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133 open-source projects relevant to oncology, 19 of them with records verified by a person at the registry, grouped by the front they serve. Viewers and archives for imaging, slide and cytometry tools for diagnostics, somatic variant callers, treatment planning and QA code for radiotherapy, data standards, and patient tools. Catalogued by the Open Medical Registry, a third party; OnCo maps each record to its fronts, technologies and cancers.
Imaging covers the ways of seeing cancer inside the body without cutting, from X-rays to tracers that light up a single protein.
Desktop platform for medical image visualisation, segmentation, registration, and image-guided therapy research.
Toolbox for computational magnetic resonance imaging, providing calibration and iterative reconstruction methods.
Collection of DICOM implementations and clinical imaging archive tooling used in production PACS deployments.
Open-source ultrasound processing modules and building blocks, analogue front ends, FPGA acquisition and pulser boards for do-it-yourself echography.
Streaming framework for medical image reconstruction, used widely for MRI reconstruction pipelines.
Embedded server component of the MaRCoS open magnetic resonance control system, running on the scanner hardware.
Open-source MRI console built on low-cost Zynq FPGA hardware, providing spectrometer and acquisition control.
Zero-footprint web-based DICOM viewer for radiology and clinical research workflows.
Build documentation for an open-source ultra-low-field MRI scanner constructed at Utrecht University, following the Open Source Imaging Initiative design.
Open-source low-field MRI scanner using a 50 mT permanent magnet, portable at roughly 150 kg, for head and extremity imaging.
Compact iCE40 FPGA and Raspberry Pi ultrasound board providing pulse-echo acquisition for imaging and non-destructive testing.
This data-centric AI repository implements a robust deep learning method (LFBNet) for fully automated tumor segmentation in whole-body [18]F-FDG PET/CT images.
Code to preprocess, segment, and fuse glioma MRI scans based on the BraTS Toolkit manuscript.
Tiny library for calculating Standardized Uptake Value for Nuclear Medicine (i.e.
Cornerstone is a set of JavaScript libraries that can be used to build web-based medical imaging applications.
dcmqi (DICOM for Quantitative Imaging) is a C++ library for conversion between imaging research formats and the standard DICOM representation for image...
A multipurpose tool for medical physics.
Dicoogle - Open Source PACS
Evaluation framework for oncology foundation models (FMs)
Code and evaluation repository for the paper
Official public repository of Gate
High-level DICOM abstractions for the Python programming language
3D medical imaging reconstruction software
Insight Toolkit (ITK) -- Official Repository.
DICOM gateway for de-identification or tag morphing
LinaQA (pronounced Linakwa) is a medical physics toolkit for radiotherapy, diagnostic radiology and nuclear medicine based on pylinac and pydicom.
mercure DICOM Orchestrator
A 3D lesion segmentation method on whole-body PET images including automated quality control.
The Medical Imaging Interaction Toolkit.
MONAI Deploy App SDK offers a framework and associated tools to design, develop and verify AI-driven applications in the healthcare imaging domain.
MONAI Label is an intelligent open source image labeling and learning tool.
Python package for programmatic access to the National Biomedical Imaging Archive (NBIA) and The Cancer Imaging Archive (TCIA)
Preprocessing 3D medical images and image archives, geared towards prostate cancer detection in MRI.
Read, modify and write DICOM files with python code
Open-source python package for the extraction of Radiomics features from 2D and 3D images and binary masks.
Software for automatic segmentation and generation of standardized clinical reports of brain tumors from MRI volumes
Deep learning-based accurate delineation of primary gross tumor volume of nasopharyngeal carcinoma on heterogeneous magnetic resonance imaging: a...
Notebooks for working with The Cancer Imaging Archive datasets.
Swift Horos/OsiriX plugin that exports active CT/MR series, provisions an isolated Python TotalSegmentator environment, runs segmentation, and imports...
Domain Generalization for Prostate Segmentation in Transrectal Ultrasound Images: A Multi-center Study
Home for the unified VICTRE pipeline for in silico breast imaging.
Weasis is a web-based DICOM viewer for advanced medical imaging and seamless PACS integration.
Tests on tissue and blood that say what kind of cancer it is, what is driving it, and which drugs might work.
