| Redistribution | allowed |
| Licence note | CC BY 4.0 on the Zenodo record (checked 2026-10-14). The TotalSegmentator model weights are a separate work under their own (non-commercial) terms. |
| Terms | https://zenodo.org/records/10047292 |
| Homepage | https://github.com/wasserth/TotalSegmentator |
| Cite | Wasserthal J., Breit H.-C., Meyer M.T., et al. TotalSegmentator: Robust Segmentation of 104 Anatomic Structures in CT Images. Radiology: AI 5(5), 2023. |
| Samples grouped by | id |
Roles (what each sample contains)¶
| Role | Type | Frame | Units | Labels / layout | Pattern or file |
|---|---|---|---|---|---|
ct |
volume (CT) | from the file header | from the file header | {id}/ct.nii.gzCT image (NIfTI, LPS mm from the header) |
|
adrenal_gland_left |
labels | from the file header | from the file header | 1=adrenal_gland_left | {id}/segmentations/adrenal_gland_left.nii.gz |
adrenal_gland_right |
labels | from the file header | from the file header | 1=adrenal_gland_right | {id}/segmentations/adrenal_gland_right.nii.gz |
aorta |
labels | from the file header | from the file header | 1=aorta | {id}/segmentations/aorta.nii.gz |
atrial_appendage_left |
labels | from the file header | from the file header | 1=atrial_appendage_left | {id}/segmentations/atrial_appendage_left.nii.gz |
autochthon_left |
labels | from the file header | from the file header | 1=autochthon_left | {id}/segmentations/autochthon_left.nii.gz |
autochthon_right |
labels | from the file header | from the file header | 1=autochthon_right | {id}/segmentations/autochthon_right.nii.gz |
brachiocephalic_trunk |
labels | from the file header | from the file header | 1=brachiocephalic_trunk | {id}/segmentations/brachiocephalic_trunk.nii.gz |
brachiocephalic_vein_left |
labels | from the file header | from the file header | 1=brachiocephalic_vein_left | {id}/segmentations/brachiocephalic_vein_left.nii.gz |
brachiocephalic_vein_right |
labels | from the file header | from the file header | 1=brachiocephalic_vein_right | {id}/segmentations/brachiocephalic_vein_right.nii.gz |
brain |
labels | from the file header | from the file header | 1=brain | {id}/segmentations/brain.nii.gz |
clavicula_left |
labels | from the file header | from the file header | 1=clavicula_left | {id}/segmentations/clavicula_left.nii.gz |
clavicula_right |
labels | from the file header | from the file header | 1=clavicula_right | {id}/segmentations/clavicula_right.nii.gz |
colon |
labels | from the file header | from the file header | 1=colon | {id}/segmentations/colon.nii.gz |
common_carotid_artery_left |
labels | from the file header | from the file header | 1=common_carotid_artery_left | {id}/segmentations/common_carotid_artery_left.nii.gz |
common_carotid_artery_right |
labels | from the file header | from the file header | 1=common_carotid_artery_right | {id}/segmentations/common_carotid_artery_right.nii.gz |
costal_cartilages |
labels | from the file header | from the file header | 1=costal_cartilages | {id}/segmentations/costal_cartilages.nii.gz |
duodenum |
labels | from the file header | from the file header | 1=duodenum | {id}/segmentations/duodenum.nii.gz |
esophagus |
labels | from the file header | from the file header | 1=esophagus | {id}/segmentations/esophagus.nii.gz |
femur_left |
labels | from the file header | from the file header | 1=femur_left | {id}/segmentations/femur_left.nii.gz |
femur_right |
labels | from the file header | from the file header | 1=femur_right | {id}/segmentations/femur_right.nii.gz |
gallbladder |
