Catalog entries
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Total entries
203
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Dutch national health research data catalogue built on the FAIR Data Point (FDP) specification. Metadata is described using HealthDCAT-AP, t…
Swiss national health research metadata catalog operated by the SIB Swiss Institute of Bioinformatics for the Swiss Personalized Health Netw…
ELIXIR's registry of bioinformatics and life science software, hosting over 33,000 tools. Each entry is structured using biotoolsSchema and …
The world's largest repository of biomedical ontologies and terminologies, maintained by the National Center for Biomedical Ontology (NCBO) …
Manually curated database of bioactive molecules with drug-like properties, maintained by EMBL-EBI. Integrates chemical, bioactivity, and ge…
The world's largest public registry of clinical studies — 500,000+ registered trials covering interventional and observational studies, elig…
Freely accessible public archive of human genomic variants classified for disease and drug response, maintained by NCBI/NLM/NIH. Contains 4.…
CMS Medicare Coverage Database
The authoritative US federal database of Medicare coverage determinations — National Coverage Determinations (NCDs) and Local Coverage Deter…
European Medicines Agency open data covering all EU-authorised medicines — approved and withdrawn applications, post-authorisation procedure…
Automated global disease surveillance system developed at Boston Children's Hospital in 2006 by Clark Freifeld and John Brownstein. Aggregat…
WHO REST API providing programmatic access to the ICD-11 Mortality and Morbidity Statistics (MMS) linearization — including entity lookups, …
Open science platform for systematic identification and prioritisation of drug targets using human genetic, genomic, and disease evidence. I…
Free, fully open academic knowledge graph covering 250M+ scholarly works, 250M+ authors, 100K+ institutions (with ROR IDs), and 30K+ journal…
Scottish Health and Social Care Open Data
Open data platform managed by Public Health Scotland providing 104 health and social care datasets covering Scotland's NHS. Topics include e…
FDA public data API providing structured access to drug adverse event reports (FAERS), drug labeling, drug recalls, medical device adverse e…
Open data portal of the Pan American Health Organization (PAHO), the WHO regional office for the Americas. Provides 140+ core health indicat…
Open repository of freely available physiological signals and related clinical data, maintained by the MIT Laboratory for Computational Phys…
swhInternet-based outbreak surveillance system launched in 1994 by the International Society for Infectious Diseases (ISID). Operated 24/7 by a…
The authoritative biomedical and life sciences literature index maintained by the US National Library of Medicine (NLM/NCBI). Covers 35M+ ci…
Open research data platform by Sage Bionetworks for storing, sharing, and collaborating on scientific data. Hosts DREAM Challenge datasets, …
Open repository of de-identified cancer imaging data funded by the National Cancer Institute (NCI) and hosted at the University of Arkansas …
Global clinical trial data sharing platform operated as an independent nonprofit. Hosts 8,000+ clinical trials representing 5.2 million part…
Official WHO publication series reporting confirmed and potential acute public health events of international concern across all hazards — i…
Multimodal medical agent benchmark that simulates end-to-end clinical workflows. Presents AI agents with patient-facing dialogue, EHR record…
The first freely accessible European intensive care database. Contains de-identified clinical data from 23,106 ICU and high-dependency unit …
Benchmark series for automated detection of breast cancer metastases in H&E-stained whole-slide images of sentinel lymph nodes — the first a…
Benchmark evaluating AI agents on end-to-end, long-horizon, policy-rich healthcare workflow automation. Covers three domains: provider prior…
Few-shot evaluation benchmark for EHR foundation models from the Shah Lab at Stanford Medicine. Contains 6,739 de-identified longitudinal pa…
eICU Collaborative Research Database
Multi-center ICU database containing data from 200,000+ admissions of 139,000+ patients across 335 ICU units at 208 hospitals across the con…
Benchmark for evaluating LLM agent ability to retrieve and answer clinical questions from FHIR-structured EHR data. Contains approximately 3…
Physician-curated benchmark for evaluating large language models on realistic health conversations. Contains 5,000 multi-turn conversations …
hfFHIR-native benchmark for evaluating AI agents on real-world clinical tasks authored by practising physicians. Contains 300 tasks across 10 …
