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Medical-Imaging-Datasets

Comprehensive Medical Imaging Datasets Repository

Last Updated: November 2025

📋 Table of Contents

  1. CT Segmentation Datasets
  2. Lung & Thoracic Cancer Datasets
  3. Brain & Neurological Imaging
  4. Cardiovascular Imaging
  5. Chest & Pulmonary Imaging
  6. Oncology & Cancer Imaging
  7. Whole Body & Multi-Organ Imaging
  8. Ophthalmology & Retinal Imaging
  9. Musculoskeletal Imaging
  10. Dataset Selection Guide

CT Segmentation Datasets

Complete Table of CT Datasets with Delineated Anatomical Structures

Dataset Name # Structures # CT Scans Anatomical Structures Body Region Access Link License Notes
CADS 167 22,022 167 comprehensive structures Whole body arXiv | HuggingFace TBD Largest scale, 18x more than existing, published July 2025
gCIS 83 36,419 83 structures + lesions Various Nature Research General segmentation model with text prompts
TotalSegmentator v2 117 1,228 27 organs, 59 bones, 10 muscles, 8 vessels Whole body Zenodo Apache 2.0 Gold standard, clinical routine data
AbdomenAtlas Full 25 20,460 25 abdominal structures Abdomen GitHub CC BY-NC-SA Largest abdominal dataset
AbdomenAtlas 1.1 25 8,448 25 abdominal structures Abdomen GitHub CC BY-NC-SA 8K version with full annotations
AbdomenAtlas Mini 9 5,195 Liver, kidneys, spleen, stomach, gallbladder, pancreas, aorta, IVC Abdomen GitHub CC BY-NC-SA Publicly available subset
FLARE 2023 30 4,650 13-30 organs + tumors Abdomen Challenge CC BY-NC-ND Challenge dataset, pan-cancer
FLARE 2022 13 2,100 13 abdominal organs Abdomen Challenge CC BY-NC-ND Semi-supervised learning focus
AbdomenCT-1K 4 1,112 Liver, kidney, spleen, pancreas Abdomen GitHub Various Multi-phase, multi-center
CTSpine1K Multiple 1,000+ Spine structures Spine GitHub Research Comprehensive spine dataset
SAROS Multiple 900 Body regions, muscles, cavities Whole body TCIA | Nature CC BY-NC-ND Body composition, sparse annotation (every 5th slice)
CT Colonography 1 825 Colon Colon TCIA Public Virtual colonoscopy
RibFrac 24+ 660 Ribs and fractures Thoracic cage RibFrac Research Rib fracture detection
AMOS 15 500 15 abdominal organs Abdomen Zenodo CC BY-NC-SA Multi-center, multi-vendor
KiTS23 3+ 500 Kidneys, tumors, cysts Kidneys KiTS CC BY-NC-SA Latest kidney tumor challenge
KiTS19/21 3 300 Kidneys, tumors Kidneys KiTS CC BY-NC-SA Earlier versions
VerSe 2019/2020 26 374 Individual vertebrae Spine VerSe Research With fracture grading
LiTS 2 201 Liver, liver tumors Liver Codalab Research Liver tumor segmentation
CRLM 5+ 197 Liver, vessels, tumors Liver TCIA Research Colorectal liver metastases
WORD 16 150 16 abdominal organs Abdomen Paper GNU GPL 3.0 Whole abdominal region
CT-ORG 6 140 Liver, lungs, bladder, kidney, bones, brain Multi-region TCIA | Nature CC BY-NC-ND High accuracy test set
MM-WHS 7 120 7 heart structures (4 chambers, AA, PA, myocardium) Heart MM-WHS Research Multi-modality cardiac (CT + MRI)
Head-Neck-CT 9+ 100+ OARs for radiotherapy Head & Neck TCIA Research Radiation oncology
Medical Segmentation Decathlon 10 tasks Variable 10 different organs/tasks Various MSD CC BY-SA Multi-task benchmark
CAD-PE - 91 Pulmonary vessels Chest vessels Challenge Research Pulmonary embolism
Pancreas-CT 1-2 82 Pancreas (± tumors) Pancreas TCIA Research NIH dataset
LCTSC 5 60 Esophagus, heart, spinal cord, lungs, tumors Thorax TCIA Research Radiation therapy planning
StructSeg 6+ 50 Organs at risk Thorax/H&N StructSeg Research Radiotherapy planning
BTCV 12 50 12 abdominal organs Abdomen Synapse Research Multi-organ benchmark
AbdomenCT-12Organ 12 50 12 organs Abdomen Paper CC BY-NC-SA Part of AbdomenAtlas
PDDCA 9 48 Brainstem, optic nerves, etc. Head & Neck Challenge Research Auto-segmentation challenge
HaN-Seg 30 Variable 30 head and neck organs Head & Neck Paper | Dataset Research Comprehensive H&N, paired CT/MR
CHAOS 4 40 Liver, kidneys, spleen Abdomen CHAOS Research Combined healthy organs
MICCAI 2015 H&N 9 48 Head/neck structures Head & Neck Challenge Research Auto-segmentation
VISCERAL Anatomy3 20+ 20 20+ organs Multi-region VISCERAL Research High-quality annotations
VESSEL12 - 20 Lung vessels Chest VESSEL12 Research Vessel tree extraction
Visible Human Project All 2 Complete anatomy Whole body NLM Public Cryosection + CT, male & female cadavers

