A list of biomedical imaging datasets with a focus on segmentation. Feel free to contribute!
| Dataset | Description | Labels / Task(s) | Image Type(s) | Dim. |
|---|---|---|---|---|
| 3DTeethSeg22 | MICCAI 2022 Challenge. 1,800 scans for 900 patients covering upper and lower jaws separately. Tooth labels and instances | Instance Segmentation | Intra-oral scan | 3D |
| AbdomenCT-1K | FLARE2022 and FLARE2023 Challenges. Abdominal organ segmentation (overlap with KiTS, LiTS, MSD, NIH-PancreasCT) | Segmentation | CT | 3D |
| AbdomenAtlas | Abdominal organ segmentation. New labels for existing abdominal CT datasets. | Segmentation | CT | 3D |
| AbdominalUS | 617 real and 926 simulated US scans. Abdominal organ segmentations (liver, kidneys, gallbladder, spleen and vessels) on a subset of 61 real scans. | Segmentation | Ultrasound | 2D |
| ACDC | Left and right ventricular endocardium | Segmentation, Classification, Scribbles | Cine-MRI | 3D |
| ADHD200 | Brain | Segmentation | fMRI | 3D |
| ADNI | Brain | Segmentation | MRI, Pet | 3D |
| AirwaySeg | Airway segmentation and centerline extraction from thoracic CT | Segmentation | CT | 3D |
| AMOS | Adominal Organ Segmentation | Segmentation | CT | 3D |
| ATLAS | Lesion segmentation | Segmentation | T1-MRI | 3D |
| BBBC003 | Mouse embryo | Segmentation | Microscopy | 2D |
| BBC024 | Synthetic | Instance Segmentation | Microscopy | 3D |
| BBC038 | Kaggle 2018 Data Science Bowl. Nuclei segmentation in diverse biological images | Instance Segmentation | Microscopy | 2D |
| BBBC039 | Nuclei of U2OS cells in a chemical screen, 200 images | Instance Segmentation | Microscopy | 2D |
| BCIHM | CT images for intracranial hemorrhage detection and segmentation | Classification, Segmentation | CT | 3D |
| BCN20k | Diagnostic classification of dermatology images | Classification | Derm | 2D |
| BCSS | 20,000 segmentation annotations of tissue region from breast cancer images from TCGA | Segmentation | WSI | 2D |
| BF-TMA | Aligned Bright-Field (BF) and Second-Harmonic Generation (SHG) images | Registration | Microscopy | 2D |
| BHSD | Brain Hemorrhage Segmentation Dataset | Classification, Segmentation | CT | 3D |
| BTCV | Abdominal organ segmentation in scans from colorectal cancer patients and cervical cancer patients. Subdatasets: Abdominal and Cervix | Segmentation, Registration | CT | 3D |
| BrainMetShare | 156 whole brain MRI studies, including high-resolution, multi-modal pre- and post-contrast sequences in patients with at least 1 brain metastasis | Segmentation, Detection | Multimodal MRI | 3D |
| BrainPTM | Brain Pre-surgical white matter Tractography Mapping challenge (BrainPTM) 2021Brain | Segmentation | MRI | 3D |
| BRATS | Brain tumors | Multi-Annotator Segmentation | Multimodal MRI | 3D |
| BUID | 780 breast ultrasounds from 600 patients. Tumor segmentation with benign/malignant labels | Segmentation, Classification | Ultrasound | 2D |
| BUSIS | Breast ultrasound image segmentation | Segmentation | Ultrasound | 2D |
| BUSI | Breast ultrasound images | Segmentation | Ultrasound | 2D |
| Calgary-Campinas | T1 volumes acquired in 359 adult subjects on scanners from three different vendors (GE, Philips, and Siemens) and at two magnetic field strengths (1.5 T and 3 T). Hypothalamus and thalmus segmentation | Segmentation | T1-MRI | 3D |
| CAMUS | Four-chamber and Apical two-chamber heart | Segmentation | Ultrasound | 2D |
| CANDID-PTX | Chest X-Rays. Segmentations from CheXmask | Segmentation | X-Ray | 2D |
