Awesome Medical Tools

An awesome list of clinical and medical tools built by practicing physicians (MD/DO).

Browse the catalog interactively: sinabarimd.github.io/awesome-medical-tools (filter by specialty, application type, training stage, stars).

For a long time, building software was a specialty of its own. Doctors who wrote production code were the exception. AI is changing that calculation. Tools like Claude Code, Copilot, and Cursor compress the technical lift enough that a working physician can ship a real clinical tool in a weekend.

The result: the people closest to the problems can now build the solutions. A clinical decision-support tool written by someone who has worked a night shift, an imaging pipeline written by a radiologist, or a patient-education app written by a doctor who has had the same conversation a thousand times brings design instincts that are hard to manufacture from outside the work. This list catalogs that emerging cohort. Every entry is authored by a verified physician or physician-in-training (MD or DO) who chose to ship their work in public.

Inclusion is based on self-declared credentials in the author's GitHub bio, profile README, or linked website. See CONTRIBUTING.md for the verification policy and removal procedure.

This list is maintained by Dr. Sina Bari, MD, a Stanford-trained surgeon and Healthcare AI VP, and updated monthly via an automated pipeline with manual review.

• Cardiology (29)
• Critical Care / ICU (1)
• Cross-specialty (46)
• Dermatology (1)
• Emergency Medicine (5)
• Gastroenterology (1)
• Genomics (2)
• Neurology (26)
• Obstetrics / Gynecology (1)
• Oncology (29)
• Ophthalmology (19)
• Pathology (31)
• Pediatrics (21)
• Primary Care / Internal Medicine (9)
• Psychiatry / Mental Health (18)
• Public Health / Epidemiology (16)
• Radiology / Imaging (77)
• Rheumatology (1)
• Rheumatology / Autoimmune (1)
• Sports Medicine (1)
• Surgery (8)
• Urology (1)

• baljash-cheema/StageD_HF - Machine learning models to identify advanced heart failure (Stage C/D) using established risk factors and clinical data. By Dr. Josh Cheema, MD, MSCI, MSAI, Cardiology.
• conlinm/ARB_project_code - Analyze association between ARB antihypertensive use and renal cell carcinoma incidence using OMOP data. By Dr. Michael Conlin.
• Dai-Kusumoto/Deep-SeSMo - CNN-based quantitative scoring system for detecting cellular senescence from microscopic phase-contrast images for drug screening. By Dr. Dai Kusumoto, Cardiology.
• david-shrk/ecgaxistrainer - Web app for training ECG axis deviation interpretation across multiple languages. By Dr. David Schaack, Cardiology (invasive electrophysiology).
• drankush/LAViz - AI-powered cardiac MRI segmentation and 3D visualization tool for left atrium analysis with clinical interpretation. By Dr. Ankush, Radiology.
• drankush/MIRACLE-API - API providing peer-reviewed reference values and z-scores for standardizing cardiovascular MRI measurement interpretation. By Dr. Ankush, Radiology.
• drankush/MIRACLE-sdk - Python SDK for accessing standardized cardiovascular MRI reference values and z-score calculations for cardiac imaging research. By Dr. Ankush, Radiology.
• drankush/MIRACLE-webapp - Web calculator for pediatric cardiac MRI z-scores and percentiles using MIRACLE reference database. By Dr. Ankush, Radiology.
• ganeshbmc/DeepIVUS - Deep learning platform for segmentation and analysis of coronary artery intravascular ultrasound (IVUS) images. By Dr. Ganesh Paramasivam, Interventional Cardiology.
• gcaptur/Paediatric-HCM-Proteomics - Analyze plasma proteomics data to identify diagnostic and prognostic biomarkers for pediatric hypertrophic cardiomyopathy using machine learning. By Dr. Gabriella Captur, Cardiology.
• Gizmopath/Cardiac-Amyloid - Neural network for detecting and segmenting amyloid deposits in cardiac tissue from digital pathology slides. By Dr. Giorgio Cazzaniga, Pathology (Digital/Anatomic).
• jgourassas/corsim - Simulate coronary angiographic views and fluoroscopic angles to train cardiology fellows on optimal imaging projections. By Dr. John Gourassas, Cardiology (Invasive).
• jgourassas/zao_ecg_axis - Determine electrocardiographic QRS axis from frontal ECG leads using circular reference system. By Dr. John Gourassas, Cardiology (Invasive).
• jphdotam/cwspy - Parse cardiac MR contours from CVI42 proprietary files for research workflows. By Dr. James, Cardiology (Cardiac MRI).
• MargoSolo/PAHminer - Literature-mining pipeline discovering causal genes for pulmonary arterial hypertension beyond standard diagnostic panels. By Dr. Margarita, Pediatrics / Clinical Genetics.
• mepepin/AVS_Epigenomics - Reproducible analysis pipeline for circulating T-cell epigenomics in aortic valve stenosis with methylation-based severity scoring. By Dr. Mark E. Pepin, Cardiovascular disease / Cardiology (based on repo focus on HCM, aortic valve stenosis, cardiovascular risk), Fellow.
• mepepin/CVD_RISK - Shiny app computing 10 and 30-year cardiovascular risk scores using validated AHA PREVENT and ACC/AHA algorithms. By Dr. Mark E. Pepin, Cardiovascular disease / Cardiology (based on repo focus on HCM, aortic valve stenosis, cardiovascular risk), Fellow.
• mepepin/HCM_CPX.Diastology - Analyze left ventricular diastolic dysfunction and cardiopulmonary fitness in hypertrophic cardiomyopathy using exercise testing and echocardiography data. By Dr. Mark E. Pepin, Cardiovascular disease / Cardiology (based on repo focus on HCM, aortic valve stenosis, cardiovascular risk), Fellow.
• mepepin/NNT_HFpEF - RNA-sequencing analysis pipeline for NNT gene and heart failure with preserved ejection fraction (HFpEF) research. By Dr. Mark E. Pepin, Cardiovascular disease / Cardiology (based on repo focus on HCM, aortic valve stenosis, cardiovascular risk), Fellow.
• mepepin/snRNA_ACTA2.p.Met49Thr - Single-nucleus RNA-seq analysis of ACTA2 mutation in thoracic aortic tissue for inherited aortic disease research. By Dr. Mark E. Pepin, Cardiovascular disease / Cardiology (based on repo focus on HCM, aortic valve stenosis, cardiovascular risk), Fellow.
• Oristrell/CHADS - Calculate CHADS2-VASc and HAS-BLED stroke and bleeding risk scores simultaneously for atrial fibrillation patients. By Dr. Joaquim Oristrell, MD, PhD, Internal Medicine.
• Oristrell/CHADS_ca - Calculate CHADS2-VASc and HAS-BLED stroke/bleeding risk scores simultaneously for atrial fibrillation patients. By Dr. Joaquim Oristrell, MD, PhD, Internal Medicine.
• Oristrell/CHADS_es - Calculate CHADS2-VASc and HAS-BLED stroke/bleeding risk scores simultaneously for atrial fibrillation patients. By Dr. Joaquim Oristrell, MD, PhD, Internal Medicine.
• Raffi-Hagopian/AI-CAC - Deep learning model for automated coronary artery calcium segmentation and scoring on routine chest CT scans. By Dr. Raffi Hagopian, Cardiology.
• rguide/Automated-cell-capacity-analyser - Automated analysis of cardiomyocyte cell membrane capacitance from electrophysiology recordings. By Dr. Roman Kula, Anaesthesiology; ICU Medicine; Experimental Cardiology.
• therlaup/DICOM2D-NeRF - Extract and align ECG data with rotational angiography DICOM frames for cardiac imaging analysis and 4D reconstruction. By Dr. Pascal Thériault-Lauzier, Cardiology.
• uotw/m.mode.ify - Generate M-mode ultrasound images post hoc from 2D clips by drawing a line through anatomy of interest, enabling motion-mode analysis for cardiac and fetal measurements. By Dr. Ben Smith, Emergency Medicine.
• Urban90/deepFlow - Extract aortic flow parameters from cardiac MRI using deep learning on DICOM images. By Dr. Bruna Gomes, Cardiology.
• YukiSahashi/slowmotion_echocardiography - Generate slow-motion echocardiography video frames using AI interpolation to improve diagnostic accuracy in stress testing and high heart-rate patients. By Dr. Yuki Sahashi, Cardiology.

• gweissman/micu_teaching - Curated MICU teaching resource covering sepsis, fluid resuscitation, survivorship, and clinical decision-making with evidence-based references. By Dr. Gary Weissman.

