Databases

Largest longitudinal knee imaging study with 26M+ medical images

26,626,000 images from 4,796 participants. 3T bilateral knee MRI, knee/hip/hand/pelvis radiographs, thigh MRI, and full-limb MRI. Longitudinal data 2004-2015+.

1,228 CTs with segmentations of 104 structures including 59 bones

CT scans with ground-truth segmentations covering all vertebrae, ribs, pelvis, femur, tibia, fibula, patella, humerus, scapula, clavicle, and more. Also 616 MR subjects.

40,561 musculoskeletal radiographs from 12,173 patients

Upper extremity X-rays across 7 types: elbow, finger, forearm, hand, humerus, shoulder, wrist. Labeled normal/abnormal by radiologists.

4,083 fracture X-ray images with expert annotations

Hand, shoulder, leg, hip X-rays with 922 fracture instances. COCO, VGG, YOLO, Pascal VOC annotation formats. Expert-annotated by radiologists.

14,236 pediatric hand radiographs with bone age labels

Hand X-rays labeled with skeletal maturity (0-228 months). Standard benchmark for bone age assessment algorithms.

374 CTs with voxel-level vertebral segmentations

Multi-detector CT scans from 355 patients with vertebrae segmentations and labeling, including enumeration abnormalities.

1,005 CT volumes with 11,100+ labeled vertebrae

Spine CT data covering normal, fracture, scoliosis and other conditions. Large-scale vertebral segmentation dataset.

Cancer imaging archive with bone metastasis and osteosarcoma data

Metastatic spine disease CT (55 subjects), osteosarcoma data, plus thousands of whole-body CTs with skeletal structures.

Complete male and female cadaver datasets with CT, MRI, and cryosection

Full-body CT (1mm axial), MRI, and color cryosection images. Derived 3D models include 28 bones, 76 muscles, 16 cartilages per subject.

15,243 high-resolution full-body CT scans of decedents

Bone-optimized and soft-tissue CT reconstructions. 1mm slice thickness, ~12,000 slices per individual. 69 metadata fields.

DXA scans from ~100,000 participants

Whole-body, proximal femur, spine L4-T4, and knee DXA scans using GE-Lunar iDXA. Bone area, mineral content, density, lean/fat mass.

Full-body postmortem CT scans for shape model construction

Anonymized postmortem CTs from forensic institutes. Core dataset for building statistical shape models of any bone.

1,184 CT volumes with 320K slices for pelvic bone segmentation

Data from 7 clinical sources including fracture and post-surgical cases. Zenodo download. Liu et al., IJCARS, 2021. CC BY 4.0.

150 pelvic fracture CTs + simulated X-rays from 6 clinical centers

Fragment-level annotations for pelvic fracture segmentation in CT and X-ray. MICCAI 2024 satellite challenge. 16 participating teams.

Knee MRI dataset for bone and cartilage segmentation

1.5T and 3T MRI from pre-surgery cases with severe cartilage damage. Femoral and tibial bone + cartilage segmentations. Biomet Inc.

6,288 hand radiographs with bone age annotations from two expert radiologists

Left and right hand X-rays, ages 0-20 years. Bounding boxes and keypoints for anatomical ROIs. Colombian patients, Fundación Santa Fe de Bogotá.

1,400 hand radiographs with equal racial representation for bone age

Diverse repository from Southern California. Standard reference for bone age assessment algorithms. USC Image Processing and Informatics Lab.

55 annotated CT scans of vertebrae with metastatic bone lesions

First open annotated dataset for vertebral metastasis segmentation with baseline ML model. Various cancer types. 2024.

Micro-CT scans and biomechanical tests of 15 mouse femurs

C57BL/6J ovariectomized and sham mice mimicking post-menopausal osteoporosis. Includes TIFF acquisitions, BMP reconstructions, and biomechanical data. Scientific Data.

359 pediatric chest-abdomen-pelvis CTs with expert organ contours

Ages 5 days to 16 years (180M, 179F). Up to 29 structures contoured per exam including bones. DICOM + RTSS format from 3 CT scanners. Jordan et al., Medical Physics, 2022.

660 CT scans with 5,000+ annotated rib fractures

Voxel-level instance masks with 4 clinical categories (buckle, nondisplaced, displaced, segmental). 420 training + 60 tuning + 120 test. FracNet baseline model.