Kit-form open-source spectral flow cytometer for volumetric cell counting and fluorescence panels of up to roughly ten colours.
3D-printed automated laboratory microscope with a monolithic flexure stage, designed to be built locally for a fraction of the cost of a commercial instrument.
Modular open-science microscope system built from 3D-printed cubes on a magnetic baseplate, reconfigurable for brightfield, fluorescence and light-sheet...
Fast and accurate gene fusion detection from RNA-Seq data
Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
Digital pathology image viewer with support for human/machine generated annotations and markups.
CellViT: Vision Transformers for Precise Cell Segmentation and Classification
Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other...
ClairS: a deep-learning method for long-read tumor, normal pair somatic small variant calling
Open source tools for computational pathology - Nature BME
A web platform for collaborative analysis of very large bio-medical images
DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.
DeepSpot: Deep learning model for predicting spatial transcriptomics from H&E histopathology images.
Web-based DICOM slide microscopy viewer library
DISCOVER co-occurrence and mutual exclusivity analysis for cancer genomics data
Identification of gene-fusions, including EML4-ALK
EpiMethEx (Epigenetic Methylation and Expression), a R package to perform a large-scale integrated analysis by cyclic correlation analyses between...
Evaluation framework for oncology foundation models (FMs)
Data intensive science for everyone.
Interactive flow and mass cytometry gating in R/Shiny on SingleCellExperiment objects, with Gating-ML round-trip.
Official code repository for GATK versions 4 and up
A structural variation pipeline for short-read sequencing
A public reference implementation of HL7 FHIR Genomics Operations (http://build.fhir.org/ig/HL7/genomics-reporting/operations.html)
Machine learning tool for analysis of lung adenocarcinoma tumors
Official code for Prediction of molecular subtypes for endometrial cancer based on hierarchical foundation model.
High-level DICOM abstractions for the Python programming language
Histomic Prognostic Signature (HiPS): A population-level computational histologic signature for invasive breast cancer prognosis
Open Source GUI App for Cytometry Acquisition and Analysis
IHC image real time analyzer
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
Nextflow bioinformatics pipeline for large-scale analysis of Multiple Myeloma genomes
A Patient-First Foundation Model for Computational Pathology
cBioPortal is a data visualization tool for cancer genomics.
A panoptic segmentation approach for tumor-infiltrating lymphocyte assessment: development of the MuTILs model and PanopTILs dataset.
Onconova is an open-source data platform aiming to enable reliable, structured data collection and analysis in precision oncology.
A modular annotation tool for genomic variants
An open, collaborative project to analyze data from the Single-cell Pediatric Cancer Atlas (ScPCA) Portal
Tools for computational pathology
Crossmapped phenotype ontologies for the oncology domain
CNN ensemble for prostate cancer Gleason grading
QuPath - Open-source bioimage analysis for research
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells.
SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format.
SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations.
Interoperable web-based DICOM slide microscopy viewer and annotation tool
Solid Tumor Associative Modeling in Pathology
SurvivMIL: A multimodal, Multiple Instance Learning pipeline for survival outcome of Neuroblastoma Patients
Computational Pathology Toolbox developed by TIA Centre, University of Warwick.
package: An R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq...
Detect somatic SNVs from deep targeted UMI-seq cfDNA
vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration
Python package for reading DICOM WSI file sets.
Early detection and screening means finding cancer before it causes symptoms, when it is most curable.
Deep Neural Networks Improve Radiologists' Performance in Breast Cancer Screening
An interpretable classifier for high-resolution breast cancer screening images utilizing weakly supervised localization
Human Papillomavirus (HPV) testing on self-collected samples allows for improved coverage rates of cervical cancer (CC) screening programs.
Deep learning on dermatoscopic images, with a browser demo that lets you try the task against the model.
Meta-repository of screening mammography classifiers
Preprocessing 3D medical images and image archives, geared towards prostate cancer detection in MRI.
Silicone Breast Phantoms for use with Digital Imaging Elasto-Tomography Breast Cancer Screening
Home for the unified VICTRE pipeline for in silico breast imaging.
Removing or destroying tumours physically, increasingly with robots, image guidance, and heat or cold instead of a knife.