| CannabisT1 | Brain | Just Images | T1-MRI | 3D |
| cDEMRIS | Fibrosis and scar segmentation in Late Gadolinium enhancement (LGE) cardiovascular magnetic resonance (CMR) of the left atrium (LA) myocardium | Segmentation | CMR | 3D |
| CHAOS | Abdominal organ segmentation (liver, kidneys and spleen) | Segmentation | CT, T2-MRI | 3D |
| CHASE | Retinal vein segmentation | Multi-annotator Seg. | Retinal | 2D |
| ChestX-Det | ~3500 images of 13 common disease categories with instance level bounding boxes and masks. Images from NIH ChestX-ray8 | Segmentation | X-Ray | 2D |
| ChestX-ray14 | Expansion of ChestX-ray8. 112,120 frontal-view X-rays with text-mined labels | Segmentation | X-Ray | 2D |
| CheXmask | Anatomical segmentations (polygons) for a bunch of chest X-Raychest x-ray imagesMasks corresponding to images in a bunch of public datasets | Segmentation | X-Ray | 2D |
| CheXpert | 224,316 Chest X-Rays with labels for 14 observations from reports. Segmentations from CheXmask | Segmentation, Classification | X-Ray | 2D |
| CheXLocalize | Segmentations for 10 pathologies in Chest X-Rays. Images from CheXpert | Segmentation | X-Ray | 2D |
| COBRE | Brain MRI from patients with Schizophrenia and healthy controls | Just Images | MRI | 3D |
| COCA | 1) gated coronary CTs with corresponding coronary artery calcium segmentations and scores 2) non-gated chest CTs with coronary artery calcium scores | Segmentation | CT | 3D |
| CoNSeP | Histopathology Nuclei | Segmentation | Microscopy | 2D |
| Couinaud | Liver and couinaud segments on images from MSD (task 8, hepatic vessels and tumor) | Segmentation | CT | 3D |
| COVID-CT | CT images of subjects with confirmed lung infections after positive Covid-19 diagnosis | Just Images | CT | 3D |
| COVID-19 | Chest CT from patients with COVID-19. Some longitudinal scans. | Just Images | CT | 3D |
| CQ500 | 491 Brain scans and the corresponding radiologists' reads | Classification | CT | 3D |
| CT-ORG | CT volumes with multiple organ segmentations. Overlap with LiTS. | Segmentation | CT | 3D |
| CT2US | CT2USforKidneySeg. 4586 images synthesized US using a GAN trained on KiTS CT and other US | Segmentation | Ultrasound | 2D |
| CTooth | Tooth segmentation | Segmentation | CBCT | 3D |
| CTSpine1k | Individual vertebra segmentations. Images from COLONOG, HNSCC-3DCT-RT, MSD T10 and COVID-19 | Segmentation | CT | 3D |
| CT-RATE | chest CT volumes paired with corresponding radiology text reports, multi-abnormality labels, and metadata | Classification, Text | CT | 3D |
| CXLSeg | Chest X-ray Dataset with Lung Segmentation. Images from MIMIC-CXR dataset | X-Ray | 2D | |
| DDI | Diverse skin dataset with biospy-proven disease labels | Classification | 2D | |
| DDR | Diabetic Retinopathy Classification, Lesion Segmentation and Lesion Detection | Segmentation, Classification, Detection | Retinal | 2D |
| DDTI | Thyroid ultrasound segmentation | Segmentation | Ultrasound | 2D |
| DenseVNet | Abdominal organ segmentation (spleen, left kidney, gallbladder, esophagus, liver, stomach, pancreas and duodenum). Overlap with BTCV and TCIA Pancreas CT | Segmenttion | CT | 3D |
| DENTEX | Dental Enumeration and Diagnosis on Panoramic X-rays Challenge | Detection | X-Ray | 2D |
| DermNet | 19,500 images of 23 types of skin diseases | Classification | Derm | 2D |
| DirLab | Thoracic 4DCT images. Inspiratory and expiratory breath-hold CT image pairs | Registration | CT | 3D |
| DRIVE | Retinal vein segmentation | Segmentation | Retinal | 2D |