320 annotated MRI volumes for bone segmentation across 17 body parts

T1 MRI sequences covering humerus, spine, pelvis, knee, foot, ankle, and more. SAM-based universal bone segmentation model included. Mazurowski Lab, Duke University.

140 CT scans with segmentations of 6 organ classes including bones

Multi-organ segmentation dataset including liver, bladder, lungs, kidneys, bone, and brain. NIfTI format. Rister et al., Scientific Data, 2020.

22,022 CT volumes with segmentations of 167 anatomical structures

Largest whole-body CT segmentation dataset. 100+ imaging centers across 16 countries. Includes all bones, organs, and vessels. HuggingFace download. 2025.

660 CT scans with 15,466 individually labeled ribs

Rib segmentation and anatomical centerline extraction. Expert-inspected annotations. Zenodo data. MICCAI 2021 + TMI 2023.

20,327 pediatric wrist trauma X-rays with 74,459 annotations

6,091 patients aged 0-19 from University Hospital Graz. Fracture classifications (AO), implant detection, bone lesions. PNG 16-bit. Scientific Data, 2022.

4,963 annotated cervical spine X-rays with 77 quantitative parameters

23 keypoints per image covering C2-C7 vertebrae. Automated parameter extraction. Scientific Data, 2024.

660 patient dental CBCT volumes with expert medical records

3D CBCT images of teeth with mandible, maxilla segmentations. First large-scale multimodal dental dataset. Scientific Data, 2025.

Knee X-rays graded by Kellgren-Lawrence severity (0-4) from OAI

Organized knee radiographs for osteoarthritis classification and AI benchmarking. KL grades 0 (normal) through 4 (severe). Mendeley Data.

8 high-resolution 3D temporal bone models with inner ear structures

CBCT + micro-slicing fusion. Segmented cochlea, ossicles, nerves, vessels. Color 3D models for surgical training. Scientific Data, 2019.

23 temporal bone specimens with co-registered CT and micro-CT

Clinical CT + high-res micro-CT, 3D surface models of bony labyrinth, anatomical landmarks. Free download from Zenodo.

H&E stained osteosarcoma histology images from 50 patients

Labeled as Non-Tumor, Viable Tumor, and Necrosis. 1,144 image tiles with 65 ML features. UT Southwestern, Children's Medical Center Dallas.

Pelvic CT scans with bone tumour segmentations

Annotated pelvic bone tumour dataset for AI research. Zenodo open access.

Open-access quantitative spinal cord MRI from 42 centers, 3 MRI manufacturers

260 participants across GE, Philips, Siemens scanners. T1w, T2w, diffusion, MT sequences. Git-annex download. Scientific Data, 2021.

447 lumbar spine MRI series with vertebrae, disc, and canal segmentations

218 patients from 4 hospitals. T1 and T2 sagittal MRI. Vertebra + IVD + spinal canal masks. Scientific Data, 2024. Zenodo download.

515 lumbar spine MRIs with Pfirrmann disc degeneration grading

1,000 intervertebral disc levels graded I-V by radiologist. T2-weighted sagittal images. PLOS ONE, 2024.

18,000 chest X-rays with radiologist annotations for 28 findings including rib fractures

Bounding box annotations for 28 abnormalities. Two radiologists per image. Includes fracture, bone lesion labels. VinBigData, PhysioNet.

3,746 radiographs for primary bone tumor classification, localization, and segmentation

1,879 normal + 1,867 tumor images from multiple hospitals. Clinical info, global labels, instance masks, and bounding boxes per tumor. Scientific Data, 2025.

High-resolution micro-CT 3D models of zebrafish skeletal development

Segmented 3D models from 12-25mm standard length. Skeletal density and volume quantification. Interactive 3D PDFs at key stages. Developmental biology model.

2,156 pelvic X-rays for developmental dysplasia of the hip diagnosis

1,250 images with quality evaluation + DDH landmarks. 906 images with keypoint annotations. Pediatric hip screening. Scientific Data, 2025.

1,000 intra-oral periapical radiographs with landmark annotations and tooth segmentation

Marked landmarks + metadata for dental and periapical disease analysis. Scientific Data, 2025.

Panoramic dental radiographs with automated dental condition detection labels

Annotated panoramic dental X-rays for multiple dental conditions. Zenodo open access. 2024.