labels | from the file header | from the file header | 1=gallbladder | {id}/segmentations/gallbladder.nii.gz |
gluteus_maximus_left |
labels | from the file header | from the file header | 1=gluteus_maximus_left | {id}/segmentations/gluteus_maximus_left.nii.gz |
gluteus_maximus_right |
labels | from the file header | from the file header | 1=gluteus_maximus_right | {id}/segmentations/gluteus_maximus_right.nii.gz |
gluteus_medius_left |
labels | from the file header | from the file header | 1=gluteus_medius_left | {id}/segmentations/gluteus_medius_left.nii.gz |
gluteus_medius_right |
labels | from the file header | from the file header | 1=gluteus_medius_right | {id}/segmentations/gluteus_medius_right.nii.gz |
gluteus_minimus_left |
labels | from the file header | from the file header | 1=gluteus_minimus_left | {id}/segmentations/gluteus_minimus_left.nii.gz |
gluteus_minimus_right |
labels | from the file header | from the file header | 1=gluteus_minimus_right | {id}/segmentations/gluteus_minimus_right.nii.gz |
heart |
labels | from the file header | from the file header | 1=heart | {id}/segmentations/heart.nii.gz |
hip_left |
labels | from the file header | from the file header | 1=hip_left | {id}/segmentations/hip_left.nii.gz |
hip_right |
labels | from the file header | from the file header | 1=hip_right | {id}/segmentations/hip_right.nii.gz |
humerus_left |
labels | from the file header | from the file header | 1=humerus_left | {id}/segmentations/humerus_left.nii.gz |
humerus_right |
labels | from the file header | from the file header | 1=humerus_right | {id}/segmentations/humerus_right.nii.gz |
iliac_artery_left |
labels | from the file header | from the file header | 1=iliac_artery_left | {id}/segmentations/iliac_artery_left.nii.gz |
iliac_artery_right |
labels | from the file header | from the file header | 1=iliac_artery_right | {id}/segmentations/iliac_artery_right.nii.gz |
iliac_vena_left |
labels | from the file header | from the file header | 1=iliac_vena_left | {id}/segmentations/iliac_vena_left.nii.gz |
iliac_vena_right |
labels | from the file header | from the file header | 1=iliac_vena_right | {id}/segmentations/iliac_vena_right.nii.gz |
iliopsoas_left |
labels | from the file header | from the file header | 1=iliopsoas_left | {id}/segmentations/iliopsoas_left.nii.gz |
iliopsoas_right |
labels | from the file header | from the file header | 1=iliopsoas_right | {id}/segmentations/iliopsoas_right.nii.gz |
inferior_vena_cava |
labels | from the file header | from the file header | 1=inferior_vena_cava | {id}/segmentations/inferior_vena_cava.nii.gz |
kidney_cyst_left |
labels | from the file header | from the file header | 1=kidney_cyst_left | {id}/segmentations/kidney_cyst_left.nii.gz |
kidney_cyst_right |
labels | from the file header | from the file header | 1=kidney_cyst_right | {id}/segmentations/kidney_cyst_right.nii.gz |
kidney_left |
labels | from the file header | from the file header | 1=kidney_left | {id}/segmentations/kidney_left.nii.gz |
kidney_right |
labels | from the file header | from the file header | 1=kidney_right | {id}/segmentations/kidney_right.nii.gz |
liver |
labels | from the file header | from the file header | 1=liver | {id}/segmentations/liver.nii.gz |
lung_lower_lobe_left |
labels | from the file header | from the file header | 1=lung_lower_lobe_left | {id}/segmentations/lung_lower_lobe_left.nii.gz |
lung_lower_lobe_right |
labels | from the file header | from the file header | 1=lung_lower_lobe_right | {id}/segmentations/lung_lower_lobe_right.nii.gz |
