Awesome Healthcare Overview

Curated list of awesome open source healthcare software, libraries, tools and resources.

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Awesome Health

Curated list of awesome open source healthcare software, libraries, tools and resources. Each link has been vetted to ensure the project is active and provides value to healthcare facilities, providers, developers, policy experts, and/or research scientists.

Contents

• EHR
• Scribe
• Specifications
• Nursing
• Imaging
• Dental
• Laboratory
• Libraries
• Frameworks
• Applications
• Personal Health Record
• Telemedicine
• Integration
• Research
• Hardware
• Bioinformatics
• Books
• Data
• Datasets
• Design
• Enterprise Master Patient Index
• Machine Learning
• Compliance
• Asset Management
• Logistics

EHR

• Akello (⭐42) - Integrated Mental Health Infrastructure
• Bahmni - Electronic Medical Record and hospital system.
• Beda EMR (⭐132) - EMR built natively on FHIR.
• BHIMA (⭐234) - Hospital information and accounting system for rural hospitals.
• CARE (⭐419) - Digital public good for hospital administration and decentralized patient care.
• Cottage Med - Electronic Medical Record software designed by physicians.
• EHRBase OpenEHR Clinical Data Repository.
• EHRServer (⭐207) - CaboLabs EHRServer.
• ERPNext (⭐41k) - Modules that help manage patients, appointments, consultations, lab tests, and billing.
• FerroEHR (⭐85) - openEHR Clinical Data Repository written in Rust, with ITS-REST and AQL support on PostgreSQL.
• FreeMedForms EMR - Electronic Medical Record software.
• GitEHR (⭐6) - Patient-owned, self-hostable EHR stored as plain-text files in a Git repository. Append-only journal, immutable documents, offline-first, no database.
• GNU Health - Electronic Health Record, Hospital Management, and Health Information System.
• GNUmed - Electronic Medical Record software.
• HasteHealth (⭐85) - Scalable FHIR server and clinical data repository.
• HospitalRun - Helps provide the most modern Hospital Information System possible to the least resourced environments.
• HOSxP - Thai Hospital Information System that aims to ease the healthcare workflow of health centers and central hospitals.
• ICTHospital (⭐115) - Hospital management software with built-in unified communications, built on Laravel.
• LibreHealth EHR - Clinically-focused Electronic Health Record System.
• Marley (⭐555) - Health information system built on the Frappe framework.
• Medplum (⭐2.8k) - Developer platform that enables flexible and rapid development of healthcare apps.
• Odoo Medical (⭐297) - Universal Health and Hospital Information System.
• Open Hospital (⭐638) - Electronic Medical Record software for underprivileged rural hospitals.
• OpenClinic (⭐39) - Medical Records System.
• openMAXIMS (⭐64) - Full Patient Administration System designed for the NHS.
• OpenEMR - Electronic Health Records and Medical Practice Management application.
• OpenEyes - Electronic Medical Record application for ophthalmology.
• OpenMRS - Enterprise Electronic Medical Record System platform.
• OSCAR EMR - OSCAR McMaster Project.
• Ottehr (⭐343) - Modular, Production-Ready, Open-Source EHR
• Ozone HIS - The entreprise-grade integrated health information system built with OpenMRS 3
• Ripple - NHS-funded, community led initiative working towards an integrated Digital Care Record Platform.

Scribe

• OpenScribe (⭐225) - Open source, local-first medical scribe platform for recording clinical encounters, transcribing audio, and generating structured draft clinical notes.
• Phlox (⭐110) - Open source (MIT), self-hosted AI medical scribe with realtime note drafting, RAG, and MCP-extensible agents; runs as a desktop app or Docker image.

Specifications

• Continuity of Care Document - Continuity of Care Document specifications
• DICOM Standards Browser - Provides an effective way to learn the DICOM standard and inspect DICOM attributes.
• FHIR - Fast Health Interoperability Resources.
• HL7 Version 2 - Specifications for all versions of HL7v2
• OHDSI OMOP Common Data Model - Standardized data model for many healthcare concepts, awesome Github presence including scripts for many major relational databases.
• OpenEHR - Open specification upon which software can be built.
• Open mHealth - Open Standard For Mobile Health Data.
• SMART on FHIR - Open standards based technology platform.

Nursing

• open-eObs - Observation and clinical assessment platform that offers a real-time view of all patients across a ward.