Clinician-curated benchmark for evaluating LLM instruction-following on real clinical tasks. Contains 983 natural-language instructions auth…
Benchmark dataset for evaluating LLM ability to perform clinical calculator tasks — a common but under-tested dimension of medical reasoning…
Comprehensive evaluation framework for benchmarking LLMs on medical tasks, built on Stanford CRFM's HELM platform. Covers 121 clinician-vali…
The largest publicly available consolidated dataset for type 1 diabetes management. Aggregates 21 source datasets into a standardised schema…
Large de-identified EHR dataset from 364,627 patients across 546,028 hospital admissions and 94,458 ICU stays at Beth Israel Deaconess Medic…
MLOmics Cancer Multi-Omics Benchmark
Standardised multi-omics benchmark dataset covering all 32 TCGA cancer types across four omics modalities: mRNA expression, microRNA, DNA me…
MICCAI 2018 grand challenge dataset for nucleus instance segmentation in H&E-stained histology images across multiple organs (breast, liver,…
Cloud-native NCI cancer imaging platform providing programmatic access to 176 collections, 85,682 cases, 1,032,911 image series, and 99+ TB …
100,000 colour-normalised H&E image patches (224×224 px, 0.5 µm/px) from colorectal cancer and normal colon tissue across 9 tissue classes: …
NHS England Synthetic Clinical Notes
Synthetic clinical notes dataset generated by NHS England Data Science to support clinical NLP research and model development without exposi…
The largest publicly available whole-slide imaging dataset, containing ~11,000 H&E-stained prostate biopsy WSIs with Gleason grading annotat…
Pan-cancer nucleus instance segmentation and classification dataset covering ~200,000 nuclei across 5 clinically important classes (neoplast…
Binary image classification benchmark derived from CAMELYON16, consisting of 327,680 colour patches (96×96 px) extracted from H&E-stained ly…
PhysioNet Sepsis Challenge 2019
Benchmark dataset for early prediction of sepsis from hourly ICU clinical measurements, from the PhysioNet/Computing in Cardiology Challenge…
Large publicly available 12-lead ECG dataset containing 21,799 clinical recordings from 18,869 patients (ages 0–95, 52% male) collected at t…
Landmark cancer genomics program that comprehensively characterised the molecular landscape of 33 cancer types across 20,000+ primary tumour…
The largest publicly available clinical EEG database, containing 60,000+ recordings from Temple University Hospital (2002–present) across 7 …
Exposes any FHIR R4/R5 server as an MCP server, enabling LLM agents to perform CRUD operations on FHIR resources through natural language vi…
Model Context Protocol (MCP) server for the OMOP Common Data Model. Provides a structured, secure interface for LLM agents to query and anal…
openEHR Assistant MCP (Cadasto)
MCP server bridging AI assistants with openEHR design-time workflows. Exposes CKM archetype and template search, openEHR terminology concept…
MCP server for runtime interaction with EHRbase via openEHR REST APIs. Exposes 11 MCP tools covering template operations, EHR lifecycle mana…
Experimental MCP server exposing SNOMED CT concept lookup to LLM agents via any FHIR R4 terminology server. Enables AI agents to resolve cli…
Native MCP server exposing 211+ expert-curated biomedical tools to any MCP-compatible AI agent. Tools span drug discovery, therapeutic reaso…
Multimodal biological reasoning model fusing a DNA foundation model with a large language model to generate interpretable, step-by-step mech…
Vision Transformer-based framework for precise nucleus instance segmentation and classification in whole-slide histology images. U-Net encod…
Vision-language foundation model for histopathology pretrained on 1.17 million image-caption pairs from PubMed Central open-access articles …
Open foundation model for electrocardiogram (ECG) analysis with 90.9 million parameters built on the wav2vec 2.0 architecture. Pre-trained o…
Foundation model for electrocardiogram analysis pretrained on over 10 million ECG recordings. Evaluated across multiple clinical domains inc…
Latent predictive foundation model for echocardiography trained on 18 million cardiac ultrasound images using joint-embedding predictive arc…
State-of-the-art protein language model family from Meta AI, trained on 250 million protein sequences using masked language modelling. Avail…
State-of-the-art protein language model from EvolutionaryScale (Biohub) trained on ~2.8 billion protein sequences. Generates embeddings that…
Self-verifying LLM agent for gene-set analysis that autonomously queries domain databases (Gene Ontology, KEGG, NCBI Gene, PubMed) to annota…
1.1-billion parameter vision transformer foundation model for histopathology — the largest publicly available pathology FM by parameter coun…
Multi-resolution convolutional neural network for semantic segmentation of whole-slide histopathology images. Uses two parallel U-Net-style …