• 2023Anita/codex-dynamic-workflows-enhanced - AI workflow framework for doctors and clinical educators to decompose complex medical decisions into visible, verifiable, approval-gated work packets. By Dr. Lixin2026, Anesthesiology.
• AkpuruenyaChukwu/ippoint - Patient appointment scheduling and stratification system to reduce waiting room time in clinical settings. By Dr. Queen UgoChinyere Alu ( Enya AkpuruenyaChukwu ), Cardiology (in training), Resident.
• andrew10043/bayesian_trials - Interactive Shiny application for Bayesian statistical re-analysis of clinical trial data. By Dr. Ben Andrew, Anesthesiology, Resident.
• BryanTegomoh/citation-audit - Detect hallucinated and unsupported citations in LLM-generated medical content using automated verification pipeline. By Dr. Bryan Tegomoh, MD, MPH, Epidemiology.
• DACWB/medicinove-quiz - SOAPIA-based onboarding quiz system for physician mentorship program with progress tracking and learning pathway recommendation. By Dr. Danilo Aedo, Ophthalmology.
• dgrisafe/cprs_templates - Keyboard shortcuts and template tips for efficient CPRS (VA clinical EHR) navigation and documentation. By Dr. Dom Grisafe, Psychiatry, Resident.
• dgrisafe/rookie-researcher - Educational guide teaching clinical research fundamentals including citation management, scientific writing, data science, and statistical methods. By Dr. Dom Grisafe, Psychiatry, Resident.
• dr-russo/physutils - MATLAB utilities for processing and analyzing physiological time-series data from clinical monitoring. By Dr. Marco, Neurology.
• DrJohnMelville/PresentationHelp - Audience response system for tracking physician sentiment during medical case review presentations. By Dr. John Melville, Child Abuse Pediatrics.
• drpedapati/homebrew-tools - CLI tools for literature search, document review, and clinical text de-identification to support research and clinical workflows. By Dr. Ernie Pedapati, Neuroscience (Autism, Fragile X, TMS, EEG).
• dylkot/cNMF - Pipeline for inferring gene expression programs from single-cell RNA-sequencing data using consensus matrix factorization. By Dr. Dylan Kotliar, Systems immunology, autoimmune disease.
• dylkot/Corall - Personalized research paper recommendation engine using citation networks and semantic matching for Zotero libraries. By Dr. Dylan Kotliar, Systems immunology, autoimmune disease.
• Enesimus/SAC_Markdown_WF - Markdown-based workflow for authoring structured clinical notes outside EHR systems, then exporting to limited clinical record interfaces. By Dr. Juan Sepulveda, Pediatrics, Pediatric Critical Care.
• ericdunipace/causalOT - R package implementing optimal transport methods for estimating causal effects in observational studies. By Dr. Eric Dunipace, Psychiatry, Resident.
• ganeshbmc/med-brief - Aggregate and summarize recent medical research from PubMed and top journals into weekly briefs for clinicians. By Dr. Ganesh Paramasivam, Interventional Cardiology.
• hsinming/AI-At-Hand - AutoHotkey script for querying AI models with built-in PHI de-identification for Taiwanese patient data. By Dr. HsinMing Chen, Radiology.
• jgourassas/icd10cm - ICD-10-CM and ICD-10-PCS code lookup and visualization tool with QR code generation for clinical coding. By Dr. John Gourassas, Cardiology (Invasive).
• kbressem/LongHealth - Benchmark dataset evaluating large language models on clinical document comprehension and information extraction tasks. By Dr. Keno, Radiology (Cardiovascular and Oncological Imaging).
• kgraph57/evidentia - Verifies medical citations against PubMed, CrossRef, and OpenAlex to detect AI-fabricated references before publication. By Dr. AMPLIFIRE, Pediatrics.
• kgraph57/medical-slide-templates - Collection of 63 medical presentation slide templates for conferences, case reports, and journal clubs following international guidelines. By Dr. AMPLIFIRE, Pediatrics.
• kgraph57/paper-writer-skill - AI-assisted pipeline for generating and managing medical research manuscripts from discovery through peer review with quality gates and literature management. By Dr. AMPLIFIRE, Pediatrics.
• lancereinsmith/claude-qgenda-plugin - Claude plugin for querying QGenda physician scheduling system to check schedules, staffing, shifts, and time-off requests. By Dr. Lance Reinsmith, Radiology.
• marcelosilva2604/llmjudge - Benchmark study evaluating LLMs as judges for medical content across answer quality, research appraisal, and emergency triage tasks. By Dr. Marcelo Silva MD, Neonatology / Pediatrics.
• MargoSolo/PhenoLag - Analyze time lag between clinical description and genetic discovery across 1,533 rare Mendelian diseases using survival analysis. By Dr. Margarita, Pediatrics / Clinical Genetics.
• medmen/dienstplan - Generate fair duty rosters for clinical staff with scheduling rules and preference constraints. By Dr. medmen, Radiology.
• mulain/docpille-backend - Backend infrastructure for private practice telemedicine platform enabling remote patient consultations. By Dr. mulain, Surgery.
• ncborcherding/WUSTL-IHIW_HLA - Analyze HLA NGS concordance across labs using GL-strings, consensus genotyping, and mixed-model variance decomposition. By Dr. theHumanBorch, Clinical Pathology, Computational Immunology.
• nicolasleenaerts/NLMLapplive - Browser-based tool for building person-specific and pooled prediction models using elastic net regression for clinical research. By Dr. Nicolas Leenaerts, Psychiatry, Fellow.
• Oristrell/Prophet - Forecasts hospital discharge volumes using time-series prediction to support capacity planning. By Dr. Joaquim Oristrell, MD, PhD, Internal Medicine.
• philipchung/verifact - Fact-checks LLM-generated clinical text against EHR data to verify accuracy of patient care documentation. By Dr. Philip Chung, Surgery (perioperative medicine implied).
• PouriaRouzrokh/LatteReview - Automate systematic literature review screening and abstract evaluation using AI agents for medical research workflows. By Dr. Pouria Rouzrokh, Radiology, Resident.
• rayolddog/PainIndexForClinicalUseOfAI - Calculator converting diagnostic AI model performance metrics into clinically actionable predictive values and false-positive burden. By Dr. rayolddog, Radiology.
• rmoldwin/SDC_ObjectModel - Serialize, deserialize, validate, and compare Structured Data Capture (SDC) XML templates for clinical data collection. By Dr. Richard Moldwin, Pathology Informatics.
• rmvpaeme/clinAnnotR - Generate publication-quality clinical figures combining lab time-series with treatment timelines for case reports. By Dr. Ruben, Pediatrics, pediatric oncology.
• shihjay2/hieofone-as - Patient-controlled health information exchange authorization server using OAuth2 and User Managed Access protocols. By Dr. Michael Shihjay Chen, MD, Family Medicine.
• shihjay2/hieofone-directory - OAuth2/OpenID Connect directory server aggregating patient health information exchange across multiple HIE authorization servers for clinical workflow. By Dr. Michael Shihjay Chen, MD, Family Medicine.
• shihjay2/nosh2 - Open-source electronic health record system with FHIR, Blue Button, ICD-10, and pharmacy API integrations for clinicians and patients. By Dr. Michael Shihjay Chen, MD, Family Medicine.
• shihjay2/nosh3 - Open-source electronic health record system for outpatient practices with FHIR-native architecture and offline capabilities. By Dr. Michael Shihjay Chen, MD, Family Medicine.
• sxg/science - AI-powered plugins for drafting biomedical research manuscripts with specialist agent review and literature analysis. By Dr. Satyam G., Resident.
• thenineteen/Deep-Covariant-Structure-of-Comorbidities - Deep learning models using autoencoders and VAEs to identify predictive patterns in medical comorbidities. By Dr. thenineteen, Neurology (Epilepsy Surgery).
• turkalpmd/claude-scientific-writer-skills - Claude.ai skill for scientific and clinical writing, peer review, case reports, and research manuscript preparation. By Dr. Izzet Turkalp Akbasli, Pediatrics, PICU and critical care.
• umeshramya/gcp-nrces-fhir - TypeScript wrapper for Google Cloud Healthcare API FHIR store integration with NRCES support. By Dr Umesh R Bilagi, Cardiology.
• walehn/PubmedSubs - Auto-search PubMed for latest papers in a specialty, translate abstracts to Korean, and deliver daily summaries via email. By Dr. H.Kim, Abdominal Radiology.
• wardle/dmd - Lightweight library and microservice for accessing UK NHS dictionary of medicines and devices (dm+d) with SNOMED CT integration. By Dr. Mark Wardle, Neurology.
• wardle/hades - HL7 FHIR terminology server providing standardized clinical code lookup, validation, and mapping across SNOMED CT, LOINC, and FHIR packages. By Dr. Mark Wardle, Neurology.
• wardle/hermes - SNOMED CT terminology server with full-text search, inference, and cross-mapping for clinical coding and interoperability. By Dr. Mark Wardle, Neurology.

• maryamhjb/dermatologist-appointment-app - Web app for online dermatology appointment booking with patient dashboard and practice admin panel. By Dr. Maryam Hajibabaei, Dermatology.

• mac389/dnp_ner_public - NER model analyzing social media reports of 2,4-DNP use to characterize dose-toxicity patterns and adverse effects in nonlethal exposures. By Dr. Michael Chary, Emergency Medicine / Medical Toxicology.
• mac389/INTOXICATE - Predict ICU admission need for poisoned patients using clinical scoring from initial ER presentation. By Dr. Michael Chary, Emergency Medicine / Medical Toxicology.
• pnlawlor/GWTG_RDD_public - Power analysis scripts for regression discontinuity design study of alteplase effectiveness in acute stroke. By Dr. Patrick Lawlor, Pediatric Neurology, Resident.
• sethuramana/2025_PEC_1 - Analysis scripts for national EMS call epidemiology in children during COVID-19 pandemic and reopening. By Dr. Arvinth Sethuraman, Pediatrics.
• turkalpmd/SOSAFED - Forecast pediatric ED crowding and optimize physician shift schedules using machine learning to reduce patient boarding time. By Dr. Izzet Turkalp Akbasli, Pediatrics, PICU and critical care.