Imaging

• 3D Slicer - Cross-platform application for analyzing, visualizing and understanding medical image data.
• Cornerstone3D (⭐1.2k) - JavaScript libraries for building web-based medical imaging platforms.
• dcm2niix (⭐1.2k) - DICOM to NIfTI converter.
• dcm4che - Clinical Image and Object Management.
• Dicoogle (⭐536) - Dicoogle is an extensible, platform-independent and open-source PACS
• Drishti (⭐205) - Tomography and electron-microscopy data visualizer for both scientists and lay people.
• DICOMcloud (⭐235) - A standalone DICOMweb server with RESTful implementation of the DICOMweb/WADO services.
• DICOM Server (⭐516) - OSS Implementation of DICOMweb standard.
• DICOM Web Viewer - JavaScript/HTML5-based DICOM viewer with standard tools and a focus on supporting various screen sizes.
• Fiji - Open-source platform for biological-image analysis.
• highdicom (⭐241) - High-level DICOM abstractions for Python, including segmentations, structured reports and annotations.
• Horos (⭐643) - Medical image viewer.
• InVesalius - Open source software for reconstruction of computed tomography and magnetic ressonance images.
• ITK - Toolkit used for the development of image segmentation and image registration programs with leading-edge algorithms in 2 and 3 dimensions.
• ITK-SNAP - Interactive software for 3 dimensional image navigation, annotation, and automatic segmentation with an emphasis on user-friendliness.
• LibreHealth Radiology - Customized version of LibreHealth Toolkit with additional tools for radiology and imaging professionals.
• Kaapana (⭐276) - Open source toolkit for state of the art platform provisioning in the field of medical data analysis.
• Kheops - Open source platform for sharing medical images
• MedPy (⭐623) - Python library for medical image processing, supporting DICOM and NIfTI formats with tools for segmentation, filtering, and feature extraction.
• mercure (⭐104) - DICOM orchestrator for routing and processing imaging studies.
• MONAI Label (⭐908) - AI-assisted image labeling tool that works with 3D Slicer and OHIF.
• OHIF (⭐4.4k) - OHIF zero-footprint DICOM viewer and oncology specific Lesion Tracker.
• Omero (⭐222) - open source client/server system written in Java for visualizing, managing, and annotating microscope images and metadata
• OpenREM - Radiation Exposure Monitoring for physicists.
• OpenSlide (⭐518) - is a C library for reading whole slide image files.
• Orthanc - Lightweight DICOM server for healthcare and medical research.
• Papaya (⭐582) - Pure JavaScript medical research image viewer.
• PyMedPhys (⭐368) - Community library for medical physics.
• QuPath (⭐1.5k) - Bioimage analysis and whole slide image analysis for digital pathology.
• SlicerDMRI (⭐86) - Extension for 3D Slicer focused on diffusion MRI analysis and visualization, supporting neuroscience research.
• Slim (⭐173) - Interoperable web viewer and annotation tool for computational pathology.
• Viv (⭐372) - multiscale visualization of high-resolution multiplexed bioimaging data on the web.
• VTK - 3 dimensional visualization toolkit supporting a variety of algorithms and modeling techniques.
• Weasis (⭐1.4k) - Standalone and web-based DICOM viewer.

Dental

• DentalPin (⭐110) - Dental practice management with an AI agent that runs real operations.
• Open Dental - Dental Practice Management Software.
• OpenMolar - Dental Practice Management Software.

Laboratory

• MISO (⭐316) - Laboratory information management system for NGS sequencing centres.
• OpenELIS - Laboratory Information System for Global Health.
• SENAITE - Laboratory Information Management System.