| DLDS | Duke Liver DataSet (DLDS). 2,000 anonymized MRI image series acquired in routine liver MRI protocols across 105 subjects | Segmentation, Series Identification | MRI | 2D |
| EchoNet | 10,030 labeled echocardiogram videos and human expert annotations (measurements, tracings, and calculations) to provide a baseline to study cardiac motion and chamber sizes | Segmentation | Echo | 2D + Time |
| Endoscapes2023 | laparoscopic video dataset for surgical anatomy and tool segmentation, object detection, and Critical View of Safety (CVS) assessment | Instance Segmentation, Bounding Boxes | Surgical video | 2D + Time |
| EOphtha | Eye Microaneurysms and Diabetic Retinopathy | Segmentation | Retinal | 2D |
| EPISURG | Postoperative MRI for quantitative analysis of resection neurosurgery for refractory epilepsy | Segmentation, Classification | T1-MRI | 3D |
| EyePacs | Diabetic Retinopathy Detection | Classification | Retinal | 2D |
| fastMRI | Knee, Brain and Prostate MRI | Just Images | Multimodal MRI | 3D |
| FDG-PET-CT-Lesions | Lesions in full-body CT | Segmentation | PET/CT | 3D |
| FeTA | Fetal brain structures | Segmentation | MRI | 3D |
| Feto_Plac | 483 frames with ground-truth vessel segmentation annotations taken from six different in vivo fetoscopic procedure videos and 6 unannotated clips | Segmentation | Fetoscopic Video | 2D + Time |
| FLARE21 | Abdominal organ segmentation (liver, kidney, spleen, and pancreas). 511 cases | Segmentation | CT | 3D |
| GlaS | Gland segmentation in images of Hematoxylin and Eosin (H&E) stained slides | Segmentation, Classification | WSI | 2D |
| GMSC | Grey Matter Spinal Cord segmentation challenge | Segmentation | MRI | 3D |
| HAM10k | Human Against Machine with 10,000 training images. Dermatoscopic images of common pigmented skin lesions | Classification | Derm | 2D |
| HaN-Seg | Head/neck organs at risk. CT & MRI of the same patient | Segmentation | MRI, CT | 3D |
| HC18 | Fetal head circumference measurements (ellipses) | Other | Ultrasound | 2D |
| HECKTOR | Head and neck tumor segmentation in PET/CT: The HECKTOR challenge | Segmentation | PET/CT | 3D |
| HippoSeg | 50 T1-weighted MR images with 25 Hippocampus Masks for Segmentation | Segmentation | MRI | 2D |
| HipXRay | X-Ray examinations of the lower legs performed as part of routine medical service with illium and femur segmentations | Segmentation | X-Ray | 2D |
| HMC-QU | 4-chamber (A4C) and apical 2-chamber (A2C) left wall | Segmentation, Detection | Ultrasound | 2D |
| HRF | Retinal vessel segmentation | Segmentation | Retinal | 2D |
| I2CVB | Prostate (peripheral zone central gland) | Segmentation, Detection | T2-MRI | 3D |
| ICCVB | Initiative for Collaborative Computer Vision Benchmarking Prostate | Segmentation | MRI | 3D |
| IDRID | Diabetic Retinopathy | Segmentation | Retinal | 2D |
| InBreast | Mamograms | Segmentation | X-Ray | 2D |
| INSPECT | longitudinal records from a large cohort of pulmonary embolism (PE) patients, along with ground truth labels for multiple outcomes | Classification, Text, EHR, Vitals, Other | CT | 3D |
| INSTANCE | The 2022 Intracranial Hemorrhage Segmentation Challenge on Non-Contrast head CT (NCCT) Brain | Segmentation | CT | 3D |
| IRCADb | CT-scans of 10 women and 10 men with hepatic tumours in 75% of cases. Liver size or the location of tumours according to Couninaud’s segmentation | Segmentation | CT | 3D |