• luisnakayama/barrett-autofill-app - Automates data extraction from endoscopy reports and population of Barrett's esophagus risk calculator via OCR. By Dr. Luis Nakayama, Ophthalmology.

• kwongj/gene-puller - Extract and align gene sequences from genomic assemblies using BLAST and multiple sequence alignment. By Dr. Jason Kwong, Infectious Diseases, Fellow.
• mhalushka/gtex_contamination_code - Analyzes RNA sequencing contamination in GTEx dataset to identify tissue-specific contamination patterns affecting gene expression studies. By Dr. Marc Halushka, Cardiovascular Pathology.

• AdamKalina/Cuculus - Convert BrainLab SIG neurophysiology recordings to EDF format for analysis and archival. By Dr. Adam Kalina, Neurology, Resident.
• AdamKalina/NicOne-reader - CLI tool to read and parse NicoletOne EEG file headers for neurophysiology research and clinical data access. By Dr. Adam Kalina, Neurology, Resident.
• AshOswal/ROI-tSSS - MATLAB implementation of tSSS algorithm for artifact suppression in MEG brain imaging data within regions of interest. By Dr. Ashwini Oswal, Neurology (with interest in Deep Brain Stimulation and Movement Disorders).
• aso-toshihiko/drPrintSurf - Render cortical surface maps from 360-parcel brain atlases for neuroimaging visualization and analysis. By Dr. Toshihiko ASO, Neurology.
• chuyungtsai/Taiwan_PD_GWAS - GWAS analysis scripts and polygenic risk scores for Parkinson's disease in Taiwanese populations from the GP2 consortium. By Dr. Yung-Tsai Chu, Neurology.
• dr-russo/importaxo - MATLAB function to import Axograph X electrophysiology data files into standardized format for analysis. By Dr. Marco, Neurology.
• dr-russo/nsd-iss_biofind - Applies NSD-ISS diagnostic staging framework to BioFIND Parkinson's disease cohort with alpha-synuclein biomarker analysis. By Dr. Marco, Neurology.
• eduardocaminha/tc-cranio-legado-atendti - Pipeline extracting 29 specific clinical findings from legacy cranial CT scan reports using normalized text search. By Dr. Eduardo Caminha, Radiology.
• EGOstinelli/NMA-on-migraine - Network meta-analysis dataset and reproducible code comparing pharmacological treatments for acute migraine in adults. By Dr. Edoardo G. Ostinelli, Psychiatry.
• euabela/alpha_temporal_dynamics - Analyze alpha-band EEG dynamics in idiopathic generalized epilepsy patients versus healthy controls. By Dr. Eugenio Abela, Neurology.
• freemanwd/ABC-ICH-Calc - Calculate intracerebral hemorrhage volume from CT scan measurements using ellipsoid formula. By Dr. W David Freeman, Neurology / Neurocritical Care (Neurointensivist).
• freemanwd/sahvai - AI system for detecting subarachnoid hemorrhage and quantifying blood volume on head CT to improve triage and research standardization. By Dr. W David Freeman, Neurology / Neurocritical Care (Neurointensivist).
• gen4ro/polyA - Analysis and visualization scripts for poly(A) knock-in study modeling hibernation-like states in mice. By Dr. Genshiro A. Sunagawa, Pediatrics.
• jmstujenske/Matlab_FastTiffReadWrite - Fast read/write and memory-mapped viewer for large two-photon calcium imaging TIFF stacks with ROI analysis. By Dr. Joseph M. Stujenske, MD, PhD, Psychiatry.
• jmstujenske/Motion-Correction-Phase-Correlation - Motion correction and registration tool for two-photon microscopy imaging with subpixel accuracy and drift compensation. By Dr. Joseph M. Stujenske, MD, PhD, Psychiatry.
• MargoSolo/landuzi - Reproducible analysis pipeline for Russian FSHD patient registry cohort study with automated figure and statistics generation. By Dr. Margarita, Pediatrics / Clinical Genetics.
• marsipu/mne-nodes - Node-based GUI for neurophysiological data processing with MNE-Python, making EEG/MEG analysis accessible to non-programmers. By Dr. Martin G. Schulz, Neurology/Clinical Neurophysiology (MEG/EEG implied).
• marsipu/mne-pipeline-hd - GUI pipeline for magnetoencephalography (MEG) data processing and analysis using MNE-Python. By Dr. Martin G. Schulz, Neurology/Clinical Neurophysiology (MEG/EEG implied).
• Neuro-Kim/svvweb - Web-based subjective visual vertical and horizontal test for assessing vestibular and visual perception function with quantified results. By Dr. Junhyun Kim, Neurology.
• nwolpe/emotion_recognition - Analysis pipeline for Cam-CAN emotion recognition study using fMRI, VBM, and behavioral data. By Dr. Noham Wolpe, Psychiatry.
• pnlawlor/LNTWP - Model neural activity variability using linear-nonlinear-time-warp-Poisson framework for premotor cortex data. By Dr. Patrick Lawlor, Pediatric Neurology, Resident.
• saitosatoshi-1/BTCS_PNES_optical_flow - Quantify motor patterns in seizures vs psychogenic nonepileptic seizures using video optical flow analysis for diagnostic differentiation. By Dr. Satoshi Saito, Neurology/Epilepsy.
• saitosatoshi-1/EEG_EMG_FBTCS - Analyze high-frequency EMG components in scalp EEG during seizures to improve detection and lateralization of focal-to-bilateral tonic-clonic seizures. By Dr. Satoshi Saito, Neurology/Epilepsy.
• thenineteen/Epilepsy-Repository - Extract clinical data from medical documents to build predictive models for epilepsy surgery outcomes. By Dr. thenineteen, Neurology (Epilepsy Surgery).
• thenineteen/Semio2Brain-Database - Database mapping seizure semiologies to brain localization and lateralization from 4643 patients across 309 studies. By Dr. thenineteen, Neurology (Epilepsy Surgery).
• thenineteen/Semiology-Visualisation-Tool - Visualize seizure semiology patterns on 3D brain maps to localize epileptogenic zones using data from 4,600+ patients. By Dr. thenineteen, Neurology (Epilepsy Surgery).

• alexandrecc/Echographie-Obstetricale - Windows-based obstetrical ultrasound reporting workflow that retrieves DICOM reports from PACS and provides an HTML form for review and editing. By Dr. Alexandre Cadrin-Chênevert, Radiology.