Desktop platform for medical image visualisation, segmentation, registration, and image-guided therapy research.
Extensive mandibular defects caused by malignant tumors, trauma, or severe inflammatory diseases represent one of the most complex challenges in modern...
3D medical imaging reconstruction software
Dataset accompanying the paper Objective speech outcomes after surgical treatment for oral cancer: An acoustic analysis of a spontaneous speech corpus...
Dataset Description : This dataset contains 99,522 episodes of RGB-based state-action-reward expert demonstrations collected from a reaching task within a...
Using focused beams or radioactive particles to kill tumour cells while sparing healthy tissue.
This is a repository to host the Contour Metrics (COMET) application for computing spatial overlap metrics for segmentations
A multipurpose tool for medical physics.
Official public repository of Gate
LinaQA (pronounced Linakwa) is a medical physics toolkit for radiotherapy, diagnostic radiology and nuclear medicine based on pylinac and pydicom.
Develop dose prediction models for knowledge-based planning in radiotherapy
Opensource Python project for cancer radiation treatment planning [AAPM'23]
A community effort to develop an open standard library for Medical Physics in Python.
PyRaDiSe: A Python package for DICOM-RT-based auto-segmentation pipeline construction and DICOM-RT data conversion
Online Radiation Therapy BED EQD2 comparision schemes and Reirradiation analysis based on Python and Streamlit
Deep learning-based accurate delineation of primary gross tumor volume of nasopharyngeal carcinoma on heterogeneous magnetic resonance imaging: a...
A minimal Python library to facilitate the creation and manipulation of DICOM RTStructs.
3D Slicer extension for Radiotherapy clinical re-irradiation analysis.
Statistical Toolkit for Analysis of Radiotherapy DICOM Data
Drugs that kill fast-dividing cells. Still the backbone of many cures, and now the warhead inside smarter drugs.
Targeted and non-targeted anticancer drugs and drug regimens
Targeted therapies are drugs designed to switch off a specific broken protein that a cancer depends on.
CancerFoundation: A single-cell RNA sequencing foundation model to decipher drug resistance in cancer
Synthetic lethality (SL) is a promising gold mine for the discovery of anti-cancer drug targets.
Open-source precision oncology platform that ranks FDA-approved and repurposing drug candidates from a patient's variant profile using OncoKB...
Targeted and non-targeted anticancer drugs and drug regimens
Immunotherapy helps the patient's own immune system recognise and destroy the cancer.
Mouse nEoanTigen pRedictOr
A panoptic segmentation approach for tumor-infiltrating lymphocyte assessment: development of the MuTILs model and PanopTILs dataset.
A molecule that homes to the tumour carries a radioactive atom. The same molecule with a different atom lets you see the tumour first.
This data-centric AI repository implements a robust deep learning method (LFBNet) for fully automated tumor segmentation in whole-body [18]F-FDG PET/CT images.
Tiny library for calculating Standardized Uptake Value for Nuclear Medicine (i.e.
Official public repository of Gate
LinaQA (pronounced Linakwa) is a medical physics toolkit for radiotherapy, diagnostic radiology and nuclear medicine based on pylinac and pydicom.
A 3D lesion segmentation method on whole-body PET images including automated quality control.
Epigenetic and transcriptional therapy changes how genes are read rather than the genes themselves.
EpiMethEx (Epigenetic Methylation and Expression), a R package to perform a large-scale integrated analysis by cyclic correlation analyses between...
Supportive care and survivorship covers everything that keeps a patient well enough to receive treatment, and well afterwards.
Deep learning for cancer symptoms monitoring on the basis of EHR unstructured clinical notes
Medical records scattered across Gmail and Google Drive?
AI patient advocacy tool for cancer treatment.
Dataset accompanying the paper Objective speech outcomes after surgical treatment for oral cancer: An acoustic analysis of a spontaneous speech corpus...
Software that reads scans and slides, predicts outcomes, designs drugs, and matches patients to trials.
Standard for exchanging healthcare information electronically, defining resources and a REST API for clinical data.
Web application for designing and executing observational studies against OMOP-standardised patient data.
Standardised relational model and DDLs for representing observational health data across institutions.