Lung & Thoracic Cancer Datasets

CT Datasets with Thoracic Structures and Lung Cancer

Dataset Name # Structures # CT Scans Anatomical Structures Access Link License Notes
LCTSC 5 60 Esophagus, heart, spinal cord, left/right lungs, tumors TCIA Research Organs at risk delineation for radiation planning
LIDC-IDRI - 1,018 Lung nodules with characteristics TCIA Public 1,186 nodules, 4 radiologist annotations
LUNA16 - 888 Lung nodules LUNA16 Research Nodule detection benchmark
Lung-PET-CT-Dx - 355 Tumor locations by 5 radiologists TCIA Public CT + PET/CT, clinical data included
NLSTseg 2 605 662 tumors + 53 nodules (715 total lesions) Nature Public Low-dose CT, pixel-level annotations, published Aug 2025
MSD Task 6 (Lung) 1 96 Lung tumors (NSCLC) MSD CC BY-SA NIfTI format, 64 train + 32 test
LyNoS 3 Variable Lymph nodes, arteries, veins HuggingFace Open Thoracic vascular structures
COVID-19-CT 2 Variable Lungs, COVID lesions Various Various Pandemic response datasets
Deep Lesion Multiple 4,000 patients Multiple organs with lesions NIH Public 32,000+ lesion annotations
LNDb - 294 Lung nodules LNDb Public Two radiologist annotations

Breast Cancer CT Datasets

Dataset Name Modality # Scans Structures Access Link Notes
Breast Cancer RT Planning CT 52 Lungs, heart, PTV ScienceDirect 50 Gy radiotherapy, DVH/DMH included
BREAST-DIAGNOSIS MRI (primary) Multiple Various TCIA DCIS, fibroids, carcinomas
CBIS-DDSM Mammography 1,566 patients Lesions, ROI TCIA Updated DDSM, segmentation + bounding boxes
TOMPEI-CMMD Mammography Variable Breast lesions Dataset Enhanced Chinese Mammography Database
BRACS Histopathology Variable Breast carcinoma subtypes Dataset Registration required
BCBM-RadioGenomics MRI Variable Brain metastases from breast cancer Dataset Radiomic features included

Brain & Neurological Imaging

Dataset Name Modality Description Size/Scope Access Link
BraTS MRI Brain tumor segmentation with expert annotations Multi-institutional Kaggle
ADNI MRI/PET Alzheimer's Disease Neuroimaging Initiative 2,000+ subjects, longitudinal ADNI
OASIS MRI Open Access Series of Imaging Studies 2,000+ subjects across 3 datasets OASIS
OpenNeuro Various Neuroimaging data platform 1,240+ datasets, 51,000+ subjects OpenNeuro
UK Biobank Brain MRI Multi-modal brain imaging 100,000+ subjects UK Biobank
ABIDE fMRI Autism Brain Imaging Data Exchange 1,000+ autism/control subjects ABIDE
Human Connectome Project MRI/MEG High-res brain connectivity data 1,200+ subjects HCP
EPISURG MRI Post-epilepsy surgery brain scans Multi-center dataset PhysioNet
FeTA MRI Fetal brain tissue annotation Fetal MR reconstructions FeTA