| ISBI_EM | 30 sections from a serial section Transmission Electron Microscopy (ssTEM) data set of the Drosophila first instar larva ventral nerve cord (VNC) | Instance Segmentation | Electron Microscopy | 2D |
| ISIC | Multiple challenges on Melanoma lesions segmentation, classification and detection | Classification, Segmentation, Detection | Derm | 2D |
| ISLES | Ischemic stroke lesion segmention challenge in Brain | Segmentation | Multimodal MRI | 3D |
| JSRT | Chest X-Rays with and without lung nodules, XY coordinates for nodules. Segmentation labels from SCD | Segmentation, Detection | X-Ray | 3D |
| KiTS | KiTS 2019Kidney and kidney tumor | Segmentation | CT | 3D |
| LERA | X-Rays of lower extremities (foot, knee, ankle, or hip) with diagnosis labels | Classification | X-Ray | 2D |
| LGGFlair | TCIA lower-grade glioma brain tumor | Segmentation | MRI | 3D |
| LIDC-IDRI | Lung nodules on CT scans | Multi-Annotator Seg., Detection | CT | 2D |
| LiTS | Liver lesion segmentation in contrast-enhanced abdominal CT scans | Segmentation | CT | 3D |
| LUNA | Lung segmentation in images from LIDC-IDRI | Segmentation | CT | 3D |
| LVM-Med | A Multi-Class Image-Dataset for Computer Aided Gastrointestinal Disease Detection | Classification | Scope | 2D |
| M4Raw | A multi-contrast, multi-repetition, multi-channel MRI k-space dataset for low-field Brain MRI research | Reconstruction | T1-MRI, T2-MRI, FLAIR | 3D |
| MCIC | Multi-site Brain regions of Schizophrenic patients | Segmentation | T1-MRI | 3D |
| MCXRay | Chest X-Ray Lung segmentation | Segmentation | X-Ray | 2D |
| MESSIDOR | Contained in RIGA | Other | Retinal | 2D |
| MICA_MICs | A dataset for Microstructure-Informed Connectomics. Raw and fully processed multimodal neuroimaging data acquired in 50 healthy control participants at a filed strength of 3T. Connectomes built across multiple parcellation schemes (18 total). | Other | T1-MRI, DWI, rfMRI | 3D |
| MIDA | Head and neck with lots of labels | Segmentation | MRI | 3D |
| MIMIC-CXR | Large collection of chest X-Rays (n=377,110) with free-text reports. Segmentations available in CheXmask | Text, Segmentation | X-Ray | 2D |
| Mindboggle-101 | individually labeled human brain surfaces and volumes, templates (unlabeled images combining the individual brains, used for registration), atlases (anatomical labels combining the individual brains, used for labeling) | Segmentation, Other | T1-MRI | 3D |
| MitoEM | Mitoem dataset: Large-scale 3d mitochondria instance segmentation from em images | Instance Segmentation | EM | 3D |
| MM-WHS | MM-WHS: Multi-Modality Whole Heart Segmentation | Segmentation | CT, MRI | 3D |
| MMOTU | Multi-Modality Ovarian Tumor Ultrasound (MMOTU) image dataset. Subdatasets: Ultrasounds and Contrast Enhanced Ultrasounds | Segmentation | Ultrasound/CEUS | 2D |
| MNMS | Multi-Centre, Multi-Vendor & Multi-Disease Cardiac Image Segmentation Challenge (M&Ms) | Segmentation | MRI | 4D |
| MoNuSeg | Nucleus segmentation | Segmentation | Miscroscopy | 2D |
| MouseBrainAtlas | Mouse Brain MRI atlas (both in-vivo and ex-vivo) | Segmentation | MRI | 3D |
| MRNet | Knee MRI | Classification | MRI | |
| MRSpineSeg | Thoracic and lumbar vertebrae, sacrum | Segmentation | MRI | 3D |
| MS_CMR | Cardiac MRI | Segmentation, Scribbles | MRI | 3D |
| MS_MRI | Segmentation | MRI | ||
| MSD | Subdatasets: Brain Tumor, Colon, Hepatic Vessel, Hippocampus, Liver, Lung, Pancreas, Prostate, Spleen | Segmentation | Multimodal MRI, CT | 3D |
| MURA | Classifying whether bone xrays are normal/abnormal | Classification | X-Ray | 2D |