Simultaneous nucleus instance segmentation and classification model for H&E histology images. Uses horizontal and vertical distance maps (Ho…
Google's family of Gemma 3 variants fine-tuned for medical text and image comprehension, released under the Health AI Developer Foundations …
Universal medical image segmentation model adapting Meta's Segment Anything Model (SAM) to 30+ imaging modalities including CT, MRI, ultraso…
Extension of MedSAM to 3D volumetric medical imaging and video sequences, built on Meta's SAM2 architecture. Handles instance-level segmenta…
Self-configuring framework for 3D volumetric medical object detection, applying the same automated configuration philosophy as nnU-Net to de…
Self-configuring framework for medical image segmentation that automatically adapts its architecture, preprocessing, training, and post-proc…
Production-ready medical NLP toolkit providing state-of-the-art encoder transformers (BERT, ELECTRA, DeBERTa families) for biomedical named …
Family of Time Series Language Models (TSLMs) from Stanford Biodesign for Digital Health (BDHG) that integrate time series as a native modal…
The first vision-language foundation model for computational pathology — a CLIP-based contrastive model fine-tuned on 208,414 pathology imag…
Whole-slide pathology foundation model trained on real-world clinical data from Providence Health System — the first WSI-level foundation mo…
Generative foundation model for single-cell multi-omics analysis. Pre-trained on 33 million normal human cells from CellXGene across brain, …
Automated segmentation tool for 100+ anatomical structures in CT and MRI scans — covering abdominal organs (liver, spleen, pancreas, kidneys…
Automated segmentation of 72 white matter fibre bundles from diffusion MRI tractograms, directly from raw peaks (fibre orientation distribut…
LLM-based AI agent for therapeutic reasoning that orchestrates 211 biomedical tools spanning drug databases, genomic repositories, clinical …
The largest pretrained vision foundation model for computational pathology — a ViT-L/16 encoder trained with DINOv2 self-supervised learning…
Successor to UNI — a ViT-H/14 vision foundation model for computational pathology from the Mahmood Lab at Harvard/BWH. 681M parameters, trai…
Self-supervised vision transformer (ViT-H/14, 632M parameters) pretrained on 1.5M whole-slide histopathology images from Memorial Sloan Kett…
Second-generation Virchow pathology foundation model — ViT-H/14 (632M parameters) pretrained on 3.1M whole-slide images from Memorial Sloan …
Free, open-source platform for medical image informatics, image processing, and three-dimensional visualisation. Supports segmentation, regi…
Google's open-source suite of Kotlin libraries for building offline-capable, mobile-first healthcare applications on Android using the HL7 F…
Open-source automated insulin delivery (AID) system for Android implementing the OpenAPS oref0/oref1 algorithm. Manages insulin pump communi…
Framework-agnostic Python data augmentation library for 2D and 3D medical imaging. Provides spatial transforms (elastic deformations, rotati…
Open-source access negotiation platform for biobank and research infrastructure data requests. Manages the full Data Access Request (DAR) li…
Java library for reading and writing life sciences image file formats, developed by the Open Microscopy Environment (OME) consortium. Suppor…
General-purpose biomedical AI agent framework from Stanford SNAP Lab. Combines LLM reasoning with retrieval-augmented planning and code exec…
High-performance FHIR R4 server with an integrated CQL (Clinical Quality Language) evaluation engine, designed for population-wide aggregate…
FHIR R5-powered, modular open-source electronic health management information system (HMIS) developed by Open Healthcare Network Foundation …
Open-source Python platform for automated quantitative measurement of biological phenotypes from microscopy images. Enables biologists witho…
High-performance TypeScript framework for building web-based medical imaging applications, providing the rendering engine underlying the OHI…
Open-source NLP platform for extracting clinical information from unstructured clinical text — radiology reports, discharge summaries, and E…
Infrastructure and R package suite enabling non-disclosive federated analysis of sensitive research data across distributed sites. Analysts …
De facto standard tool for converting DICOM neuroimaging data to NIfTI format with BIDS-compliant JSON sidecars. Handles vendor-specific DIC…
The de-facto open-source Java DICOM toolkit and library, providing a comprehensive implementation of the DICOM standard for medical imaging.…
Reference C/C++ implementation of the DICOM standard — a comprehensive collection of libraries and command-line tools covering DICOM data en…