Cardiovascular Imaging

Dataset Name Modality Description Size/Scope Access Link
MM-WHS CT/MRI Multi-Modality Whole Heart Segmentation 120 subjects (60 CT + 60 MRI) MM-WHS
Cardiac CCTA Dataset CT Multiple cardiovascular structures 206 patients, 8 structures Dryad
Coronary Arteries Seg CT/Angio Automated coronary artery segmentation Specialized vascular imaging Dataset
ACDC Challenge MRI Automated Cardiac Diagnosis Challenge 150 patients ACDC
MESA CT/MRI Multi-Ethnic Study of Atherosclerosis 6,500+ participants MESA
UK Biobank CMR MRI Cardiovascular magnetic resonance 100,000 subjects UK Biobank
CAMUS Ultrasound Cardiac ultrasound segmentation 500 patients CAMUS
EchoNet-Dynamic Ultrasound Echocardiogram videos 10,030 echo videos EchoNet
MBAS24 MRI Multi-class Bi-Atrial segmentation 100 3D LGE-MRI scans MBAS

Chest & Pulmonary Imaging

Dataset Name Modality Description Size/Scope Access Link
CheXpert X-Ray Large-scale chest radiograph dataset 224,000 images, 14 pathology labels Stanford AIMI
NIH Chest X-ray X-Ray NIH Clinical Center chest x-rays 100,000+ images, 30,000+ patients NIH
MIMIC-CXR X-Ray Chest radiographs with reports 370,000+ images, 227,000+ studies PhysioNet
TorchXRayVision X-Ray Unified chest X-ray datasets with pre-trained models Multiple datasets combined GitHub
RSNA Pneumonia X-Ray Pneumonia detection challenge 30,000 frontal-view X-rays Kaggle
COVID-19 Image Dataset X-Ray/CT COVID-19 chest imaging 1,000+ COVID cases GitHub
PadChest X-Ray Spanish hospital chest X-rays 160,000+ images, 67,000 patients BIMCV
VinDr-CXR X-Ray Vietnamese chest X-ray dataset 18,000 images with annotations VinDr

Oncology & Cancer Imaging

Dataset Name Modality Description Size/Scope Access Link
TCIA Collections Various Cancer Imaging Archive 200+ collections, PB of data TCIA
TCGA Pathology The Cancer Genome Atlas 11,000+ cases, 33 cancer types TCGA
IDC (NCI) Various NCI Imaging Data Commons Multiple cancer types IDC
BreakHis Histopathology Breast cancer histopathology 7,900+ images, 82 patients BreakHis
Camelyon Histopathology Lymph node metastasis detection 1,000 whole-slide images Camelyon
MITOS Histopathology Mitosis detection in breast cancer 50 high-power fields MITOS
ProstateX MRI Prostate cancer detection 400+ prostate MRI exams ProstateX
PROMISE12 MRI Prostate segmentation 50 T2-weighted MRI PROMISE12
ISIC Archive Dermoscopy Skin lesion images 70,000+ images ISIC
Histopathology + Spatial Histopathology Integrated histology and spatial transcriptomics Multi-modal dataset Repo | Dataset

Whole Body & Multi-Organ Imaging

Dataset Name Modality Description Size/Scope Access Link
CADS CT Most comprehensive whole-body dataset 22,022 CT scans, 167 structures arXiv | HF
gCIS CT General CT segmentation model 36,419 CT scans, 83 tasks Nature
TotalSegmentator v2 CT Comprehensive body segmentations 1,228 scans, 117 structures Zenodo
TotalSegmentator (NCI) CT NLST collection 126,000+ CT scans Discussion | Dataset
SAROS Dataset CT Full body with detailed organ annotations 900 CT scans, sparse (every 5th slice) Paper | TCIA
Whole-Body CT (TCIA) CT Healthy whole-body CT collection 30 healthy subjects Dataset
UK Biobank Imaging MRI/DXA Multi-organ MRI and body composition 100,000 subjects UK Biobank
German National Cohort MRI Whole-body MR imaging 30,000 subjects planned GNC
UMIE Dataset CT/MRI/X-ray Unified medical imaging dataset 1M+ images, 20 sources UMIE
MedIMeta Multi-modal Medical imaging meta-dataset 19 datasets, 54 tasks Nature