lung_middle_lobe_right |
labels | from the file header | from the file header | 1=lung_middle_lobe_right | {id}/segmentations/lung_middle_lobe_right.nii.gz |
lung_upper_lobe_left |
labels | from the file header | from the file header | 1=lung_upper_lobe_left | {id}/segmentations/lung_upper_lobe_left.nii.gz |
lung_upper_lobe_right |
labels | from the file header | from the file header | 1=lung_upper_lobe_right | {id}/segmentations/lung_upper_lobe_right.nii.gz |
pancreas |
labels | from the file header | from the file header | 1=pancreas | {id}/segmentations/pancreas.nii.gz |
portal_vein_and_splenic_vein |
labels | from the file header | from the file header | 1=portal_vein_and_splenic_vein | {id}/segmentations/portal_vein_and_splenic_vein.nii.gz |
prostate |
labels | from the file header | from the file header | 1=prostate | {id}/segmentations/prostate.nii.gz |
pulmonary_vein |
labels | from the file header | from the file header | 1=pulmonary_vein | {id}/segmentations/pulmonary_vein.nii.gz |
rib_left_1 |
labels | from the file header | from the file header | 1=rib_left_1 | {id}/segmentations/rib_left_1.nii.gz |
rib_left_10 |
labels | from the file header | from the file header | 1=rib_left_10 | {id}/segmentations/rib_left_10.nii.gz |
rib_left_11 |
labels | from the file header | from the file header | 1=rib_left_11 | {id}/segmentations/rib_left_11.nii.gz |
rib_left_12 |
labels | from the file header | from the file header | 1=rib_left_12 | {id}/segmentations/rib_left_12.nii.gz |
rib_left_2 |
labels | from the file header | from the file header | 1=rib_left_2 | {id}/segmentations/rib_left_2.nii.gz |
rib_left_3 |
labels | from the file header | from the file header | 1=rib_left_3 | {id}/segmentations/rib_left_3.nii.gz |
rib_left_4 |
labels | from the file header | from the file header | 1=rib_left_4 | {id}/segmentations/rib_left_4.nii.gz |
rib_left_5 |
labels | from the file header | from the file header | 1=rib_left_5 | {id}/segmentations/rib_left_5.nii.gz |
rib_left_6 |
labels | from the file header | from the file header | 1=rib_left_6 | {id}/segmentations/rib_left_6.nii.gz |
rib_left_7 |
labels | from the file header | from the file header | 1=rib_left_7 | {id}/segmentations/rib_left_7.nii.gz |
rib_left_8 |
labels | from the file header | from the file header | 1=rib_left_8 | {id}/segmentations/rib_left_8.nii.gz |
rib_left_9 |
labels | from the file header | from the file header | 1=rib_left_9 | {id}/segmentations/rib_left_9.nii.gz |
rib_right_1 |
labels | from the file header | from the file header | 1=rib_right_1 | {id}/segmentations/rib_right_1.nii.gz |
rib_right_10 |
labels | from the file header | from the file header | 1=rib_right_10 | {id}/segmentations/rib_right_10.nii.gz |
rib_right_11 |
labels | from the file header | from the file header | 1=rib_right_11 | {id}/segmentations/rib_right_11.nii.gz |
rib_right_12 |
labels | from the file header | from the file header | 1=rib_right_12 | {id}/segmentations/rib_right_12.nii.gz |
rib_right_2 |
labels | from the file header | from the file header | 1=rib_right_2 | {id}/segmentations/rib_right_2.nii.gz |
rib_right_3 |
labels | from the file header | from the file header | 1=rib_right_3 | {id}/segmentations/rib_right_3.nii.gz |
rib_right_4 |
labels | from the file header | from the file header | 1=rib_right_4 | {id}/segmentations/rib_right_4.nii.gz |
rib_right_5 |
labels | from the file header | from the file header | 1=rib_right_5 | {id}/segmentations/rib_right_5.nii.gz |
rib_right_6 |