1,382 foot X-rays with hallux valgus angle annotations

1,150 patients. Foot localization + HVA/IMA angles + phalanx line segments. First large-scale HV dataset. Scientific Data, 2025.

83 annotated mouse bone micro-CT scans for growth plate detection

3D micro-CT bone scans with growth plate annotations. Internal challenge for automatic bone quantification. 6 baseline solutions included. 2024.

225 murine whole-body micro-CT scans with organ segmentations

3D micro-CT with manual segmentations of various organs and tissues. Figshare download. Scientific Data, 2018.

Micro-CT of 21 mouse tibiae: wild-type, osteogenesis imperfecta, and stem cell treated

Reconstructed micro-CT images + 3D PLY bone models. OI mouse model with stem cell transplantation. Figshare. Scientific Data, 2018.

10,000+ pediatric ulna and radius fracture X-rays

De-identified forearm X-rays from Shenzhen Children's Hospital 2013-2024. First large-scale dedicated pediatric forearm fracture dataset. Scientific Data.

Lumbar spine MRI dataset for disc herniation, stenosis, and facet arthropathy

Multi-site, multi-continent dataset curated by RSNA + ASNR + ASSR. Graded by severity per vertebral level. Kaggle challenge 2024.

Lumbar spine MRI dataset for disc and vertebral analysis

Sagittal lumbar spine MRI images curated for AI research. Mendeley Data.

112,120 frontal chest X-rays from 30,805 patients with 14 disease labels

Includes fracture labels. Expert-annotated test set with 4,374 images for rib fracture detection. NLP-mined labels >90% accurate. NIH Clinical Center.

10,466 spine X-rays with bounding box annotations for 13 abnormality types

5,000 studies manually annotated by radiologists. Largest spine X-ray detection dataset. Object detection + multi-label classification. PhysioNet.

1,000 synthetic whole-body bone scans generated by AI for 3 clinical conditions

250 bone metastasis + 250 cardiac amyloidosis + 500 normal. Generated from 9,170 real scans. For data augmentation and AI training. Zenodo, 2024.

176 knee MRI scans with semi-manual cartilage and meniscus segmentations

88 subjects from OAI. DESS MRI. Tibial/femoral cartilage, menisci, patellar cartilage segmented by iMorphics. NIH Data Archive.

1,611 whole-body PET/CT studies for tumor lesion segmentation

1,014 FDG + 597 PSMA studies from 2 clinical sites. Multi-tracer challenge. NIfTI nnUNet format. MICCAI 2024 satellite event.

185 semantic-segmented bone marrow biopsy images for cellularity analysis

High-resolution H&E stained bone marrow biopsies with pixel-level annotations of haematological components. Automated cellularity calculation. 2024.

25,009 bone marrow cell images from 125 myelodysplastic syndrome patients

27 cell categories including normal and abnormal MDS cells. Image tags for classification. Scientific Data, 2025.

2,332 panoramic dental X-rays with tooth detection, numbering, and diagnosis

Three annotation tiers: quadrant detection (693), tooth enumeration (634), abnormal tooth diagnosis (1,005). FDI numbering. Multi-institutional.

1,000 panoramic dental radiographs with expert abnormality labels

Multimodal annotations including teeth numbering, abnormalities, and expert labels. Tufts University.

1,370 knee MRIs with ACL tear and meniscal tear labels

Sagittal T2, coronal T1, axial PD views. 319 ACL tears, 508 meniscal tears. Largest publicly annotated knee MRI dataset. Stanford AIMI.

1,500+ fully sampled knee MRIs for accelerated MRI reconstruction

Raw k-space + DICOM. 1.5T and 3T. PD, PD-FS, T2-FS sequences. fastMRI+ adds 16,154 pathology bounding box annotations across 22 categories.

1,014 whole-body FDG-PET/CT studies with manually annotated tumor lesions

501 lymphoma/melanoma/NSCLC + 513 negative controls. 3D lesion segmentations. 419 GB DICOM. NIfTI conversion scripts included. Scientific Data, 2022.

3,026 participants with knee X-rays and MRIs over 84-month follow-up

Ages 50-79 with OA or risk factors. Bilateral knee X-rays + MRI at baseline, 15, 30, 60, 84 months. Bone/cartilage/meniscus assessment.