• jebibault/CancerSatellite - Predict cancer prevalence at high spatial resolution using satellite imagery and deep learning for epidemiological mapping. By Dr. Jean-Emmanuel Bibault, Radiation Oncology.
• jebibault/CRCSurvival - Predicts 10-year cancer-specific survival in colorectal cancer patients using XGBoost with interpretable features. By Dr. Jean-Emmanuel Bibault, Radiation Oncology.
• jebibault/DeepRadiomicsRectalCancer - Deep radiomics model to predict pathologic complete response to neoadjuvant chemoradiation in locally advanced rectal cancer. By Dr. Jean-Emmanuel Bibault, Radiation Oncology.
• jebibault/Radiation-Oncology-Structures-Ontology - Standardized ontology for radiation oncology anatomical structures to enable multicentric clinical research and data integration. By Dr. Jean-Emmanuel Bibault, Radiation Oncology.
• JiaruiMi/ChIPseeker - Annotate genomic coordinates from ChIP-seq experiments to identify regulatory regions and associated genes. By Dr. GaryRice, Cardio-electrophysiology, MD-PhD Candidate.
• kbressem/oncorounds - Interactive benchmark for evaluating LLM clinical reasoning through multi-round oncology case simulations. By Dr. Keno, Radiology (Cardiovascular and Oncological Imaging).
• mhalushka/miRge - Comprehensive microRNA sequencing analysis pipeline for annotation, novel miRNA detection, and isomiR characterization. By Dr. Marc Halushka, Cardiovascular Pathology.
• mhalushka/miRge3.0 - Analyze small RNA sequencing data for miRNA annotation, editing detection, novel discovery, and isomiR characterization. By Dr. Marc Halushka, Cardiovascular Pathology.
• p4rkerw/dpcr_design - Design and optimize multiplex ddPCR primer sets for digital PCR experiments with automated parameter checking. By Dr. Parker C. Wilson, MD, PhD, Renal and Molecular Genetic Pathology.
• p4rkerw/longread_rcc - Pipeline for long-read sequencing analysis of clear cell renal cell carcinoma genomics using Oxford Nanopore data. By Dr. Parker C. Wilson, MD, PhD, Renal and Molecular Genetic Pathology.
• p4rkerw/qpcr_design - Design and optimize qPCR primers for gene expression and genomic analysis in research and diagnostic workflows. By Dr. Parker C. Wilson, MD, PhD, Renal and Molecular Genetic Pathology.
• p4rkerw/willoytec_cna - Whole-genome sequencing analysis pipeline for detecting somatic copy-number alterations and chromosomal instability in kidney cancer cell lines. By Dr. Parker C. Wilson, MD, PhD, Renal and Molecular Genetic Pathology.
• riazn/biallelic_hr - Reproducible analysis pipeline for pan-cancer bi-allelic homologous recombination gene alterations using TCGA data. By Dr. Nadeem Riaz, Computational Oncology.
• riazn/bms038_analysis - Reproducible analysis pipeline for tumor evolution and immune microenvironment changes during nivolumab immunotherapy from genomic and transcriptomic data. By Dr. Nadeem Riaz, Computational Oncology.
• riazn/facets_wrapper - Wrapper for FACETS algorithm to segment tumor/normal BAM pairs and compute HRD scores for cancer genomics. By Dr. Nadeem Riaz, Computational Oncology.
• sbpatel2009/NGS-Panel-Analyzer - Shiny app for analyzing next-generation sequencing panel data against COSMIC mutation database. By Dr. Snehal Patel, Molecular Pathology.
• scat2801/CosMx - Analyze and visualize single-cell spatial transcriptomics data from CosMx platform with QC, normalization, and differential expression workflows. By Dr. Mitch Chen, Cardiothoracic Radiology.
• scat2801/egfr-rpv - Radio-genomics analysis pipeline identifying EGFR mutation predictors in non-small cell lung cancer for precision therapy targeting. By Dr. Mitch Chen, Cardiothoracic Radiology.
• scat2801/nhoc-rpv - Radiomics analysis code for explainable PET/CT imaging biomarker predicting non-small cell lung cancer outcomes. By Dr. Mitch Chen, Cardiothoracic Radiology.
• scat2801/sarcAI - Automated sarcopenia measurement on CT imaging to predict cancer patient survival and drug toxicity outcomes. By Dr. Mitch Chen, Cardiothoracic Radiology.
• semenko/liquidqc - Quality control and fragmentomics analysis for cell-free RNA sequencing in a single BAM pass. By Dr. Nick Semenkovich, Liquid biopsy analysis / Deep learning for clinical diagnostics.
• svarady/gdsc-exploratory-analysis - Exploratory analysis and integration of cancer cell line drug sensitivity, genomic, and clinical data for predictive oncology modeling. By Dr. Soledad Varady, Pediatrics.
• tejas05in/survival-analysis-with-AIDS-data - Compare survival analysis models (Cox, random forest, DeepSurv, DeepSurvivalMachines) on AIDS patient data. By Dr. TEJAS. J, Forensic Pathology.
• tony-zhelonkin/RNAseq-toolkit - Modular R toolkit for bulk RNA-seq differential expression and gene set enrichment analysis in genomics research. By Dr. Anton Zhelonkin, Dermatology.
• tony-zhelonkin/scbio-docker - Docker environment for reproducible single-cell and bulk RNA sequencing analysis in R and Python. By Dr. Anton Zhelonkin, Dermatology.
• tony-zhelonkin/TE-RNAseq-toolkit - Analyze transposable element expression in bulk RNA-seq data with dual statistical modes and enrichment visualization. By Dr. Anton Zhelonkin, Dermatology.
• walehn/new-onset-liver-metastasis - Detect new liver metastases on follow-up CT scans using deep learning with image registration and subtraction imaging. By Dr. H.Kim, Abdominal Radiology.
• wenzel-liu/piranha-ripseq-pipeline - Reproducible RIP-seq peak-calling pipeline for identifying RNA-binding protein interaction sites from immunoprecipitation data. By Dr. Wenzel, Cardiology.
• yjcyxky/IgGM - Generative AI model for designing antibodies, including novel sequences, affinity maturation, and humanization for therapeutic development. By Dr. Jingcheng Yang, Cardiothoracic Surgery.

• gdebel/pearldgs_toolbox - Python toolbox for machine-learning-based intraocular lens power calculation using the PEARL-DGS formula. By Dr. Guillaume Debellemanière, Ophthalmology.
• giovmontesano/shinyCMP_OPI - Shiny app for OCT-informed perimetry testing with the Compass fundus perimeter to assess visual fields. By Dr. Giovanni Montesano, Ophthalmology (glaucoma).
• GulumimiRen/CorDeflVol - Calculate corneal deflection volume from Corvis ST biomechanical measurements using spherical geometry models. By Dr. GulumimiRen, Ophthalmology.
• luisnakayama/BRSET - Brazilian multilabel retinal fundus image dataset with quality assessment and diagnostic labeling for ophthalmology AI model development. By Dr. Luis Nakayama, Ophthalmology.
• luisnakayama/mBRSET - Benchmark dataset of 5164 retinal fundus images from Brazilian patients with diabetes for developing portable retinal imaging AI models. By Dr. Luis Nakayama, Ophthalmology.
• luisnakayama/portable_mydriasis - Research dataset and code evaluating mydriasis impact on portable retinal imaging and AI-based diabetic retinopathy screening in resource-limited settings. By Dr. Luis Nakayama, Ophthalmology.
• megane0-0/VI-Classification-Tool - Interactive visual field calculator for sports classification of visually impaired athletes based on Humphrey and Esterman testing. By Dr. Satoshi Y., Ophthalmology (glaucoma).
• megane0-0/VIClassificationField - Calculate maximum visual field diameter from Humphrey perimetry test results to support sports classification for visually impaired athletes. By Dr. Satoshi Y., Ophthalmology (glaucoma).
• mglraimundo/aletheia - Client-side informed consent form generator for ophthalmology procedures, compliant with Portuguese DGS regulations. By Dr. Miguel Raimundo, Ophthalmology.
• mglraimundo/biomapi-cli - Extract biometry measurements from optical biometry reports to support IOL power calculations and surgical planning. By Dr. Miguel Raimundo, Ophthalmology.
• mglraimundo/cyl - Compute corneal astigmatism corrections for toric IOL planning from keratometry data via BiomAPI integration. By Dr. Miguel Raimundo, Ophthalmology.
• mglraimundo/escrsiolcalcstats - Analytics dashboard tracking usage of ESCRS IOL Calculator for cataract surgery lens selection across patients and formulas. By Dr. Miguel Raimundo, Ophthalmology.
• mglraimundo/escrsmockup - IOL power calculator mockup for intraocular lens selection in cataract surgery. By Dr. Miguel Raimundo, Ophthalmology.
• mxxene13/vasc_enface_choroidal_analizer_UWF - MATLAB tool for batch quantitative analysis of widefield OCT-A choroidal vascular imaging with automated segmentation and morphometric metrics. By Dr. mxxene13, Ophthalmology, Vitreoretinal Surgery.
• romero-ophthalmology/Lens-Equator-Finder - Extract and measure anterior segment parameters from SS-OCT images for cataract surgery planning and IOL calculations. By Dr. romero-ophthalmology, Ophthalmology (Cornea and Anterior Segment).
• romero-ophthalmology/TORIC-IOL-ROTATION - Calculate optimal toric IOL rotation axis to correct astigmatism during cataract surgery. By Dr. romero-ophthalmology, Ophthalmology (Cornea and Anterior Segment).
• TaeKeunToo/HypertensiveRetinopathy - Web calculator predicting hypertensive retinopathy risk using logistic regression from Korean population health data. By Dr. Tae Keun Yoo, Ophthalmology.
• tkredd2/MobileNet_corneal_ulcers - MobileNet model to classify bacterial vs fungal keratitis from handheld camera images for rapid point-of-care diagnosis. By Dr. Travis Redd, MD, MPH, Ophthalmology.
• Winduu/tesis-oftalmologia-2026 - Reproducible R analysis of corneal sensitivity prevalence and clinical predictors in type 2 diabetes patients. By Dr. Wainer Manuel Sena Rivas, Ophthalmology, MD Student (clinical).