labels | from the file header | from the file header | 1=rib_right_6 | {id}/segmentations/rib_right_6.nii.gz |
rib_right_7 |
labels | from the file header | from the file header | 1=rib_right_7 | {id}/segmentations/rib_right_7.nii.gz |
rib_right_8 |
labels | from the file header | from the file header | 1=rib_right_8 | {id}/segmentations/rib_right_8.nii.gz |
rib_right_9 |
labels | from the file header | from the file header | 1=rib_right_9 | {id}/segmentations/rib_right_9.nii.gz |
sacrum |
labels | from the file header | from the file header | 1=sacrum | {id}/segmentations/sacrum.nii.gz |
scapula_left |
labels | from the file header | from the file header | 1=scapula_left | {id}/segmentations/scapula_left.nii.gz |
scapula_right |
labels | from the file header | from the file header | 1=scapula_right | {id}/segmentations/scapula_right.nii.gz |
skull |
labels | from the file header | from the file header | 1=skull | {id}/segmentations/skull.nii.gz |
small_bowel |
labels | from the file header | from the file header | 1=small_bowel | {id}/segmentations/small_bowel.nii.gz |
spinal_cord |
labels | from the file header | from the file header | 1=spinal_cord | {id}/segmentations/spinal_cord.nii.gz |
spleen |
labels | from the file header | from the file header | 1=spleen | {id}/segmentations/spleen.nii.gz |
sternum |
labels | from the file header | from the file header | 1=sternum | {id}/segmentations/sternum.nii.gz |
stomach |
labels | from the file header | from the file header | 1=stomach | {id}/segmentations/stomach.nii.gz |
subclavian_artery_left |
labels | from the file header | from the file header | 1=subclavian_artery_left | {id}/segmentations/subclavian_artery_left.nii.gz |
subclavian_artery_right |
labels | from the file header | from the file header | 1=subclavian_artery_right | {id}/segmentations/subclavian_artery_right.nii.gz |
superior_vena_cava |
labels | from the file header | from the file header | 1=superior_vena_cava | {id}/segmentations/superior_vena_cava.nii.gz |
thyroid_gland |
labels | from the file header | from the file header | 1=thyroid_gland | {id}/segmentations/thyroid_gland.nii.gz |
trachea |
labels | from the file header | from the file header | 1=trachea | {id}/segmentations/trachea.nii.gz |
urinary_bladder |
labels | from the file header | from the file header | 1=urinary_bladder | {id}/segmentations/urinary_bladder.nii.gz |
vertebrae_c1 |
labels | from the file header | from the file header | 1=vertebrae_c1 | {id}/segmentations/vertebrae_C1.nii.gz |
vertebrae_c2 |
labels | from the file header | from the file header | 1=vertebrae_c2 | {id}/segmentations/vertebrae_C2.nii.gz |
vertebrae_c3 |
labels | from the file header | from the file header | 1=vertebrae_c3 | {id}/segmentations/vertebrae_C3.nii.gz |
vertebrae_c4 |
labels | from the file header | from the file header | 1=vertebrae_c4 | {id}/segmentations/vertebrae_C4.nii.gz |
vertebrae_c5 |
labels | from the file header | from the file header | 1=vertebrae_c5 | {id}/segmentations/vertebrae_C5.nii.gz |
vertebrae_c6 |
labels | from the file header | from the file header | 1=vertebrae_c6 | {id}/segmentations/vertebrae_C6.nii.gz |
vertebrae_c7 |
labels | from the file header | from the file header | 1=vertebrae_c7 | {id}/segmentations/vertebrae_C7.nii.gz |
vertebrae_l1 |
labels | from the file header | from the file header | 1=vertebrae_l1 | {id}/segmentations/vertebrae_L1.nii.gz |
vertebrae_l2 |
labels | from the file header | from the file header | 1=vertebrae_l2 | {id}/segmentations/vertebrae_L2.nii.gz |