CT metal artifact reduction dataset with orthopedic implant images

Image pairs and sinogram pairs for training and testing metal artifact reduction algorithms. Released publicly post-challenge. AAPM 2024.

82,544 whole-body bone scan images from 3,247 patients

Anterior and posterior views with 13 region-wise body part slices per view. West China Hospital. Bone metastasis detection benchmark.

55 CT scans with annotated spinal metastatic bone lesions

Vertebrae classified as normal, osteolytic, osteosclerotic, or mixed. Various primary cancers. Baseline ML model included. TCIA.

100,000 ultrasound images of lower limb bones with CT-derived labels

Ex-vivo US images of tibia, fibula, foot bones from 14 cadavers. Automatic bone surface labels from tracked CT models. Pretrained segmentation models included. 2025.

900 CTs with muscle, bone, and body region annotations from TCIA

882 patients, 20,150 annotated slices. 13 semantic labels including bones, muscle, subcutaneous tissue. Sarcopenia assessment. 28 TCIA collections.

Open-access lumbosacral spine MRI with enhanced nerve root resolution

High-resolution MRI dataset of the lumbosacral spine with spinal nerve root structure annotations. Available on Figshare.

In vivo joint loading data from instrumented implants (Charité Berlin)

30+ years of measured hip, knee, shoulder, spine forces during daily activities. Includes load-time diagrams, synchronized videos, and numerical force data.

120 subjects performing 7 locomotion tasks with EMG, motion capture, and force plates

Level walking, stairs, slopes, sit-to-stand. 6,882 movement cycles. Lower limb sEMG + full-body kinematics + GRF. Males aged 20-59. Scientific Data, 2025.

64-channel high-density EMG with IMU and force plates during locomotion

Level-ground, slopes, stairs, side stepping, transitions. All major surface muscles. For prosthetics, exoskeletons, and motor control research. Scientific Data, 2023.

200,000+ footsteps from 150 individuals with high-resolution plantar pressure

4 sensors/cm2 pressure walkway. 4 speeds x 4 footwear conditions. 1,400 steps per individual. Gait recognition and biomechanics. Scientific Data, 2025.

30 transtibial prosthesis users with optical camera and IMU kinematics

Joint angles from IMU sensors + optical motion capture raw marker data. C3D and CSV formats. Scientific Data, 2024.

1,798 healthy and injured subjects during treadmill walking and running

Raw marker trajectories + metadata at various gait speeds. Young and older adults. Figshare download. Scientific Data, 2024.

Comprehensive lower limb biomechanics during stairs, ramps, and level walking

Motion capture, EMG, and ground reaction forces during multiple ambulation conditions and transitions. Georgia Tech. Camargo et al., J. Biomech., 2021.

Full-body motion capture of 138 healthy adults and 50 stroke survivors

C3D marker data across the lifespan. Healthy controls aged 18-85 and hemiplegic stroke patients. Scientific Data, 2023.

63-marker motion capture of 30 subjects walking and running at multiple speeds

4,840 overground + 18,159 treadmill gait cycles. C3D and CSV formats with 3D GRF. Scientific Data, 2024.

75,732 bilateral walking trials from 2,084 patients

Ground reaction force data from patients with musculoskeletal impairments and 211 healthy controls. Largest gait GRF dataset.

GRF and COP data from 350 healthy individuals

Ages 11-64, up to 8 sessions with 8+ trials each. Raw and processed CSV with MATLAB/Python scripts.

Complete lower extremity musculoskeletal geometry

Segmented CT/MRI with 55 muscle actuators, 12 ligaments, bony landmarks. 12 segments, 11 joints, 21 DOF, 166 muscle-tendon elements per leg.

US population-representative DXA bone density data

Proximal femur and lumbar spine BMD from thousands of participants. Reference data for T-score and Z-score calculations.

Validated musculoskeletal models with bone geometries

Lower extremity, spine, upper extremity, full-body models. Includes bone geometries, joint definitions, muscle paths and parameters.

108,623+ 3D skeletal models from museum collections

CT/MRI volumetric data, 3D surface models, photogrammetry. Primarily biological skeletal material. Hosts oVert project data.

13,000+ CT scans of vertebrate specimens

Covers >50% of genera of amphibians, reptiles, fishes, mammals. Raw CT and 3D mesh models from US natural history museums.