Frameworks

• API Server (⭐113) - FHIR Server to support patient- and clinician-facing apps.
• Blaze (⭐231) - A FHIR Store with internal, fast CQL Evaluation Engine
• CareKit (⭐2.5k) - Open source software framework for creating apps that help people better understand and manage their health.
• CHT - Community Health Toolkit - set of Open Source tools that support community healthcare
• Clinical Meteor project - Meteor for FDA, HIPAA, and HL7 compliant applications.
• Clinical Quality Language (⭐338) - Clinical Quality Language is a HL7 standard for the expression of clinical knowledge.
• CyclOps (⭐97) - Framework for healthcare ML implementation.
• FHIRBase - Storage based on the FHIR Standard.
• FHIR Proxy (⭐75) - secure application that acts as an intermediary in the transfer of FHIR data to and from Azure API.
• FHIR Works on AWS (⭐302) - FHIR Works on AWS deployment.
• FHIR Server for Azure (⭐1.4k) - A .NET Core implementation of the FHIR standard.
• HAPI FHIR JPA Server Starter (⭐544) - Ready-to-deploy FHIR server built on HAPI FHIR.
• Helios FHIR Server (⭐57) - FHIR server written in Rust, optimized for clinical analytics workloads.
• Inferno - providing testing tools for the FHIR
• Intervention Engine FHIR Server (⭐113) - Generic FHIR server implementation in GoLang.
• LinuxForHealth FHIR Server (⭐375) - Modular Java implementation of version 4 of the HL7 FHIR specification.
• Medblocks UI (⭐74) - Web Components for rapid development of openEHR and FHIR systems.
• Opal (⭐288) - Framework for building clinical applications.
• ResearchKit (⭐5.8k) - Software framework that makes it easy to create apps for medical research or for other research projects.
• Spark (⭐285) - Public domain FHIR server developed in C#.
• Spezi (⭐261) - Stanford framework for building interoperable digital health apps on Apple platforms.
• Sushi (⭐190) - a reference implementation command-line interpreter/compiler for FHIR
• Swift-SMART (⭐140) - Swift SMART on FHIR framework for iOS and OS X.

Libraries

• Android FHIR SDK (⭐608) - The Android FHIR SDK
• Archie (⭐71) - OpenEHR Library written in Java.
• Asymmetrik FHIR API Server (⭐415) - A secure REST implementation for the HL7 FHIR Specification.
• Datamol (⭐557) - Molecular Manipulation Made Easy. A light Python wrapper build on top of RDKit.
• dcmjs (⭐356) - JavaScript implementation of DICOM manipulation.
• DCMTK - DICOM Toolkit.
• deid (⭐182) - De-identification of DICOM images in Python.
• dicom (⭐1.1k) - High Performance DICOM Medical Image Parser in GoLang.
• dicom-rs (⭐570) - Rust implementation of the DICOM standard.
• ehrapy (⭐369) - Electronic Health Record analysis in Python.
• Evil-DICOM (⭐193) - C# DICOM Library.
• Fellow Oak DICOM (⭐1.2k) - DICOM for .NET, .NET Core, Universal Windows, Android, iOS, Mono, and Unity.
• FHIRKit Client (⭐188) - Node FHIR client library.
• FHIRModels (⭐210) - FHIRModels is a Swift library for FHIR resource data models.
• FHIR .NET API (⭐941) - The official .NET API for HL7 FHIR.
• fhir.js (⭐438) - JavaScript client for FHIR.
• fhir.resources (⭐543) - Pydantic-based FHIR resource models for Python.
• fhir-py (⭐218) - Async and sync FHIR client for Python.
• FHIR protocol buffers (⭐963) - A Google implementation of protocol buffers for FHIR.
• Graphir (⭐63) - GraphQL interface over FHIR API
• HAPI FHIR (⭐2.4k) - Java API for HL7 FHIR Clients and Servers.
• Hearth (⭐26) - A fast FHIR-compliant server focused on longitudinal data stores.
• Health data standards (⭐0) - Ruby library for generating and consuming various healthcare related formats. These include HITSP C32, QRDA Category I, and QRDA Category III.
• HealthChain (⭐230) - Python SDK for building healthcare AI applications with FHIR tools and real-time EHR connectivity.
• Hermes (⭐239) - a SNOMED CT terminology server.
• Metriport (⭐797) - Open-source universal API for healthcare data.
• MITK - The Medical Imaging Interaction Toolkit.
• nHapi (⭐313) - .NET port of the HAPI HL7 v2 library.
• nhs-number (⭐6) - A Clojure/Script library providing validation, formatting and generation of UK NHS Numbers
• nhs-number (⭐14) - Python package to provide utilities for NHS Numbers, including validity checks, normalisation, and generation.
• Node HL7 (⭐59) - Node module that is bridged with the Java Hapi HL7 library.
• Node-hl7-parser (⭐53) - Open source version of Redox's HL7 v2 to schema-fied JSON parser.
• php-fhir (⭐152) - Tools for creating PHP classes from the HL7 FHIR Specification.
• Pydicom (⭐2.2k) - Pure Python package for working with DICOM files, enabling reading, writing, and manipulation of medical imaging data.
• pynetdicom (⭐577) - A Python implementation of the DICOM networking protocol.
• Python HL7 (⭐318) - Simple library for parsing messages of HL7 version 2.x into Python objects.
• Python SMART on FHIR client (⭐697) - Flexible Python client for FHIR servers supporting the SMART on FHIR protocol.
• Python 835 Parser (⭐113) - A simple-to-use Python interface to EDI 835 Health Care Claim Payment and Remittance Advice files.
• Ruby FHIR (⭐176) - FHIR client implementation in Ruby.
• Ruby HL7 (⭐96) - Ruby HL7 library.
• Rust FHIR (⭐17) - Rust SDK for HL7 FHIR
• sct (⭐32) - File-based SNOMED-CT toolset built in Rust.
• Scanpy - Single-cell RNA-seq analysis library in Python.
• SMART on FHIR JavaScript client (⭐355) - JavaScript client for SMART on FHIR apps.
• TorchXRayVision (⭐1.2k) - A library for chest X-ray datasets and models. Including pre-trained models.