| MuscleUS | Transverse Musculoskeletal Ultrasound Image SegmentationsMuscle segmentation. 3917 images of biceps brachii, tibialis anterior and gastrocnemius medialis acquired on 1283 subject | Segmentation | Ultrasound | 2D |
| NCI_ISBI | NCI-ISBI 2013 challenge: automated segmentation of prostate structures | Segmentation | T1-MRI | 3D |
| NerveUS | Nerve segmentation in ultrasound | Segmentation | Ultrasound | 2D |
| NuInsSeg | Overlapping instance segmentation masks | Instance Segmentation | WSI | 2D |
| NukeMM | NucMM Challenge: Neuronal Nuclei Segmentation at Sub-Cubic Millimeter Scale | Segmentation | WSI | 3D |
| NYUMets_Brain | Longitudinal MRI studies for 1429 metastatic brain cancer patients (avg. 6 imaging studies per patient over an avg. of 17 months) | Just Images | T1-MRI, T2-MRI, FLAIR | 3D |
| OAI-ZIB | Knee MRI | Segmentation | MRI | 3D |
| OASIS | Brain anatomy | Segmentation | T1-MRI | 3D |
| OCMR | Open-Access Multi-Coil k-Space Dataset for Cardiovascular Magnetic Resonance Imaging | MRI | ||
| OCTA500 | Retinal vasculature | Segmentation | OCT/OCTA | 2D |
| PADCHEST | Chest X-Rays and reports. Segmentations available in CheXmask. | Segmentation, Text | X-Ray | 2D |
| PAIP | Liver cancer cell segmentation | Segmentation | WSI | 2D |
| PancreasCT | Pancreas CT | Segmentation | CT | 3D |
| PanDental | Panoramic dental X-Rays with mandible and teeth segmented | Segmentation | X-Ray | 2D |
| PanNuke | Nucleus segmentation | Segmentation | Microscopy | 2D |
| PAXRay | Chest X-Rays projected from CTs. Overlapping segmentations | Segmentation | X-Ray | 2D |
| Polyp | A multi-centre polyp detection and segmentation dataset for generalisability assessment | Detection, Segmentation | Scope | 2D |
| PPMI | Brain regions of Parkinson patients | Segmentation | MRI | 3D |
| PRIME-FP20 | Retinal vessel segmentation | Segmentation | Retinal | 2D |
| PROMISE12 | Prostate | Segmentation | T2-MRI | 2D |
| Qubiq | Collection of multi-annotator segmentation datasets (prostate, brain tumor, pancreas, kidney) | Multi-Annotator Seg. | MRI, CT | 2D, 3D |
| RadImageNet | Large collection of biomedical images | Classification | MRI, CT, PET, Ultrasound | 2D |
| REFFUGE2 | Optical disk and cup segmentation | Multi-Annotator Seg. | Retinal | 2D |
| RibFrac | Rib fracture detection, segmentation and classification. Same CTs as PAXRay, rough segmentations | Detection, Segmentation, Classification | CT | 3D |
| RibSeg | Rib segmentations and centerlines | Segmentation, Centerlines | CT | 3D |
| RIGA | Optical cup and disk boundaries | Segmentation | Retinal | 2D |
| RITE | Retinal vessel tree extraction. Same images as DRIVE | Centerlines | Retinal | 2D |
| RoboTool | Surgical tool segmentation | Segmentation | Scope | 2D |
| ROSE | Retinal vessel segmentation | Segmentation | OCT | 2D |
| RSNASpine | RSNA 2022 Cervical Spine Fracture Detection. Subset of data has bounding boxes and segmentations | Detection, Segmentation | CT | 3D |
| SCR | Chest X-Rays with segmentations for lungs, heart, clavicle (images from JSRT) | Segmentation | X-Ray | 2D |
| SegA | MICCAI 2023 Challenge. Aorta segmentation | Segmentation | CTA | 3D |
| SegPC | Segmentation of multiple myeloma cells | Segmentation | Microscopy | 2D |
| SegRap | MICCAI 2023 Challenge. Segmentation of 45 organs at risk and gross tumor volume (nasopharyngeal carcinomas) in head/neck | Segmentation | CT | 3D |