Biomedical 3D models including skeletal anatomy

Skeletal anatomy models segmented from patient CT/MRI. STL format for 3D printing and visualization.

Dictionary-type anatomy database with 3D structure data

Anatomical concepts as segmented regions of a whole-body adult male model. OBJ and STL formats.

100,000+ 3D medical shapes across 23+ datasets

Bones, organs, vessels, surgical instruments. Python API (MedShapeNetCore) for bulk download.

Community-contributed bone STL models from CT scans

Mandible, pelvis, spine, skull, foot models. Includes democratiz3D DICOM-to-STL conversion tool.

Peer-reviewed 3D models of vertebrate specimens

Osteological models from CT data with segmented bones, teeth, and cavities. Citable, ISSN 2274-0422.

8 specimen-specific knee joint FE models with all tissue structures

Femur, tibia, patella, fibula, menisci, cartilage, and ligaments. MRI-based with mechanical testing data. CC BY 4.0. Erdemir et al., Ann. Biomed. Eng., 2023.

11 clinically verified hip joint models with bone and cartilage meshes

Bilateral hip models including femur, pelvis, acetabular and femoral cartilage. Volume and surface meshes for FEA. Semi-automated workflow. University of Copenhagen.

Segmentations and surface models of all lower body bones from 20+ cadaver CTs

Complete pelvis and lower limb bone surfaces from postmortem whole-body CTs. Zenodo data. Fischer et al., Scientific Data, 2023. CC BY 4.0.

500 healthy skulls + 29 craniotomy skulls with implant designs

High-resolution skull meshes (STL) and volumetric data (NRRD) from clinical CTs. Includes expert-designed cranial implants. Medical University of Graz. CC BY 4.0.

1,800 intraoral scans with 23,999 annotated teeth

OBJ mesh files with per-tooth segmentation and labeling. First public 3D tooth segmentation dataset. MICCAI 2022 challenge.

86 3D models of lumbar vertebrae from dried specimens

Image-based 3D reconstruction of individual lumbar vertebrae. Useful for spine biomechanics and shape analysis.

STL surface models of 29 lumbar spine specimens

Individual vertebral body and disc STL files from the NCCIH Grant R01 AT006692 Data Repository. RUSH University.

Thorax, clavicle, scapula, and humerus kinematics with 3D models

3D bone models from specimen CT segmentation with landmarks. Includes kinematics data for shoulder biomechanics research.

Pre-built tibia-fibula statistical shape model (30 specimens)

Cortical and trabecular bone separated. Includes SSM + code + surface meshes. Three example applications included.

Pelvis, femur, tibia SSMs from 333 pediatric CTs

Ages 4-18 years. PCA weights with partial least squares regression. Predicts shape from age, height, weight.

30 subjects, complete lower body bone surfaces

Pelvis, femur, tibia, fibula, patella, foot bones as PLY meshes. MATLAB/Python example code. Derived from VSD cadaver CTs.

PCA-based statistical shape model of the four fingers

10 training specimens, pose-neutralized. Open for community contribution.

9,376 3D femur + cartilage shapes for ML benchmarks

Segmentation masks + 3D surface meshes. Neural shape model benchmarks, osteoarthritis B-Score.

Bone geometries from 35 healthy volunteers (MR scans)

Femur, tibia, fibula meshes (left and right). 22M, 13F. Height 155-193cm, weight 45-108kg.

High-resolution femur statistical shape model in HDF5 format

18,879 vertices, 37,754 triangles, 15 PCA modes. Built from CT scans. Used in the bone.technology SSM Explorer.

Gaussian Process Morphable Model of the femur (1,622 vertices)

Compact femur model with 15 modes. From Madsen et al., MICCAI 2020: Shape priors from partial observations. BSD-3-Clause license.

Pelvis, femur, tibia-fibula, and patella SSMs from 26 cadaver CTs

Fieldwork mesh models with PCA shape modes. Zhang et al., J. Biomechanics 49(16), 2016. Used in bone.technology SSM Explorer. GPL-3.0 license.

Sacrum, left hip, and right hip SSMs from 40 CT scans

5,000 vertices per model, 39-40 PCA modes. Built from TCIA CT data. HDF5 Scalismo format. Used in bone.technology SSM Explorer.