• ansohn88/LLM_MDL_telemetry - Extract structured clinical data from pathology reports using open-source LLMs with real-time statistical tracking. By Dr. Andrew Sohn, Molecular Genetic Pathology.
• ansohn88/MIPCL - Deep learning model for triaging and detecting pancreatic adenocarcinoma on whole-slide cytology images using multiple instance learning. By Dr. Andrew Sohn, Molecular Genetic Pathology.
• bertrandchauveau/DICOM_WSI_Deidentifier - Deidentify DICOM whole slide images to remove protected health information for pathology research and digital archival. By Dr. Bertrand Chauveau, Pathology (renal pathology subspecialty interest).
• bertrandchauveau/DICOMtoSVS - Convert DICOM whole slide images to SVS-format TIFF pyramids for pathology workflow interoperability. By Dr. Bertrand Chauveau, Pathology (renal pathology subspecialty interest).
• draaslan/blood-cell-detection-dataset - Annotated dataset of peripheral blood smear images with labeled RBC and WBC for training cell detection models. By Dr. Abdüssamet Aslan, Radiology.
• draaslan/blood-cell-detection-model - Deploy blood cell detection model on NVIDIA Jetson to identify RBCs and WBCs in peripheral blood smears. By Dr. Abdüssamet Aslan, Radiology.
• drshamsuzzaman/wsi-deid - De-identify and pseudonymize whole slide images for safe research sharing in digital pathology. By drshamsuzzaman, Pathology.
• dtruhn/PathStruct - Extract structured data from histopathology reports using GPT-4 and OCR to enable computational analysis. By Dr. Daniel Truhn, Radiology (Diagnostic and Interventional).
• endaaman/patholint - LLM-based text quality validation system for pathology reports with multi-model evaluation. By Dr. Ken Enda, Pathology.
• ftucos/dossier_medical_reports_scraping - Extract structured data from medical reports and histology exam PDFs using local LLM processing for clinical research. By Dr. Francesco A. Tucci, Surgical Pathology, MD-PhD Candidate.
• ftucos/StarDist-nuc_cyt_quantification - ImageJ macro pipeline for automated nuclear and cytoplasmic stain quantification using deep-learning segmentation. By Dr. Francesco A. Tucci, Surgical Pathology, MD-PhD Candidate.
• Gizmopath/HOTSPoT - Automated segmentation tool for identifying portal tracts in liver biopsy histology slides using deep learning. By Dr. Giorgio Cazzaniga, Pathology (Digital/Anatomic).
• Gizmopath/MIRAGE---MGRS-Interactive-Resource-for-AI-Guided-Evaluation - AI-powered clinical decision support tool predicting monoclonal gammopathy of renal significance before kidney biopsy. By Dr. Giorgio Cazzaniga, Pathology (Digital/Anatomic).
• Gizmopath/QuANTUM - QuPath-integrated pipeline for automated tumor cellularity detection in lung tissue histopathology using deep learning nuclei segmentation. By Dr. Giorgio Cazzaniga, Pathology (Digital/Anatomic).
• Gizmopath/SVM-LSTM-models-for-automated-SNOMED-CT-labeling - Automated SNOMED-CT coding of pathology reports using SVM and LSTM models trained on 283k reports. By Dr. Giorgio Cazzaniga, Pathology (Digital/Anatomic).
• Gizmopath/ZEBRA-ZEbra-Bodies-Recognition-by-Artificial-intelligence - Deep learning pipeline to detect vacuolated podocytes in kidney biopsies for early diagnosis of Fabry nephropathy. By Dr. Giorgio Cazzaniga, Pathology (Digital/Anatomic).
• jongtaek-kim/Informatics-Resource-For-Pathologists - Curated educational guide to programming, data science, and informatics resources for pathologists and healthcare professionals. By Dr. Jong Taek Kim, Molecular Pathology.
• RemiMathevet/FoetoPath_v1.2 - All-in-one fetal pathology server with case management, biometric calculations, report generation, and histologic slide viewing. By Dr. Rémi Mathevet, Fetal Pathology.
• RemiMathevet/mrxs_to_omezarr.zip - Convert and visualize digital pathology slides in OME-Zarr format with hierarchical annotation support. By Dr. Rémi Mathevet, Fetal Pathology.
• RemiMathevet/omezarr_viewer - Viewer for OME-Zarr digital pathology slide images with pyramidal zoom and GeoJSON annotation support. By Dr. Rémi Mathevet, Fetal Pathology.
• RemiMathevet/omnissiah - High-performance whole slide image reader for computational pathology pipelines, 100x faster than standard tools. By Dr. Rémi Mathevet, Fetal Pathology.
• RemiMathevet/PathologyServer - Web viewer for multiformat whole-slide pathology images with annotation and tile export for ML training. By Dr. Rémi Mathevet, Fetal Pathology.
• sbalci/ClinicoPathJamoviModule - jamovi module providing statistical methods for clinicopathological research including survival analysis, descriptive statistics, and machine learning. By Dr. Serdar Balcı, Pathology.
• sbalci/qupath-extension-workshop - QuPath extension bundling digital pathology analysis scripts for educational workshops on cell detection and immunohistochemical staining classification. By Dr. Serdar Balcı, Pathology.
• The-Obstacle-Is-The-Way/gigapixel-goblin - VLM-based navigation and reasoning system for whole-slide pathology images with diagnostic question-answering evaluation. By Dr. JJ, Psychiatry (Addiction Psychiatry focus implied by naltrexone-university repo).
• weijian/2026-USCAP-AI-Pathology-Report - Maps academic pathology AI research presented at USCAP 2026 to commercial diagnostic solutions and clinical translation pathways. By Dr. Jan, Pathology (Clinical Pathology).
• weijian/Basaloid-Squamous-Cell-Carcinoma-of-the-Uterine-Cervix - Case report and immunohistochemical analysis distinguishing basaloid squamous cell carcinoma from small cell neuroendocrine carcinoma of the cervix. By Dr. Jan, Pathology (Clinical Pathology).
• weijian/CIN3 - Pathology decision framework for distinguishing CIN3 with early invasion from benign cervical intraepithelial neoplasia using morphology and immunostaining. By Dr. Jan, Pathology (Clinical Pathology).
• weijian/Correa_Human_Gastric_Carcinogenesis - Literature-driven analysis mapping evolution of gastric cancer pathology diagnosis from morphology-based Correa cascade model to molecular mechanisms. By Dr. Jan, Pathology (Clinical Pathology).
• weijian/CSH - Diagnostic case study and morphologic analysis of crystal-storing histiocytosis in gastric mucosa with monotypic light chain restriction. By Dr. Jan, Pathology (Clinical Pathology).
• weijian/pathologistwithdigitalpathologyandAI - Educational resource on digital pathology and AI applications in breast cancer diagnosis and classification for pathologists. By Dr. Jan, Pathology (Clinical Pathology).

• ameyarad/boneagealpha - AI model for automated bone age estimation from pediatric hand X-rays using segmentation and regression. By Dr. Ameya Kawthalkar, Musculoskeletal Radiology.
• ausmeyer/RSV_timing_ppx_2026 - Analyze RSV prophylaxis timing windows and coverage using CDC surveillance data to inform infant prevention strategies. By Dr. Austin G. Meyer, Internal Medicine / Pediatrics.
• Dokotela/pythia - Immunization forecasting tool implementing CDC clinical decision support for vaccination scheduling and guidance. By Dr. Grey Faulkenberry, MD MPH, Clinical Informatics; Internal Medicine; Pediatrics, Fellow.
• drrajatsubhra/drrajatsubhra-CTEV-innovation - Document low-cost home-based method for managing flexible congenital clubfoot using cotton and tape as alternative to surgical casting. By Dr Rajatsubhra Mukhopadhyay, Pediatrics.
• drrajatsubhra/odistr-clinical-evidence - Clinical evidence repository for on-demand intranasal steroid therapy protocol for pediatric asthma and allergic conditions. By Dr Rajatsubhra Mukhopadhyay, Pediatrics.
• drrajatsubhra/RMDMCC-treatment-method - Document describing a non-surgical manual dilatation technique for treating low-set Hirschsprung's Disease in children. By Dr Rajatsubhra Mukhopadhyay, Pediatrics.
• EasterMedicalConsulting/BAMC_Pediatric_PGY3_Repo - AI agent framework and training resource for pediatric residents on LLM-assisted clinical workflows and professional development. By Dr. Easter Systems, Pediatrics.
• EasterMedicalConsulting/NEISS_Microwave_Study - Analyze pediatric microwave-related injury trends and risk factors using NEISS surveillance data with epidemiological methods. By Dr. Easter Systems, Pediatrics.
• EasterMedicalConsulting/Pediatric-LLM-Skills - LLM prompt templates for pediatric residents to generate clinical documentation, patient letters, and medical necessity notes. By Dr. Easter Systems, Pediatrics.
• Enesimus/uci-lab-navegador - Chrome extension for longitudinal visualization and analysis of pediatric ICU laboratory results to support clinical decision-making. By Dr. Juan Sepulveda, Pediatrics, Pediatric Critical Care.
• Enesimus/web-parenteral-nutrition - Web calculator for pediatric and adult parenteral nutrition formulation and dosing. By Dr. Juan Sepulveda, Pediatrics, Pediatric Critical Care.
• marcelosilva2604/clusteringeducation - Cluster analysis of pediatricians' educational priorities on breastfeeding support using MCA and K-means on Brazilian survey data. By Dr. Marcelo Silva MD, Neonatology / Pediatrics.
• marcelosilva2604/gastro-pediatria - Analysis code and data for cross-sectional study of patient-reported outcomes, disability, and substance use risk in young IBD patients in Brazil. By Dr. Marcelo Silva MD, Neonatology / Pediatrics.
• marcelosilva2604/ObesityAssociation - Machine learning evaluation of early-life predictors for childhood obesity risk using Brazilian national nutrition survey data. By Dr. Marcelo Silva MD, Neonatology / Pediatrics.
• marcelosilva2604/prescricao - Pediatric prescription generator that calculates weight-based medication doses and overlays them onto a customizable prescription template PDF. By Dr. Marcelo Silva MD, Neonatology / Pediatrics.
• rmvpaeme/bilicurve-shiny - Interactive tool for plotting neonatal bilirubin values against phototherapy thresholds by gestational age. By Dr. Ruben, Pediatrics, pediatric oncology.
• rmvpaeme/fenton-shiny - Interactive Shiny app for plotting and tracking preterm infant growth measurements against Fenton 2013 reference curves. By Dr. Ruben, Pediatrics, pediatric oncology.
• rmvpaeme/shiny_trials - Dashboard for exploring and comparing EU clinical trials with focus on pediatric drug development and trial landscape trends. By Dr. Ruben, Pediatrics, pediatric oncology.
• savior714/todo - Family medication and care coordination app preventing duplicate dosing in multi-caregiver households. By Dr. SEUNGJU LEE, Pediatrics.
• soanseng/adhd-family-plan - Structured family planning workbook for managing ADHD symptoms in children through behavioral strategies and caregiver coaching. By Dr. Soanseng Tan, Psychiatry.
• YoshifumiMiyagi/Child-Pharyngitis - Machine learning classifier to distinguish bacterial from nonbacterial pharyngitis in children. By Dr. yoshifumimiya, Pediatrics.