Deep learning-based DNA variant caller from Google Health. Processes aligned sequencing reads (BAM/CRAM), generates pileup image tensors, an…
The world's largest health management information system (HMIS) platform, deployed in over 80 countries and used by billions of people's hea…
Web-based platform for managing, annotating, and running computational algorithms on large whole-slide and microscopy images. Supports image…
PyTorch-based deep learning framework for accelerated MRI reconstruction from undersampled k-space data. Implements a range of state-of-the-…
Discharge Documentation Generator
LLM-powered tool for generating draft clinical discharge letters from electronic health record notes. Synthesises medical notes from hospita…
Lightweight Python library for identifying drug and medication names in free text, with fuzzy matching for misspellings and integration with…
Open-source openEHR Clinical Data Repository (CDR) providing a standard-based backend for interoperable clinical applications. Implements th…
Standardised evaluation framework for oncology foundation models, covering both pathology and radiology. Benchmarks patch-level, slide-level…
High-performance C++20 library for reading whole slide images (WSI) in digital pathology, with first-class Python bindings. Thread-safe, AI/…
Deep learning neuroimaging pipeline for fast and accurate whole-brain MRI analysis. Performs whole-brain segmentation of 95+ cortical and su…
Python framework for large-scale self-supervised learning on electronic health records. Provides tooling for converting raw EHR data to the …
The standard batteries-included distribution of ImageJ for life sciences research. Bundles ImageJ with 200+ curated plugins covering segment…
Robust and reproducible preprocessing pipeline for functional MRI (fMRI) data. Accepts BIDS-formatted input and performs brain extraction, s…
The industry-standard toolkit for variant discovery in high-throughput sequencing data, developed by the Broad Institute. Implements best-pr…
Libre hospital and health information system providing over 40 standard-based packages covering primary care, obstetrics, pediatrics, labora…
Open-source Django/Docker platform for end-to-end development and deployment of medical imaging AI. Provides archives for managing DICOM dat…
The most widely used open-source Java implementation of the HL7 FHIR standard. Provides both a client library and a full JPA server with dat…
Heuristic-driven DICOM-to-BIDS converter for neuroimaging. Converts raw DICOM acquisitions into BIDS-compliant datasets using customisable P…
HuggingFace-native framework for training large language models on structured electronic health records using the MEDS (Medical Event Data S…
High-level Python library built on pydicom for creating and reading derived DICOM objects — segmentations (SEG), parametric maps, structured…
Python library for whole slide image (WSI) processing in computational pathology. Provides tissue detection, tiling, stain normalisation, an…
Python toolkit for digital pathology image analysis providing colour normalisation, nuclei detection and segmentation, feature extraction, a…
Interactive machine learning toolkit for image segmentation, classification, object detection, counting, and tracking. Users interactively l…
Open-source 3D medical image reconstruction software that generates volumetric models from 2D DICOM slices (CT and MRI). Features segmentati…
Foundational open-source C++ toolkit for N-dimensional scientific image processing, with primary focus on medical imaging segmentation and r…
Widely used open-source application for interactive segmentation of 3D medical images — providing user-guided active contour and manual segm…
Kubernetes-based open-source platform toolkit for building federated medical image analysis infrastructure. Orchestrates AI workflows (nnU-N…
Clinical NLP toolkit for named entity recognition and linking in free-text clinical notes. Performs concept extraction and normalisation aga…
FHIR-native open-source developer platform for building and deploying clinical software, operated by Orangebot Inc. Provides a full-stack Ty…
Agentic AI framework for chest X-ray (CXR) interpretation that dynamically orchestrates multiple specialist models — visual QA (CheXagent, L…
Updated iteration of the MedRAX agentic chest X-ray reasoning framework from the Bo Wang Lab. Extends the multi-model orchestration approach…
.NET Core implementation of the HL7 FHIR standard maintained by Microsoft Healthcare. Supports FHIR R4 and R5 with pluggable persistence (SQ…
Python package for standardised medical image radiomics and preprocessing. Handles DICOM, NIfTI, and NRRD input, performs image preprocessin…
The most widely used open-source healthcare integration engine — routes, transforms, and filters health messages between clinical systems ac…