Statistical shape model of transtibial amputated residual limbs

33 training datasets from MRI + CT. For prosthetic socket simulation and design. SSM of limb shapes. Abel Research. CC license.

16,807 virtual thoracolumbar spine FE models from EOS-based SSM

3D surface meshes + FE models of normal and deformed spines. Generated via SSM from EOS biplanar X-rays. Zenodo download. Scientific Data, 2024.

Multi-subject spinal cord MRI database for reproducibility across sites

Standardized spinal cord MRI protocol across multiple centers. Zenodo download. Supports Spinal Cord Toolbox validation.

Skull defect and cranial implant design benchmark dataset

114+100 complete skulls with synthetic defects and matching implants. Adapted from CQ500 head CT. MICCAI 2020 AutoImplant challenge. CC BY-NC-SA 4.0.

Complete 3D lower extremity muscle, bone, cartilage from Visible Human cryosections

Pelvis to ankle: bone, muscle, cartilage, ligament, fat surfaces for male and female. Scientific Data, 2022. Useful for musculoskeletal modeling.

Open-source complete 3D human anatomy atlas with muscle attachments

Full skeleton, muscles with origins/insertions, articular cartilages at all joints. Blender format. CC BY-SA license. Community-maintained.

Head and neck organ-at-risk CT and MR segmentation dataset

42 patients with matched CT and MR. 30 structures segmented including mandible, skull base bones. Zenodo download. Medical Physics, 2023.

Complete cadaver CT, MRI (1mm), and cryosection images (0.2mm) of Korean male

Whole-body serially sectioned images with bone, muscle, organ segmentation. Higher resolution than US Visible Human. Ajou University.

Complete male (90 GB) and female (131 GB) cadaver CT + cryosection datasets

Asian population reference anatomy. CT, MRI, and gelatin-embedded cryosection photographic images. Third Military Medical University, China.

High-resolution X-ray CT archive of biological specimens including vertebrate skeletons

Slice animations, volumetric renderings, and 3D surface models of living and extinct vertebrate skulls and skeletons. NSF Digital Libraries Initiative. UT Austin HRCT Facility.

NSF-funded database of 3D digital surface models of bird skeletal bones

Laser surface scans of bird bones from Harvard MCZ, Yale Peabody, and other collections. Common and rare species. College of the Holy Cross.

3D scans of hominin fossils, ancient animals, and stone tools from Kenya

National Museums of Kenya and Turkana Basin Institute collections. Downloadable for 3D printing. CC BY-NC-SA license.

3D scans of fossil hominins from the Smithsonian Human Origins collection

Downloadable 3D models of primate and early human fossils. Non-commercial use. Smithsonian Institution.

3D skeletal reconstructions from subadult CT scans for forensic anthropology

Long bone and pelvis 3D reconstructions from pediatric medical imaging. Raw skeletal and dental data. University of Nevada, Reno.

3D carpal bone anatomy from 90 subjects (120 wrists) with kinematics

CT-derived cortical surfaces of carpal bones, radius, and ulna. 1,215 unique wrist positions with kinematics data. Useful for wrist biomechanics and SSM construction.

Humerus and scapula statistical shape and density models from 75 CTs

MATLAB SSM/SDM code + VTK output. Shape model with PCA scores and bone density distribution. Soltanmohammadi et al., J. Biomech. Eng. 142(12), 2020.

Statistical shape models of talus, calcaneus, metatarsal, and midfoot

SSMs of primary functional foot segments from 24-34 MRI scans. Built with GIAS2 toolbox. Grant et al., PeerJ, 2020.

SSM-based finite element models of normal and deformed thoracolumbar spine

3D surface meshes from EOS images with hexahedral FE mesh templates for bone and soft tissues. Zenodo data. Scientific Data, 2024.

Public dataset of tibia-fibula surface meshes and SSM

Geometric variation of the human tibia-fibula with surface meshes and statistical shape model. Zenodo data.

Combined statistical body model of skeleton, organs, and skin surface

Articulated bone model with 68 bones + organs + skin. Fit to body scans. Enables joint skeleton-organ-skin shape analysis.

Curated guide for finding 3D bone shapes and medical image datasets

AI-assisted filtering for bone type, mesh availability, and licensing. Aggregates links to dozens of bone imaging and mesh datasets.