• AkpuruenyaChukwu/Cliniq-Companion-V1 - Patient guide framework for optimizing clinic visits and self-documentation in resource-limited healthcare settings. By Dr. Queen UgoChinyere Alu ( Enya AkpuruenyaChukwu ), Cardiology (in training), Resident.
• AmarDhand/PersonalNetworks - Process and analyze personal network data from REDCap for clinical research on social determinants of health. By Dr. Amar Dhand, Neurology.
• conlinm/arb_estimation_code - OHDSI study package for angiotensin II receptor blocker (ARB) estimation using Common Data Model databases. By Dr. Michael Conlin.
• direnc/CuraLink - HIPAA-compliant telehealth platform with video consultations, appointment scheduling, EHR management, and AI-assisted symptom analysis. By Dr. Direnç Sakarya, Psychiatry.
• Dokotela/smart_scan_amr - Digitize handwritten prescriptions and track antimicrobial use across local inventory and national surveillance systems. By Dr. Grey Faulkenberry, MD MPH, Clinical Informatics; Internal Medicine; Pediatrics, Fellow.
• EasterMedicalConsulting/clinical-sql-toolkit - Production SQL templates for population health registries, care-gap identification, HEDIS measures, and quality improvement analytics. By Dr. Easter Systems, Pediatrics.
• Neuro-Kim/HomeDoc - Remote health monitoring platform for patients to log vitals (BP/glucose) and wearable data, physicians to track patients, and admins to manage accounts. By Dr. Junhyun Kim, Neurology.
• p4rkerw/zsf1_gse263155 - RNA-seq analysis pipeline for adenine-induced chronic kidney disease in rat models using public datasets. By Dr. Parker C. Wilson, MD, PhD, Renal and Molecular Genetic Pathology.
• pofeng/linebot-BW - LINE chatbot for personal weight and BMI tracking with historical charting. By Dr. Pofeng Lee, Pediatrics.

• aktivhoon/scz_bip_manifold - Analyze differential psychotic symptom patterns in schizophrenia and bipolar I disorder using manifold learning and network analysis. By Dr. Younghoon Kim, Psychiatry.
• blh101/Letter-Generator - Generate standardized clinical letters for psychiatric patients and referrals. By Dr. Brad H, Psychiatry.
• cabilover/vrabes_mri_difference - Reproducible analysis pipeline for longitudinal fMRI connectivity changes in panic disorder pharmacotherapy response. By Dr. junhyung, Psychiatry.
• corneliushennch/prethod_data_wrangling - Clinical prediction model development to identify prognostic factors for depression treatment outcomes using routine practice data. By Dr. Cornelius Hennch, Psychiatry, Resident.
• EGOstinelli/cNMA_on_adults_with_ADHD - Component network meta-analysis dataset and code comparing pharmacological, psychological, and neurostimulatory treatments for adult ADHD. By Dr. Edoardo G. Ostinelli, Psychiatry.
• ericdunipace/vitamin_meta - Meta-analysis of vitamin treatments for depression and anxiety disorders to assess clinical efficacy. By Dr. Eric Dunipace, Psychiatry, Resident.
• lorente01/Psychosis_relapse_IPDMA - Individual participant data meta-analysis of antipsychotic treatment and psychosis relapse across 19 trials with 5,130 patients. By Dr. Jose M Rubio, Psychiatry.
• MattiaMarchi/ADHD-SUD_NMA - Reproducible R code for network meta-analysis of ADHD and substance-use-disorder pharmacological treatments. By Dr. Mattia Marchi, Psychiatry.
• MattiaMarchi/Efficacy-of-CBD-for-Psychosis - Reproducible R code for meta-analysis of cannabidiol efficacy in psychotic disorders. By Dr. Mattia Marchi, Psychiatry.
• MattiaMarchi/Psychedelics-for-existential-distress-in-terminally-ill-people--network-meta-analysis - R code for reproducing systematic review and network meta-analysis of psychedelics for existential distress in terminally ill patients. By Dr. Mattia Marchi, Psychiatry.
• MattiaMarchi/Withania-somnifera_Ashwagandha_-mental-illness - R code for reproducing meta-analyses on Ashwagandha efficacy for mental illness symptoms. By Dr. Mattia Marchi, Psychiatry.
• nicolasleenaerts/GBO - Apply off-policy reinforcement learning to micro-randomized trial data for optimizing just-in-time adaptive interventions. By Dr. Nicolas Leenaerts, Psychiatry, Fellow.
• nicolasleenaerts/NLML - R machine learning tools for building prediction models from ecological momentary assessment data in substance use and eating disorders research. By Dr. Nicolas Leenaerts, Psychiatry, Fellow.
• Polyneuro/BI_To_AI - Educational framework applying neuroscience and biopsychosocial modeling to develop AI models for psychiatric prediction and personalization. By Dr. Athula Polonowita, Psychiatry.
• Polyneuro/Binomial-Genomics - Tutorials on Dirichlet-Multinomial statistical models for analyzing gene interactions in depression, anxiety, and chronic pain. By Dr. Athula Polonowita, Psychiatry.
• RenaudJA/Fisher_Task_Exp - PsychoPy implementation of the Fisher task, a probabilistic reasoning experiment used to measure jumping-to-conclusions bias in psychotic disorders. By Dr. Renaud Jardri, Child and Adolescent Psychiatry.
• RenaudJA/Necker_cube_demo - PsychoPy implementation of Necker Cube bistable perception task for assessing perceptual inference processing in cognitive research. By Dr. Renaud Jardri, Child and Adolescent Psychiatry.
• The-Obstacle-Is-The-Way/naltrexone-university - Subscription question bank for addiction psychiatry and addiction medicine board exam preparation. By Dr. JJ, Psychiatry (Addiction Psychiatry focus implied by naltrexone-university repo).

• 2023Anita/ars-research-harness - Checkpoint-first research workflow harness with reproducible NHANES diabetes epidemiology case study. By Dr. Lixin2026, Anesthesiology.
• AkpuruenyaChukwu/Outreach-Companion-V1 - Documentation framework and templates for medical outreach planners and participants to improve encounter quality and record-keeping. By Dr. Queen UgoChinyere Alu ( Enya AkpuruenyaChukwu ), Cardiology (in training), Resident.
• ausmeyer/flu_HI_lightgbm_shap - Machine learning pipeline for predicting H3N2 influenza antigenic evolution using sequence data and SHAP explainability. By Dr. Austin G. Meyer, Internal Medicine / Pediatrics.
• chrisdewa/curso_python - Educational course teaching statistical analysis with Python for biomedical professionals analyzing clinical and epidemiological data. By Dr. Christian Delaflor, Developmental Pediatrics.
• Dokotela/bw-amr-ig - FHIR implementation guide for antimicrobial resistance surveillance and data exchange in Botswana. By Dr. Grey Faulkenberry, MD MPH, Clinical Informatics; Internal Medicine; Pediatrics, Fellow.
• draaslan/covid-19-research-papers-dataset - Curated dataset of 150k+ COVID-19 research papers with metadata for literature analysis and meta-research. By Dr. Abdüssamet Aslan, Radiology.
• dylkot/lassa_fever_gwas - GWAS analysis notebooks investigating host genetic susceptibility to Lassa fever infection. By Dr. Dylan Kotliar, Systems immunology, autoimmune disease.
• eebrown/covidprobability - Calculate probability of undetected COVID-19 in a setting based on exposure, testing, and symptom status. By Dr. Eric Brown, Psychiatry.
• gcaptur/COVID-Proteomics - Identifies plasma proteomic biomarkers that predict risk of persistent COVID-19 symptoms. By Dr. Gabriella Captur, Cardiology.
• kwongj/genome-map - Visualize genome sequencing coverage depth as SVG maps from samtools output for quality control and analysis. By Dr. Jason Kwong, Infectious Diseases, Fellow.
• kwongj/kraken-extract - Extract metagenomic sequences classified to specified taxa from Kraken taxonomic profiling output. By Dr. Jason Kwong, Infectious Diseases, Fellow.
• kwongj/maskrc-svg - Masks recombinant regions in bacterial sequence alignments detected by ClonalFrameML or Gubbins, with SVG visualization. By Dr. Jason Kwong, Infectious Diseases, Fellow.
• kwongj/mlst-cc - Identifies bacterial clonal complexes from MLST allele profiles for epidemiological tracking and outbreak investigation. By Dr. Jason Kwong, Infectious Diseases, Fellow.
• pwjpwj/Benznidazole-CEA - Cost-effectiveness analysis framework for benznidazole treatment of chronic Chagas disease using calibrated Markov modeling. By Dr. Philip Erick Wikman Jorgensen, Internal Medicine / Infectious Disease.
• RodriguesJA/Cjejuni_Cattle_MI - Bioinformatics pipeline for comparative phylogenomics and antibiotic resistance profiling of Campylobacter jejuni across cattle and human populations. By Dr. Jose Rodrigues, D.O., Ph.D., Pediatrics, Resident.
• vishnuravi/hospital-capacity - Visualize real-time bed capacity and COVID-19 patient statistics across US hospitals using federal health data. By Dr. Vishnu Ravi.