Open-source medical image computing toolkit combining a full-featured desktop workbench for visualization, segmentation, and registration wi…
FAIR research data platform for building and managing biobank catalogues, rare-disease registries, and cohort data portals. Provides a flexi…
Framework for packaging, testing, and deploying medical AI applications into clinical production environments, part of the MONAI ecosystem. …
AI-assisted medical image annotation server with active learning. Runs as a lightweight server connecting to clinical viewers (3D Slicer, OH…
Curated repository of 30+ production-ready medical imaging models in standardised MONAI Bundle format, covering segmentation, detection, cla…
PyTorch-based open-source framework for deep learning in healthcare imaging, part of the PyTorch Ecosystem. Provides domain-specific transfo…
Automated MRI quality control tool that extracts image quality metrics (IQMs) and generates visual reports for structural (T1w, T2w) and fun…
Fast, interactive, multi-dimensional image viewer for Python. The standard viewer for bio-imaging and computational pathology workflows — su…
Python library for neurophysiological signal processing. Provides accessible, reproducible tools for ECG, EEG, EMG, EDA, and PPG signals — c…
Specialised MRI preprocessing pipeline for human infant neuroimaging (0–2 years old), part of the NiPreps ecosystem. Handles the unique chal…
Web platform for real-time continuous glucose monitoring (CGM) data broadcasting, storage, and visualisation. Acts as a personal diabetes da…
Browser-based medical image visualisation library supporting 30+ neuroimaging formats including NIfTI, DICOM, MGH, NRRD, tractography, and s…
R package for nonlinear mixed-effects (NLME) modelling in pharmacometrics, designed to compete with commercial tools such as NONMEM and Mono…
Machine learning model for predicting patient no-shows at clinical appointments, actively deployed at UMC Utrecht. Identifies patients at hi…
Zero-footprint, web-based medical image viewer from the Open Health Imaging Foundation (OHIF). A configurable progressive web application wi…
Open-source platform for managing, visualising, and analysing microscopy image data. Supports 150+ imaging formats, centralised storage, web…
Core database application for biobanks and epidemiological studies, developed under the OBiBa initiative (Maelstrom Research / McGill Univer…
Open-source tool for automatically extracting raw time-series voltage data from paper ECG images — scanned or photographed. Uses semantic se…
Community-built open-source reference implementation of an automated insulin delivery (AID) algorithm for Type 1 diabetes — the original DIY…
The most widely used open-source electronic health records (EHR) and medical practice management solution, governed by the OpenEMR Foundatio…
Open-source electronic medical records platform designed for resource-limited settings, deployed in 60+ countries across Africa, Asia, and L…
Open-source, local-first AI clinical scribe that records patient encounters and automatically generates structured clinical notes. Runs enti…
Low-level C library and Python bindings for reading whole-slide image (WSI) files across 11 proprietary vendor formats — including Aperio SV…
Lightweight, open-source RESTful DICOM server for medical imaging, widely used in hospitals, research institutions, and imaging workflows. P…
Canadian open-source electronic medical record system developed at McMaster University Department of Family Medicine, widely used by primary…
Open-source Health Information System distribution that integrates OpenMRS 3 (EMR/clinical records), Odoo (ERP, billing, pharmacy), SENAITE …
Open-source toolkit for computational pathology from Dana-Farber Cancer Institute. Covers the full digital pathology pipeline: whole slide i…
The standard Python library for reading, modifying, and writing DICOM files. Used in virtually every Python-based medical imaging pipeline —…
Open-source Python toolkit for clinical deep learning that unifies datasets, tasks, and ML models across EHR, physiological signals, and med…
Open-source desktop platform for digital pathology image analysis and bioimage informatics. Provides whole slide image (WSI) viewing, intera…
Open-source cheminformatics toolkit for molecule manipulation, descriptor calculation, substructure searching, and pharmacophore analysis. T…
End-to-end open-source platform for patient-specific cardiovascular blood flow simulation. Provides a complete pipeline from medical image s…
3D Slicer extension providing a toolkit for image-guided interventions (IGT). Offers real-time instrument tracking, ultrasound and needle gu…
Unified deep learning framework for digital pathology, providing a consistent API across weakly supervised, strongly supervised, multiple in…