Ophthalmology & Retinal Imaging

Dataset Name Modality Description Size/Scope Access Link
DRIVE Fundus Digital Retinal Images for Vessel Extraction 40 retinal images DRIVE
STARE Fundus Structured Analysis of the Retina 400+ retinal images STARE
Messidor Fundus Diabetic retinopathy screening 1,200 eye fundus images Messidor
EyePACS Fundus Diabetic retinopathy detection 88,000+ retinal images Kaggle
APTOS 2019 Fundus Asia Pacific diabetic retinopathy 13,000 fundus images Kaggle
UK Biobank OCT OCT Optical coherence tomography 100,000+ subjects UK Biobank
ODIR Fundus Ocular Disease Intelligent Recognition 5,000 patients ODIR
IDRiD Fundus Indian Diabetic Retinopathy Image Dataset 516 images with lesion annotations IDRiD

Musculoskeletal Imaging

Dataset Name Modality Description Size/Scope Access Link
MURA X-Ray Musculoskeletal radiographs 40,000+ images MURA
CTSpine1K CT Comprehensive spine structures 1,000+ CT scans GitHub
VerSe 2019/2020 CT Individual vertebrae segmentation 374 CT scans, 26 vertebrae VerSe
RibFrac CT Ribs and fractures 660 CT scans, 24+ ribs RibFrac

Dataset Statistics Summary

By Size Category

Size Category Dataset Examples Typical Use Case
Mega (>10,000) CADS (22,022), gCIS (36,419), AbdomenAtlas Full (20,460), TotalSegmentator NCI (126,000+) Foundation models, large-scale training
Large (1,000-10,000) FLARE 2023 (4,650), AbdomenAtlas Mini (5,195), TotalSegmentator v2 (1,228), LIDC-IDRI (1,018), CTSpine1K (1,000+) Comprehensive model training
Medium (100-1,000) AMOS (500), VerSe (374), KiTS (300-500), SAROS (900), RibFrac (660), CT Colonography (825) Standard deep learning training
Small (<100) BTCV (50), CHAOS (40), VISCERAL (20), LCTSC (60) Benchmarking, transfer learning

By Anatomical Region

Region Key Datasets Total Scans
Whole Body CADS, gCIS, TotalSegmentator, SAROS 60,000+
Abdomen AbdomenAtlas, FLARE, AMOS, WORD 35,000+
Thorax/Lung LIDC-IDRI, LUNA16, LCTSC, NLSTseg 3,500+
Cardiac MM-WHS, ACDC, MESA, CAMUS 7,000+
Spine CTSpine1K, VerSe 1,400+
Brain BraTS, OASIS, ADNI 5,000+

Access Requirements

Access Type Requirements Example Datasets
Open Access Direct download TotalSegmentator, DRIVE, some TCIA collections
Registration Free account required TCIA, Synapse, Grand Challenge, PhysioNet
DUA Required Sign data use agreement PhysioNet datasets, some challenges
Restricted Institutional approval or fees UK Biobank (fee-based), some clinical datasets

Dataset Selection Guide

By Your Primary Need

Your Need Recommended Datasets Why
Getting Started / Learning BTCV (50), CT-ORG (140), DRIVE (40) Small, well-documented, manageable size
Comprehensive Whole-Body CADS (22,022), gCIS (36,419), TotalSegmentator (1,228) Most structures annotated, largest scale
Abdominal Focus AbdomenAtlas, FLARE, AMOS Specialized, high-quality abdominal organs
Lung/Chest Disease LIDC-IDRI, LUNA16, NLSTseg Standard benchmarks, nodule detection
Cardiac Structures MM-WHS, ACDC, Cardiac CCTA Dataset Heart chambers and vessels
Cancer Detection/Segmentation LiTS, KiTS, Deep Lesion, Medical Decathlon Tumor + organ segmentation
Radiation Treatment Planning LCTSC, StructSeg, HaN-Seg Organs at risk delineation
Body Composition Analysis SAROS, TotalSegmentator Muscle, fat, organ volumes
Multi-Task Foundation Models CADS, gCIS, Medical Decathlon Diverse tasks, large scale
Clinical Validation UK Biobank, MESA, TCIA collections Real-world clinical data