• aksg87/adpkd-segmentation-pytorch - Deep learning model for automated kidney segmentation on MRI to measure total kidney volume in ADPKD patients. By Dr. Akshay Goel.
• ameyarad/Wilhelm - AI-powered radiology reporting platform with voice transcription, template matching, and multi-language report generation for educational use. By Dr. Ameya Kawthalkar, Musculoskeletal Radiology.
• draaslan/brain-tumor-classification-tao - Classify brain tumors from MRI images using NVIDIA TAO Toolkit with deep learning models. By Dr. Abdüssamet Aslan, Radiology.
• drankush/VoxRad - Voice transcription app for radiologists using locally-deployed ASR and LLM models for report generation. By Dr. Ankush, Radiology.
• drtjre/PacsCrawler - Download DICOM images and metadata from PACS servers into local database for research and analysis. By Dr. Thomas J. Re, Radiology.
• dtruhn/ODELIA - Versioned data collection templates for breast imaging and lesion documentation in clinical research. By Dr. Daniel Truhn, Radiology (Diagnostic and Interventional).
• ebaumel/radrules - Convert published radiology classification systems into structured knowledge files and LLM-ready system prompts for clinical AI applications. By Dr. Eric M. Baumel, Diagnostic Radiology.
• eduardocaminha/radiologia-extracao-mamografia - Automatically structure mammography reports into standardized JSON using large language models for clinical documentation and data extraction. By Dr. Eduardo Caminha, Radiology.
• eduardocaminha/radiologia-laudos - Streamlit application for managing radiology procedures, modalities, and report templates in a Delta Lake database. By Dr. Eduardo Caminha, Radiology.
• eduardocaminha/radiologia-pneumotorax-multiexame - Pipeline to identify pneumothorax cases across multiple imaging modalities and validate with LLM for dataset creation. By Dr. Eduardo Caminha, Radiology.
• freemanwd/HEADS-UP - Detect intracranial hemorrhage subtypes and measure volume from head CT using deep learning ensemble. By Dr. W David Freeman, Neurology / Neurocritical Care (Neurointensivist).
• hsinming/RIS-Conductor - Automates radiology report generation by extracting images from PACS and using AI to draft reports in RIS systems. By Dr. HsinMing Chen, Radiology.
• hwangsi/adrenalMRCalc - Calculator for Signal Intensity Index on adrenal chemical shift MRI to differentiate adenomas from non-adenomatous lesions. By Dr. Sungil Hwang, Radiology.
• JAbrantesRadiology/dicom-zip-fixer - Add .dcm file extensions to DICOM files exported from hospital PACS systems for compatibility with medical imaging tools. By Dr. João Maria Veigas Abrantes, Radiology.
• JAbrantesRadiology/ECR2022 - Jupyter notebooks for DICOM preparation, AI density analysis, and radiologist-AI performance comparison for ECR 2023 research. By Dr. João Maria Veigas Abrantes, Radiology.
• JaretK/ImplantDetector - Detects surgical implants in anterior-posterior chest X-rays using machine learning. By Dr. Jaret Karnuta, Orthopaedic Surgery.
• jjanizek/findings-to-impression - Fine-tuned language model that generates radiology report impressions automatically from findings text. By Dr. Joseph D. Janizek, Radiology, Resident.
• jjanizek/ms-cxr-t-bench - Benchmark suite evaluating vision-language models on temporal chest X-ray classification and ICU device/finding detection tasks. By Dr. Joseph D. Janizek, Radiology, Resident.
• jjanizek/vcr - Reproduce VCR interpretability method for medical image analysis on chest X-rays and dermatology images using vision-language models. By Dr. Joseph D. Janizek, Radiology, Resident.
• jjanizek/vcr-paper - Research tool to evaluate visual concept rankings in medical AI models trained on chest X-rays and dermatology images. By Dr. Joseph D. Janizek, Radiology, Resident.
• joytywu/PET_CT - Utilities for processing and analyzing PET-CT imaging data for research and clinical analysis. By Dr. Joy Wu, Radiology, Resident.
• kbressem/gpt4-structured-reporting - Structures unstructured radiology reports into standardized JSON format using GPT-4 prompting. By Dr. Keno, Radiology (Cardiovascular and Oncological Imaging).
• kbressem/prostate158 - Curated dataset of prostate MRI images with expert annotations for training segmentation models to detect anatomical zones and cancer lesions. By Dr. Keno, Radiology (Cardiovascular and Oncological Imaging).
• Kikubernetes/visual_bvec - Visualize and quantify gradient direction uniformity in diffusion MRI acquisitions to assess data quality. By Dr. Kikuko Kaneko, Radiology / Neuroradiology.
• lee8720/LLM_Human_Loop - Evaluates LLM-assisted diagnostic reasoning for thoracic imaging with radiologist feedback integration. By Dr. lee8720, Radiology.
• lee8720/LLM_Interaction - Investigates how radiologist expertise and LLM confidence affect diagnostic interaction and decision-making in chest imaging. By Dr. lee8720, Radiology.
• lee8720/LLM_Radlex - LLM-based expansion of RadLex medical terminology ontology for standardizing chest CT report analysis across multinational datasets. By Dr. lee8720, Radiology.
• lee8720/VLM_Benchmark - Benchmark dataset and evaluation code comparing 13 vision-language models against radiologist performance on thoracic imaging diagnostics. By Dr. lee8720, Radiology.
• lee8720/VLM_Diagnosis - Analyzes how vision-language models decouple visual parsing from diagnostic reasoning in thoracic imaging. By Dr. lee8720, Radiology.
• lee8720/VLM_VA - Generate visual abstracts from radiology journal articles using vision-language models for research communication and education. By Dr. lee8720, Radiology.
• licurgosantiago/dicom-rx-tools - Python toolkit for DICOM processing, metadata extraction, quantitative imaging analysis, and AI integration in radiology workflows. By Dr. Licurgo Santiago, Radiology.
• liyezhou/minimal-fsl - Minimal Docker container for FSL neuroimaging analysis with customizable module selection. By Dr. Yezhou Li, Neurology, Resident.
• medmen/symprot - Extract, document, and compare Siemens CT/MRI exam protocols from machine printouts for standardization and research. By Dr. medmen, Radiology.
• mirandabautistajuan-lang/calcifying-tendinopathy - AI model for detecting calcific tendinopathy of the rotator cuff on shoulder X-rays with generalization testing across imaging domains. By Dr. Juan Miranda Bautista, Musculoskeletal Radiology.
• mirandabautistajuan-lang/shoulder-volume-impact - CNN pipeline quantifying how training data volume affects detection of calcific tendinopathy in shoulder X-rays with external validation. By Dr. Juan Miranda Bautista, Musculoskeletal Radiology.
• mirandabautistajuan-lang/shoulder-xray-cnn-hybrid - AI framework for detecting calcifying tendinopathy in shoulder X-rays using CNN and hybrid deep learning approaches. By Dr. Juan Miranda Bautista, Musculoskeletal Radiology.
• mirandabautistajuan-lang/shoulder-xray-distribution-shift-architecture - Deep learning models for detecting rotator cuff calcifications on shoulder X-rays with analysis of hardware generalization and multi-view fusion strategies. By Dr. Juan Miranda Bautista, Musculoskeletal Radiology.
• noneedanick/bonefracturedetection - YOLOv7 model for automated bone fracture detection in X-ray images with Streamlit deployment. By Dr. Murat Yüce, Radiology, Fellow.
• noneedanick/DeepFakeXRay - Educational tool training radiologists and clinicians to identify AI-generated versus authentic X-ray images. By Dr. Murat Yüce, Radiology, Fellow.
• omarallouz/MRI_Threshold_selector - Select membership probability thresholds from anatomical MRI scans for tissue segmentation. By Dr. Omar Al-Louzi, Neurology.
• orthodoc/binder - Mobile app for clinicians to organize and manage clinical images for patient care. By Dr. Biswajit Dutta Baruah, Orthopedic Surgery.
• overtone1000/RadCalc - Web-based calculators for radiology measurements and diagnostic scores including DEXA, FRAX, and bone density analysis. By Dr. Tyler Moore, Radiology.
• PouriaRouzrokh/IAAII-Multiagentic-AI - Workshop materials on building multi-agent AI systems for radiology using Google's Agent Development Kit. By Dr. Pouria Rouzrokh, Radiology, Resident.
• RadEdje/Agentic_Rad_Workflow_MedGemma - Agentic AI workflow framework for radiologists to build and validate local diagnostic AI models using MedGemma. By Dr. ERWIN JOHN T. CARPIO, MD, FPCR, Radiology.
• RadEdje/Agents - Agentic AI assistant for radiologists to triage imaging, generate preliminary reports, and screen for conditions like tuberculosis. By Dr. ERWIN JOHN T. CARPIO, MD, FPCR, Radiology.
• RadEdje/RadLens - Web app for real-time object detection and classification using phone camera and TensorFlow.js models. By Dr. ERWIN JOHN T. CARPIO, MD, FPCR, Radiology.
• RadEdje/RadLens2.0 - Mobile web app using deep learning to classify forearm fracture types (Monteggia/Galeazzi) from camera images in real-time. By Dr. ERWIN JOHN T. CARPIO, MD, FPCR, Radiology.
• RadioTamerlan/DbtDenseSeg - Segmentation pipeline for Digital Breast Tomosynthesis identifying breast density, area, and pectoral muscle from DICOM/NIfTI images. By Dr. Tamerlan Mustafaev, Radiology.
• rayolddog/calibrated-ct-encoding - Preserve Hounsfield Unit calibration when preprocessing CT DICOM images for deep learning models. By Dr. rayolddog, Radiology.
• rayolddog/Denoising-DICOM-CT-exams - Adaptive denoising algorithm for CT images that preserves edges while reducing noise in homogeneous regions. By Dr. rayolddog, Radiology.
• rayolddog/DICOM_SR - Generate DICOM structured reports from voice dictation using speech-to-text and LLM formatting. By Dr. rayolddog, Radiology.
• rayolddog/ich-maxvit - AI pipeline for automated intracranial hemorrhage detection from CT head scans with radiology worklist and DICOM reporting. By Dr. rayolddog, Radiology.
• rbumm/SlicerPACSConnector - 3D Slicer extension for querying and retrieving DICOM images from local or remote PACS servers. By Dr. Rudolf Bumm, Surgery.
• robertavram-md/pydicom-batch - Batch export DICOM images from PACS servers for medical image dataset creation and AI research. By Dr. Robert Avram, Cardiology.
• scat2801/pyradiomicsBatch - Batch pipeline for extracting radiomic features from medical images using PyRadiomics. By Dr. Mitch Chen, Cardiothoracic Radiology.
• stmutasa/SODKit - Python toolkit for loading DICOM, preprocessing medical images, and building neural networks for medical imaging analysis. By Dr. Simi Mutasa, Diagnostic Radiology (MSK).
• ThalesMMS/DICOM-Swift - Parse DICOM medical images on iOS/macOS with windowing, metadata extraction, SwiftUI viewers, and CLI export tools. By Dr. Thales Santos, Radiology.
• ThalesMMS/MTK - GPU-accelerated medical volume rendering and MPR visualization toolkit for DICOM imaging on iOS and macOS. By Dr. Thales Santos, Radiology.
• ThalesMMS/MTK-Demo - iOS DICOM viewer with 3D volume rendering, MPR reconstruction, and CT/PET fusion for clinical image analysis. By Dr. Thales Santos, Radiology.
• ThalesMMS/MTKDicomBridge - Swift framework bridging DICOM parsing to Metal-based volume rendering for clinical medical imaging visualization. By Dr. Thales Santos, Radiology.
• therlaup/pydicom-batch - Batch export DICOM images from PACS servers to build local datasets for medical imaging research and AI model development. By Dr. Pascal Thériault-Lauzier, Cardiology.
• tsaiid/ahk-htch - AutoHotkey macros and templates for radiology reporting in hospital RIS/PACS workflow system. By Dr. I-Ta Tsai, Radiology.
• tsaiid/ahk-nycuh - Radiology workflow automation scripts for RIS/PACS integration, report writing, and pulmonary nodule tracking with AI assistance. By Dr. I-Ta Tsai, Radiology.
• tsaiid/radtools.tsai.it - Web-based radiology utilities including bone age assessment, cancer staging reports, and lung cancer screening tools. By Dr. I-Ta Tsai, Radiology.
• tsaiid/structured-reporting-web-tools - Web tool for radiologists to generate standardized AJCC cancer staging reports with automatic TNM calculation for RIS integration. By Dr. I-Ta Tsai, Radiology.
• tsaiid/vghks-random-duty - Schedule generator for resident on-call duty assignments with fairness constraints and holiday management. By Dr. I-Ta Tsai, Radiology.
• Tubo/radscheduler - Roster and leave management system designed for radiology registrar scheduling and automations. By Dr. Tubo, Radiology.
• turkalpmd/RadiovLLMjection - Evaluate prompt injection vulnerabilities in vision-language models used for radiology decision support and AI trustworthiness. By Dr. Izzet Turkalp Akbasli, Pediatrics, PICU and critical care.
• turtleizzy/slicer-npz-loader - 3D Slicer extension for loading volume and segmentation data from NumPy archives into medical imaging workflows. By Dr. Izzy Turtle, Radiology.
• uotw/ClipDeidentifier - Remove Protected Health Information from ultrasound media for safe educational distribution. By Dr. Ben Smith, Emergency Medicine.
• uotw/SonoClipShareUploader - Desktop app to strip PHI from ultrasound media and securely upload to SonoClipShare archive. By Dr. Ben Smith, Emergency Medicine.
• walehn/rad-conclusion - AI-assisted radiology report generator with multi-LLM support for conclusion and structured disease reporting. By Dr. H.Kim, Abdominal Radiology.
• walehn/radiology-paper-writer - AI-assisted system for drafting and reviewing radiology research papers with multi-model feedback on methodology and compliance. By Dr. H.Kim, Abdominal Radiology.
• XiaoPika/Medical-3D-Viewer - Web platform for browsing and sharing 3D medical imaging models converted from STL, designed for clinical case presentation and surgical planning. By Dr·Pika, Interventional and Diagnostic Radiology.
• ykuo2/dicom2jpg - Convert DICOM medical images to standard formats (JPG, PNG, BMP, TIFF) with proper LUT transformations for clinical viewing. By Dr. Yu Kuo, Radiology.
• Yoojin-nam/MeducAI - Governed pipeline for generating reproducible LLM-based radiology board exam study materials with validated educational effectiveness. By Dr. Yoojin Nam, Radiology.
• YoshifumiMiyagi/NIH14_CHESTXP - Classify sex from pediatric chest X-rays using deep learning with optional lung-mask cropping and image preprocessing. By Dr. yoshifumimiya, Pediatrics.