Structural MRI preprocessing pipeline from the NiPreps ecosystem. Performs skull stripping, tissue segmentation, and spatial normalisation a…
Open-source FHIR server built in C# by Firely and now maintained by Incendi. Supports FHIR R4 and STU3, available as NuGet packages or Docke…
Open-source Swift framework for rapid development of modular, interoperable digital health applications on iOS and macOS. Provides reusable …
Cell and nucleus instance segmentation library using star-convex polygon representations — predicts distances to object boundaries along fix…
Leading open-source library for PET and SPECT tomographic image reconstruction. Provides iterative and analytical reconstruction algorithms,…
High-performance Go library for reading, writing, and processing DICOM medical image files. Supports parsing of multi-frame imagery (encapsu…
Open-source Python library for generating and evaluating synthetic tabular data across multiple modalities — tabular, time series, survival …
AI agent framework for natural-language querying of systems biology models from the BioModels database (EMBL-EBI). Enables researchers to in…
End-to-end Python API for computational pathology built on PyTorch, developed by the TIA Centre at the University of Warwick. Provides a uni…
Open-source nonprofit diabetes data platform that aggregates, visualises, and shares data from 50+ diabetes devices including CGMs (Dexcom, …
Open-source Python library for efficient loading, preprocessing, augmentation, and patch-based sampling of 3D medical images in deep learnin…
End-to-end LLM framework for zero-shot patient-to-clinical-trial matching. Comprises three stages: retrieval (recalls 90%+ of relevant trial…
Large-scale whole slide image processing toolkit from the Mahmood Lab at Harvard Medical School. Provides a single-command pipeline for tiss…
Privacy Enhancing Technology (PET) operations platform enabling federated learning and multi-party computation across distributed healthcare…
Open-source Chrome extension for real-time PII detection and redaction before submission to AI chat interfaces. Monitors text inputs and ide…
The Veterans Health Information Systems and Technology Architecture — the comprehensive EHR and HIS that has run the US Department of Vetera…
Open-source browser-based 3D radiological viewer for DICOM data with interactive cinematic volume rendering. All processing runs locally in …
Comprehensive open-source DICOM viewer available as a desktop application and web-based deployment. Supports the full DICOM stack: 2D/3D ima…
Native Python implementation of the Waveform Database (WFDB) standard for reading, writing, and processing physiological signal data. The pr…
Python library for patch sampling from whole-slide images (WSI) with annotation-aware batch iteration. Handles three tightly coupled tasks: …
Open-source biomedical imaging informatics platform developed by the Neuroinformatics Research Group (NRG) at Washington University School o…
The CDISC standard for analysis-ready clinical trial datasets — the layer between raw SDTM tabulation data and the statistical analyses subm…
The regulatory standard for organising and formatting clinical trial data submitted to the FDA and EMA. SDTM defines a set of domain models …
The international standard for transmitting, storing, retrieving, printing, processing, and displaying medical imaging information. Defines …
FAIR Data Point (FDP) Specification
W3C Unofficial Proposal Draft specification for a metadata service that exposes digital objects following FAIR principles (Findable, Accessi…
The dominant healthcare interoperability standard, defining a RESTful API and JSON/XML resource formats for exchanging clinical and administ…
The official EU metadata specification for describing health datasets for secondary use, extending DCAT-AP 3.0 with health-domain semantics.…
OWL ontology for systematically describing and classifying health IT application systems and software products. Defines classes and relation…
A minimal, specialty-agnostic FHIR R4 Implementation Guide defining a structured electronic health record extract containing essential healt…
The international quality management system (QMS) standard for organisations in the medical device lifecycle — design, production, storage, …
The international standard for risk management of medical devices, including software as a medical device (SaMD) and AI/ML-enabled devices. …
The international accreditation standard for medical laboratories, defining requirements for quality and competence in clinical testing. Cov…
W3C recommendation for expressing policies over data assets — permissions, prohibitions, and obligations. In healthcare, used to encode data…
Open Nursing Core Implementation Guide
FHIR R4 implementation guide defining a standardised nursing data model covering the complete nursing process (ADPIE — Assessment, Diagnosis…