vertebrae_l3 |
labels | from the file header | from the file header | 1=vertebrae_l3 | {id}/segmentations/vertebrae_L3.nii.gz |
vertebrae_l4 |
labels | from the file header | from the file header | 1=vertebrae_l4 | {id}/segmentations/vertebrae_L4.nii.gz |
vertebrae_l5 |
labels | from the file header | from the file header | 1=vertebrae_l5 | {id}/segmentations/vertebrae_L5.nii.gz |
vertebrae_s1 |
labels | from the file header | from the file header | 1=vertebrae_s1 | {id}/segmentations/vertebrae_S1.nii.gz |
vertebrae_t1 |
labels | from the file header | from the file header | 1=vertebrae_t1 | {id}/segmentations/vertebrae_T1.nii.gz |
vertebrae_t10 |
labels | from the file header | from the file header | 1=vertebrae_t10 | {id}/segmentations/vertebrae_T10.nii.gz |
vertebrae_t11 |
labels | from the file header | from the file header | 1=vertebrae_t11 | {id}/segmentations/vertebrae_T11.nii.gz |
vertebrae_t12 |
labels | from the file header | from the file header | 1=vertebrae_t12 | {id}/segmentations/vertebrae_T12.nii.gz |
vertebrae_t2 |
labels | from the file header | from the file header | 1=vertebrae_t2 | {id}/segmentations/vertebrae_T2.nii.gz |
vertebrae_t3 |
labels | from the file header | from the file header | 1=vertebrae_t3 | {id}/segmentations/vertebrae_T3.nii.gz |
vertebrae_t4 |
labels | from the file header | from the file header | 1=vertebrae_t4 | {id}/segmentations/vertebrae_T4.nii.gz |
vertebrae_t5 |
labels | from the file header | from the file header | 1=vertebrae_t5 | {id}/segmentations/vertebrae_T5.nii.gz |
vertebrae_t6 |
labels | from the file header | from the file header | 1=vertebrae_t6 | {id}/segmentations/vertebrae_T6.nii.gz |
vertebrae_t7 |
labels | from the file header | from the file header | 1=vertebrae_t7 | {id}/segmentations/vertebrae_T7.nii.gz |
vertebrae_t8 |
labels | from the file header | from the file header | 1=vertebrae_t8 | {id}/segmentations/vertebrae_T8.nii.gz |
vertebrae_t9 |
labels | from the file header | from the file header | 1=vertebrae_t9 | {id}/segmentations/vertebrae_T9.nii.gz |
Standardized layout¶
Files are fetched on first access into the dataset cache and stay in their original format; ds.export(folder) writes every sample as standard files (PLY for points and meshes, MetaImage for volumes and label maps) with a .pardesline.json sidecar carrying frame, units, labels, licence and provenance, plus a manifest for the folder. Label maps become exact surfaces with to_mesh(label=k), DICOM series become one volume, raw arrays are decoded through the layout above.
ds = pl.load("totalsegmentator_ct").take(2)
ds.export("./standardized") # PLY / MetaImage + sidecars + manifest.json
Algorithms and models that run on it¶
- labels roles:
mask.to_mesh(label=k),mask.to_numpy(), metrics:dice,hd95(evaluation-metrics-3d) ; catalog modules:pyvista_volume_processing,simpleitk_registration,simpleitk_segmentation - volume roles:
volume.align(moving),volume.segment(lower, upper),volume.to_mesh(isovalue=...),volume.to_sitk(); catalog modules:pyvista_volume_processing,simpleitk_registration,simpleitk_segmentation - Supervised segmentation:
prepare_nnunet_dataset.pywrites this dataset in the nnU-Net v2 raw layout; PointNet trains on the label surfaces. - Self-supervised pretraining: 3D JEPA reads the volumes directly.
Related¶
- Datasets catalog · How to download a medical imaging dataset in Python · Add a dataset
- Tags:
medical,ct,segmentation,nifti,whole-body,totalsegmentator
Generated from src/pardesline/data/manifests/totalsegmentator_ct.json on 2026-10-14.