WHO fracture risk assessment tool for 80+ countries

10-year probability of major osteoporotic and hip fracture from clinical risk factors and optional BMD.

Clinical standards for bone densitometry practice

Official positions on DXA reporting, reference databases, T-score calculation, body composition analysis.

Open-source MATLAB toolbox for FEA, meshing, and biomechanical modeling

Includes bone mesh generation from segmented images, hex/tet meshing, FEBio integration. Moerman, JOSS, 2018. Widely used in bone biomechanics.

Open-source ImageJ plugin for bone image analysis

Measures thickness, connectivity, anisotropy, and moments of inertia from micro-CT and clinical CT. Standard tool for trabecular bone analysis.

Open-source deep learning tool for mandible and maxilla segmentation

Segments maxilla/upper skull, mandible, upper/lower teeth, and mandibular canal from CT/CBCT. 3D Slicer extension available.

Open-source toolkit for statistical shape modeling and analysis

Automated particle-based SSM construction from meshes/images. Includes Studio GUI, Python API, and example datasets. SCI Institute, University of Utah.

Scala library for statistical shape modeling and registration

Gaussian Process Morphable Models, shape registration, fitting algorithms. HDF5 model format. Tutorial datasets included. University of Basel. Apache 2.0.

Open-source platform for medical image analysis and 3D visualization

DICOM viewer, segmentation, registration, mesh generation, and 100+ extensions. Used for bone segmentation, implant planning, and SSM construction.

Open-source finite element solver for biomechanics and biophysics

Nonlinear FEA for bones, joints, soft tissues. Includes FEBio Studio GUI, tissue material models, and contact mechanics. University of Utah + Columbia.

Open-source software for spinal cord MRI processing and analysis

Segmentation, registration, atlas-based analysis, and metrics for spinal cord and canal. Includes SCIseg for injury lesion detection. NeuroPoly Lab.

R package for long bone cortical thickness mapping and cross-sectional geometry

Extracts semilandmarks, builds cortical thickness maps, and calculates biomechanical parameters (CSA, Ixx, Iyy) from 3D bone models. Profico et al., AJPA, 2021.

Comprehensive Raman, X-ray diffraction, and chemistry database for minerals including bone apatite

Reference Raman spectra for hydroxyapatite, carbonated apatite, and other bone-relevant minerals. University of Arizona. Essential for bone spectroscopy research.

Open-source multi-modality framework for hip dysplasia analysis

Ultrasound + X-ray DDH analysis. Expert-annotated datasets, pre-trained models, alpha angle and acetabular index measurement. Python API.

Computational human phantoms for radiation dosimetry including skeletal models

Whole-body voxel phantoms from pediatric to adult. 100+ organs including detailed bone anatomy. NCI + University of Florida collaboration.

Open-source model segmenting 40 anatomic structures in MRI and CT

Pelvic, abdominal, thoracic structures including bones and muscles. Trained on UK Biobank + TotalSegmentator. Code + weights publicly available.

Sequence-independent segmentation of anatomic structures in MRI

Extension of TotalSegmentator to MRI. Robust across different sequences and field strengths. 616 MR subjects training data. Radiology, 2024.

Open-source system for distributing free, high-quality 3D anatomy atlases

Built on 3D Slicer. Producing open anatomy atlases for research and education. Includes brain, inner ear, and musculoskeletal models.

Open-source toolbox for IMU-based lower extremity kinematics via OpenSim

Sensor fusion + musculoskeletal model for accurate joint angles from wearable IMUs. Long-duration measurement outside lab. Stanford/OpenSim.

Open-source deep learning bone age assessment validated on skeletal dysplasias

Prior-free approach for bone age from hand X-rays. Validated on patients with skeletal dysplasias, not just healthy children. Pediatric Radiology, 2023.

Open-source deep learning tool for knee osteoarthritis KL grading

Trained on MOST, validated on OAI. Automated Kellgren-Lawrence grading from knee X-rays. University of Oulu.

Markerless motion capture using smartphone cameras

Browser-based 3D biomechanical analysis from two smartphone videos. OpenSim integration. Stanford. Uhlrich et al., PLOS Comp. Bio., 2023.

Curated master list of biomechanics datasets, tools, and resources

Links to dozens of gait, bone, musculoskeletal datasets and processing tools. Best single starting point.