Modular, extensible electronic medical record platform designed for low-resource settings.
This data-centric AI repository implements a robust deep learning method (LFBNet) for fully automated tumor segmentation in whole-body [18]F-FDG PET/CT images.
Code to preprocess, segment, and fuse glioma MRI scans based on the BraTS Toolkit manuscript.
Deep Neural Networks Improve Radiologists' Performance in Breast Cancer Screening
The Cancer Report Validator (CRV) is an interactive tool for validating the content of electronic submissions of cancer-related medical information prior to...
CancerFoundation: A single-cell RNA sequencing foundation model to decipher drug resistance in cancer
CellViT: Vision Transformers for Precise Cell Segmentation and Classification
ClairS: a deep-learning method for long-read tumor, normal pair somatic small variant calling
Open source tools for computational pathology - Nature BME
This is a repository to host the Contour Metrics (COMET) application for computing spatial overlap metrics for segmentations
Cornerstone is a set of JavaScript libraries that can be used to build web-based medical imaging applications.
dcmqi (DICOM for Quantitative Imaging) is a C++ library for conversion between imaging research formats and the standard DICOM representation for image...
The decider R package: decision making in multiple-arm oncology dose escalation trials with logistic regression
DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.
DeepSpot: Deep learning model for predicting spatial transcriptomics from H&E histopathology images.
Evaluation framework for oncology foundation models (FMs)
Code and evaluation repository for the paper
Data intensive science for everyone.
A public reference implementation of HL7 FHIR Genomics Operations (http://build.fhir.org/ig/HL7/genomics-reporting/operations.html)
Machine learning tool for analysis of lung adenocarcinoma tumors
An interpretable classifier for high-resolution breast cancer screening images utilizing weakly supervised localization
Official code for Prediction of molecular subtypes for endometrial cancer based on hierarchical foundation model.
Histomic Prognostic Signature (HiPS): A population-level computational histologic signature for invasive breast cancer prognosis
Deep learning on dermatoscopic images, with a browser demo that lets you try the task against the model.
Insight Toolkit (ITK) -- Official Repository.
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
Meta-repository of screening mammography classifiers
mercure DICOM Orchestrator
A 3D lesion segmentation method on whole-body PET images including automated quality control.
Deep learning for cancer symptoms monitoring on the basis of EHR unstructured clinical notes
MONAI Deploy App SDK offers a framework and associated tools to design, develop and verify AI-driven applications in the healthcare imaging domain.
MONAI Label is an intelligent open source image labeling and learning tool.
A Patient-First Foundation Model for Computational Pathology
cBioPortal is a data visualization tool for cancer genomics.
A panoptic segmentation approach for tumor-infiltrating lymphocyte assessment: development of the MuTILs model and PanopTILs dataset.
Python package for programmatic access to the National Biomedical Imaging Archive (NBIA) and The Cancer Imaging Archive (TCIA)
Onconova is an open-source data platform aiming to enable reliable, structured data collection and analysis in precision oncology.
Develop dose prediction models for knowledge-based planning in radiotherapy
Open-source precision oncology platform that ranks FDA-approved and repurposing drug candidates from a patient's variant profile using OncoKB...
An open, collaborative project to analyze data from the Single-cell Pediatric Cancer Atlas (ScPCA) Portal
Tools for computational pathology
Crossmapped phenotype ontologies for the oncology domain
Opensource Python project for cancer radiation treatment planning [AAPM'23]
CNN ensemble for prostate cancer Gleason grading
Read, modify and write DICOM files with python code
Open-source python package for the extraction of Radiomics features from 2D and 3D images and binary masks.
PyRaDiSe: A Python package for DICOM-RT-based auto-segmentation pipeline construction and DICOM-RT data conversion
Software for automatic segmentation and generation of standardized clinical reports of brain tumors from MRI volumes
Dataset Description : This dataset contains 99,522 episodes of RGB-based state-action-reward expert demonstrations collected from a reaching task within a...
Deep learning-based accurate delineation of primary gross tumor volume of nasopharyngeal carcinoma on heterogeneous magnetic resonance imaging: a...
A minimal Python library to facilitate the creation and manipulation of DICOM RTStructs.