| SegTHOR | ISBI 2019 Challenge. Segmentation of THoracic Organs at Risk in CT images (heart, aorta, trachea, esophagus) | Segmentation | CT | 3D |
| SegThy | Thyroid and artery/vein segmentation in neck | Segmentation | MRI,Ultrasound | 3D |
| ShenzhenXRay | Lung segmentation in chest X-Rays | Segmentation | X-Ray | 2D |
| SCD | Sunnybrook Cardiac Multi-Dataset Collection. 2009 Cardiac MR Left Ventricle Segmentation Challenge data. 45 cine-MRI images: healthy, hypertrophy, heart failure with infarction and heart failure without infarction | Segmentation | Cine-MRI | 3D |
| SKM-TEA | 155 quantitative double echo steady state MRI knee scans (incl. raw k space) acquired clinically. Segmentations of six tissues and bounding boxes for 16 pathologies | Segmentation, Detection | MRI | 3D |
| SMIR | Delineations of the cochlea and sub-compartments, a statistical shape model encoding its anatomical variability, and data for electrode insertion and electrical simulations | Segmentation, Other | CT | 3D |
| SNEMI3D | Neurites in EM | Segmentation | Electron Microscopy | 3D |
| SPIDER | Lumbar spine segmentation in MR images: a dataset and a public benchmark. Vertebra, intervertebral discs (IVDs), and spinal canal | Segmentation | T1-MRI, T2-MRI | 3D |
| SpineWeb | Collection of datasets related to spine | Segmentation | T2-MRI, CT | 2D, 3D |
| ssTEM | serial section Transmission Electron Microscopy (ssTEM) of the Drosophila melanogaster third instar larva ventral nerve cord. Dense labeling of neuron membranes (including orientation and junction), mitochondria, synapses and glia/extracellular space. 20 scans with multiple labels | Segmentation | Electron Microscopy | 2D |
| STARE | Retinal vein segmentation | Multi-annotator Seg. | Retinal | 2D |
| StructSeg | MICCAI 2019 Challenge. Organ at Risk and Gross Target Volume Segmentation in Head/Neck and Chest | Segmentation | CT | 3D |
| STS2D | MICCAI 2023 Challenge. Tooth segmentation | Segmentation | X-Rray | 2D |
| STS3D | MICCAI 2023 Challenge. Tooth segmentation | Segmentation | CBCT | 3D |
| TBI_ICH | 82 CT scans of patients with traumatic brain injury. Intracranial hemorrhage regions delineated in each slice by two radiologists | Multi-Annotator Seg. | CT | 3D |
| TDSC_ABUS | MICCAI 2023 Challenge. Tumor detection, segmentation and classification in breast ultrasound | Segmentation, Classification | Ultrasound | 3D |
| ToothFairy | MICCAI 2023 Challenge. Inferior Alveolar Nerve (IAN) canal detection. Dense and sparse annotations | Segmentation | CBCT | 3D |
| ToothSeg | Individual segmentation of teeth in dental X-Rays | Segmentation | X-Ray | 2D |
| TotalSegmentator | Segmentation of 104 Anatomical Structures in 1204 CT scans | Segmentation | CT | 3D |
| TUCC | Thyroid Ultrasounds Cine-Clip Dataset. 192 images from 167 patients with biopsy-confirmed thyroid nodules | Segmentation, Classification | Ultrasound Video | 2D + Time |
| VerSe | Individual vertebra segmentation | Segmentation | CT | 3D |
| VinDr-CXR | Prediatric chest X-Rays. Segmentations from CheXmask. | Segmentation, Detection, Bounding Boxes | X-Ray | 2D |
| VISCERAL | Anatomy3 Challenge | Segmentation | CT,MRI | 3D |
| VocalFolds | Laryngeal endoscopic images | Segmentation | Endoscopic video | 2D + Time |
| WBC | Nucleus and cytoplasm segmentation in white blood cells | Segmentation | Optical Microscope Camera | 2D |
| WMH | White Matter Hyperintensity (WMH) Segmentation Challenge | Segmentation | T1-MRI, FLAIR | 3D |
| WORD | Abdominal organ segmentation | Segmentation | CT | 3D |