Applications

• AirwayLab (⭐45) - Browser-based airway analysis dashboard for PAP therapy users with flow limitation scoring, breathing pattern analysis, and oximetry metrics.
• CommCare HQ (⭐525) - Server for CommCare, a mobile data collection platform for frontline health workers.
• Intervention Engine (⭐35) - Provides a web-application for data-driven team huddles.
• MedTimer (⭐648) - Medication reminder and tracking app for Android.
• OpenSRP FHIR Core (⭐70) - Offline-capable Android app for community health workers, built on the Android FHIR SDK.
• RCPCH Digital Growth Charts - Open source Digital Growth Charts platform with API, CLI, Python package, React chart components.
• SMART Pediatric Growth Chart (⭐71) - Pediatric growth charts.
• Simple - For clinicians to track patients with high blood pressure.
• SORMAS (⭐334) - Surveillance, outbreak response management and analysis system.

PHR

• AndroidAPS (⭐1.2k) - Open source automated insulin delivery system for Android.
• HealthLocker (⭐72) - Elixir-based personal health record.
• Loop (⭐1.8k) - Automated insulin delivery app for iOS.
• Nightscout (⭐2.9k) - Web monitor for continuous glucose monitor data.
• OpenHealth (⭐4k) - Privacy-first AI health assistant that interprets personal health data (blood tests, checkups, family history, symptoms) with local LLM support via Ollama.
• Tidepool - Data platform to reduce the burden of Type 1 Diabetes.
• Trio (⭐419) - Automated insulin delivery system for iOS based on the OpenAPS algorithm.
• xDrip+ (⭐1.8k) - Android app for collecting and displaying continuous glucose monitor data.

Telemedicine

• Healthcare worker at home - ​ Open Source Telehealth software

Research

• admiral (⭐324) - R package from pharmaverse for creating ADaM clinical trial datasets.
• i2b2 - Research data warehouse.
• LabKey Server - Platform for Translational Research.
• LibreClinica (⭐83) - Electronic data capture for clinical trials, community successor of OpenClinica.
• OHDSI ATLAS (⭐335) - Web tool for observational research on OMOP CDM data.

Integration

• FHIR Converter (⭐532) - an open source project that enables conversion of health data from legacy formats to FHIR.
• Google HCLS Data Harmonization (⭐250) - an engine that converts data of one structure to another
• LinuxForHealth HL7v2-FHIR Converter (⭐110) - Converts HL7 v2 messages to FHIR resources.
• mirthSync (⭐104) - CLI for putting Mirth Connect and Open Integration Engine configuration under version control.
• NextGen Connect Integration Engine (⭐1.2k) - The swiss army knife of healthcare integration.
• Open eHealth Integration Platform (⭐194) - An extension of the Apache Camel routing and mediation engine
• Open Integration Engine (⭐240) - Community open source fork of Mirth Connect.
• OpenHIM - Health information mediator.
• OpenWearables (⭐2.7k) - Self-hosted platform to unify wearable health data through one AI-ready API.
• Zato - A Python-based ESB and integration platform for healthcare interoperability, automation and orchestration.

Hardware

• Gluco (⭐52) - Glucometer.
• Murgen - Ultrasound imaging development kit.
• OpenAPS - The Open Artificial Pancreas System project is an open and transparent effort to make safe and effective basic Artificial Pancreas System.

