Open tools you can use or build

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.

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.

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.

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...

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

Targeted and non-targeted anticancer drugs and drug regimens

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

Mouse nEoanTigen pRedictOr

A panoptic segmentation approach for tumor-infiltrating lymphocyte assessment: development of the MuTILs model and PanopTILs dataset.

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.

EpiMethEx (Epigenetic Methylation and Expression), a R package to perform a large-scale integrated analysis by cyclic correlation analyses between...

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...

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

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...

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.

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

Substitution of red meat with legumes and risk of primary liver cancer in UK Biobank participants: A prospective cohort study