Solid Tumor Associative Modeling in Pathology
Bulk access and download state cancer profiles data.
SurvivMIL: A multimodal, Multiple Instance Learning pipeline for survival outcome of Neuroblastoma Patients
SynProtX is a deep learning model leveraging large-scale proteomics, molecular graphs, and fingerprints to enhance the prediction of synergistic effects in...
Notebooks for working with The Cancer Imaging Archive datasets.
Computational Pathology Toolbox developed by TIA Centre, University of Warwick.
Swift Horos/OsiriX plugin that exports active CT/MR series, provisions an isolated Python TotalSegmentator environment, runs segmentation, and imports...
TrialMatchAI leverages large language models to streamline clinical trial matching by evaluating patient-specific clinical characteristics against trial...
package: An R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq...
vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration
Drug discovery platforms are the tools used to find the next drug: gene screens, organoids, models in mice, and AI.
Software for authoring and running protocols on Opentrons liquid-handling laboratory robots.
Software for the automated analysis of in cellulo high-throughput drug screening
Official Python client for accessing ChEMBL API
The decider R package: decision making in multiple-arm oncology dose escalation trials with logistic regression
Synthetic lethality (SL) is a promising gold mine for the discovery of anti-cancer drug targets.
Mouse nEoanTigen pRedictOr
Targeted and non-targeted anticancer drugs and drug regimens
SynProtX is a deep learning model leveraging large-scale proteomics, molecular graphs, and fingerprints to enhance the prediction of synergistic effects in...
Stopping cancer from starting: vaccines, germline testing, lifestyle, and preventive drugs or surgery.
Substitution of red meat with legumes and risk of primary liver cancer in UK Biobank participants: A prospective cohort study
Bulk access and download state cancer profiles data.
Devices and physical therapies treat cancer with electric fields, heat, or sound rather than chemicals.
Kit-form open-source spectral flow cytometer for volumetric cell counting and fluorescence panels of up to roughly ten colours.
Open-source ultrasound processing modules and building blocks, analogue front ends, FPGA acquisition and pulser boards for do-it-yourself echography.
Embedded server component of the MaRCoS open magnetic resonance control system, running on the scanner hardware.
Open-source MRI console built on low-cost Zynq FPGA hardware, providing spectrometer and acquisition control.
3D-printed automated laboratory microscope with a monolithic flexure stage, designed to be built locally for a fraction of the cost of a commercial instrument.
Modular open-science microscope system built from 3D-printed cubes on a magnetic baseplate, reconfigurable for brightfield, fluorescence and light-sheet...
Build documentation for an open-source ultra-low-field MRI scanner constructed at Utrecht University, following the Open Source Imaging Initiative design.
Open-source low-field MRI scanner using a 50 mT permanent magnet, portable at roughly 150 kg, for head and extremity imaging.
Compact iCE40 FPGA and Raspberry Pi ultrasound board providing pulse-echo acquisition for imaging and non-destructive testing.
Silicone Breast Phantoms for use with Digital Imaging Elasto-Tomography Breast Cancer Screening
What people eat, drink, weigh and do affects who gets cancer, how treatment goes, and who relapses. Those questions are answerable, and the good studies answer them with the rigour of a drug trial.
Substitution of red meat with legumes and risk of primary liver cancer in UK Biobank participants: A prospective cohort study
From the Open Medical Registry (openmedical.sh), an MIT-licensed catalogue of open-source medicine. Blurbs are one line from each registry record; every project keeps its own licence.
OnCo also keeps its own, wider catalogue of open source in oncology: pipelines, knowledge bases, imaging, planning, pathology, single-cell, chemistry, trials, data commons, standards and hardware, with licence, openness, stars and last activity read from each repository.
Snapshot taken 2026-09-10; refresh with npm run fetch:openmedical. The mapping to fronts is OnCo's and lives in scripts/fetch-openmedical.ts; a project appears only after its record was read and judged relevant. Several well-known oncology tools are not yet in the registry (for example MONAI core, TotalSegmentator, matRad, OpenTPS, cBioPortal core, CanReg5 and mCODE); add them at openmedical.sh/contribute and they will be picked up on the next refresh. Missing a mapping? Suggest an edit.