• Oristrell/ESSPRI_es - Patient-reported outcome index for Sjögren's syndrome disease activity assessment using EULAR ESSPRI tool. By Dr. Joaquim Oristrell, MD, PhD, Internal Medicine.

• Oristrell/ESSPRI_ca - Web-based implementation of ESSPRI patient-reported outcome index for Sjögren's syndrome symptom assessment. By Dr. Joaquim Oristrell, MD, PhD, Internal Medicine.

• JaretK/BaseballInjuryLearning - Machine learning analysis of MLB player injury patterns to identify risk factors and predictive signals. By Dr. Jaret Karnuta, Orthopaedic Surgery.

• ChiariRay/surgical-video-annotation - Platform for annotating surgical videos using AI-assisted segmentation for training and research. By Dr. Ray Yin, Orthopedic Surgery.
• gmarzloff/p24_beginners_guide - Installation and setup guide for the Hasomed P24 functional electrical stimulation device for research and clinical use. By Dr. George Marzloff, Spinal Cord Injury Medicine / Physical Medicine and Rehabilitation.
• Kolinzoviola/ClinicData - Web-based clinic management system for tracking orthopaedic patient registrations, visits, diagnoses, and treatment plans. By Dr. Emeka Elumelu, Orthopedic Surgery.
• lancereinsmith/AOSpine - Web calculator for AOSpine thoracolumbar injury severity scoring to guide trauma management decisions. By Dr. Lance Reinsmith, Radiology.
• lancereinsmith/qgendapy - Python client library for QGenda OR scheduling and staff management API integration. By Dr. Lance Reinsmith, Radiology.
• murad-alqadi/chiara - Question-bank study app for plastic surgery in-training exams with custom tests, timed mode, and performance analytics. By Dr. Murad M. Alqadi, MD, Surgery.
• ncborcherding/immApex_manuscript - TCR repertoire network analysis pipeline for predicting kidney transplant rejection and monitoring graft outcomes. By Dr. theHumanBorch, Clinical Pathology, Computational Immunology.
• philipchung/llm-periop-prediction - Evaluate LLM capability to predict perioperative risk, ASA classification, and postoperative outcomes from clinical notes. By Dr. Philip Chung, Surgery (perioperative medicine implied).

• hwangsi/ProstateMRICalculator - Android app that uses on-device AI to extract MRI measurements and classify prostate volume for benign prostatic hyperplasia severity assessment. By Dr. Sungil Hwang, Radiology.