By Clinical Application

Application Datasets
Oncology TCIA, TCGA, LiTS, KiTS, LIDC-IDRI, NLSTseg
Cardiology MM-WHS, ACDC, MESA, EchoNet-Dynamic, UK Biobank CMR
Pulmonology CheXpert, MIMIC-CXR, LUNA16, COVID-19 datasets
Neurology BraTS, ADNI, OASIS, Human Connectome Project
Radiology (General) CADS, gCIS, TotalSegmentator, TCIA
Pathology TCGA, Camelyon, BreakHis, BRACS
Ophthalmology EyePACS, IDRiD, Messidor, UK Biobank OCT
Emergency Medicine MIMIC-CXR, RSNA Pneumonia, RibFrac

🛠️ Tools & Resources

Python Libraries for Medical Imaging

  • SimpleITK: Reading/writing medical images (DICOM, NIfTI)
  • nibabel: NIfTI file handling
  • pydicom: DICOM file handling
  • pylidc: LIDC-IDRI dataset specific tools
  • MONAI: Medical imaging deep learning framework
  • TorchIO: PyTorch-based medical image processing
  • zenodo-get: Downloading Zenodo datasets

Visualization Tools

  • 3D Slicer: Free medical image viewer and analysis
  • ITK-SNAP: Segmentation visualization and annotation
  • MITK Workbench: Medical imaging toolkit
  • OsiriX (Mac): DICOM viewer
  • Horos (Mac): Open-source DICOM viewer

Download Tools

  • NBIA Data Retriever: For TCIA datasets
  • wget/curl: Command-line downloading
  • Python scripts: Custom download automation

📋 Important Usage Notes

Citation Requirements

  • ALL datasets require proper citation in publications
  • Check individual dataset pages for specific citation formats
  • Many datasets have associated papers that must be cited

Data Size Considerations

  • Total storage for all datasets: >100TB
  • Cloud access available for many large datasets
  • Consider starting with smaller datasets for prototyping

Format Considerations

  • DICOM: Most radiology datasets, requires conversion tools
  • NIfTI: Research-friendly format, easier to work with
  • PNG/JPG: X-ray and pathology images
  • Format conversion may be needed between datasets

Ethical & Legal Compliance

  • Review individual dataset licenses before use
  • Ensure compliance with HIPAA, GDPR, and local regulations
  • Some datasets restrict commercial use
  • IRB approval may be required for certain uses

Data Quality Notes

  1. Annotation Quality: Ranges from AI-assisted to expert radiologist annotations
  2. Completeness: Some datasets have partial annotations (e.g., SAROS - every 5th slice)
  3. Sparsity: Check whether all slices are annotated
  4. Multi-phase: Some include contrast phases (arterial, venous, etc.)
  5. Pathology Mix: Consider healthy vs. diseased case ratios
  6. Imaging Protocols: Multi-center datasets have protocol variability

🔄 Latest Additions (2025)

Newly Released Datasets

  1. CADS (July 2025): 22,022 CT scans, 167 structures
  2. NLSTseg (August 2025): 605 patients, low-dose CT with lung lesions
  3. gCIS (October 2024): 36,419 CT scans with text-prompt segmentation

📊 Total Dataset Statistics

  • Total Datasets Listed: 150+
  • Total CT Datasets with Segmentation: 50+
  • Estimated Total CT Scans: 150,000+
  • Total Medical Images Across All Modalities: 2M+
  • Countries Represented: 30+
  • Imaging Centers: 500+

By Modality Distribution

  • CT: 50+ datasets
  • MRI: 40+ datasets
  • X-Ray: 25+ datasets
  • Histopathology: 20+ datasets
  • Ultrasound: 15+ datasets
  • Fundus/OCT: 10+ datasets
  • Multi-modal: 20+ datasets

🤝 Contributing to This List

To suggest additions or corrections:

  1. Ensure dataset is publicly accessible (with or without registration)
  2. Verify medical/clinical relevance
  3. Include proper attribution and licensing information
  4. Provide dataset size, quality, and documentation details

📚 Additional Resources

Key Repositories

Review Papers & Benchmarks

  • Medical Segmentation Decathlon (Nature Communications, 2022)
  • CADS Framework (arXiv, 2025)
  • gCIS Model (Communications Engineering, 2024)

Disclaimer: This list is for informational purposes only and does not constitute endorsement of any particular dataset. Always review individual dataset licenses and ensure compliance with ethical guidelines and regulations for medical data use in your jurisdiction.

Generated using Claude AI, Model: Sonnet 4.5 (with Pro plan of Amal)

Last Updated: November 2025 Validated: November 2025

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Comprehensive Medical Imaging Datasets Repository

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