Bioinformatics

• ADAM (⭐1.1k) - Genomics analysis platform.
• Bcbio (⭐1k) - Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis.
• cBioPortal (⭐1.1k) - Platform for exploring and visualizing cancer genomics data.
• FlashDeconv (⭐26) - High-performance spatial transcriptomics deconvolution for cell type mapping in tissue samples.
• Galaxy - Open web-based platform for data intensive biomedical research.
• GATK (⭐2k) - Broad Institute toolkit for variant discovery in high-throughput sequencing data.
• Hail (⭐1.1k) - Scalable genomic data analysis.
• nf-core/sarek (⭐616) - Pipeline to detect germline and somatic variants from sequencing data.
• scikit-bio (⭐1.3k) - Python library for bioinformatics, providing tools for sequence analysis, microbiome studies, and statistical analysis of biological data.
• Wregex - Amino acid motif searching software with optional Position-Specific Scoring Matrix.

Books

• Inspired EHRs (⭐134) - Ideas, designs, and techniques for designing an Electronic Health Record (EHR).

Data

• Atlas BI Library (⭐17) The unified report library.
• Cedar (⭐8) - Open source tool for testing the strength of Electronic Clinical Quality Measure.
• cTAKES - Natural Language Processing System for extraction of information from Electronic Medical Record clinical free-text.
• DHIS2 (⭐360) - Health information management platform used by national health systems.
• EDS_NLP (⭐167) - provides a set of spaCy components to extract information from clinical notes written in French
• eds-scikit (⭐45) - a tool to assist data scientists working on the AP-HP's Clinical Data Warehouse. It is specifically targeted for OMOP-standardized data.
• IHRIS - Health Information System for management of human resources for health.
• medspaCy (⭐684) - Library for clinical NLP with spaCy.
• OpenMRS FHIR Analytics (⭐228) - Pipeline tools for transforming OpenMRS data to FHIR-based analytics using Apache Beam.
• OpenSAFELY - Secure analytics platform for Electronic Health Records in the NHS.
• Pathling (⭐140) - FHIR and clinical terminology analytics on Apache Spark.
• Snow Owl (⭐292) - Highly scalable, open source terminology server with revision-control capabilities and collaborative authoring platform features.
• Snowstorm (⭐399) - SNOMED International's SNOMED CT terminology server.
• Synthea Patient Generator (⭐3.4k) - Synthetic patient generator that models the medical history of synthetic patients.
• Tuva (⭐333) - Open source data model, data marts and data quality tests for claims and clinical data.

Datasets

• Medical Data for Machine Learning (⭐6k) - Curated list of medical data for machine learning.

Design

• Determinants of Health (⭐95) - Determinants of Health Visualization.
• Health Icons (⭐879) - A collection of open source icons for public health projects.

EMPI

• MEDIC Client Registry RI (⭐15) - The Mohawk College MARC-HI/MEDIC Client Registry EMPI Implementation.

Machine learning

• MedicalGPT (⭐5.9k) - Training Your Own Medical GPT Model with ChatGPT Training Pipeline.
• MONAI (⭐8.8k) - AI Toolkit for Healthcare Imaging.
• nnU-Net (⭐9k) - Self-configuring deep learning framework for biomedical image segmentation.
• Odyssey (⭐63) - Interpretable foundation model of the patient clinical timeline for event forecasting and time-to-event prediction.
• OpenMed (⭐5.8k) - Local clinical named-entity recognition and PHI de-identification models.
• PathML (⭐467) - Python library for digital pathology image analysis, providing tools for preprocessing, model training, and analysis of histological slides.
• PyHealth (⭐1.7k) - A Deep Learning Python Toolkit for Healthcare Application.
• seismometer (⭐272) - Epic's framework for evaluating AI models in healthcare.
• TorchIO (⭐2.5k) - Medical image preprocessing and augmentation for deep learning.
• TotalSegmentator (⭐3.1k) - Segmentation of more than 100 anatomical structures in CT and MR images.

Compliance

• HealthStack (⭐94) - Terraform modules for secure and compliant healthcare infrastructure on AWS.

Asset Management

• Tapirx (⭐42) - Networked medical device discovery and identification.

Logistics

• ID3C (⭐22) - Data logistics system enabling real-time genomic epidemiology.
• OpenBoxes (⭐920) - an Open Source Inventory and Supply Chain Management System.
• OpenLMIS - Open source, web-based, electronic logistics management information system (LMIS) software, purpose-built to manage health commodity supply chains.