Open source software

Learn out about researchers' work on open source software.

Open research software, or open-source research software, refers to the use and development of software for analysis, simulation, visualisation, etc. where the full source code is available. (...) open-source software must be distributed in source and/or compiled form (with the source code available in the latter case), and must be shared under a licence that allows modification, derivation and redistribution.

FOSTER Open Science Training Handbook

Discover CMVM researchers' publications on the topic of open source software. Names in bold denote CMVM authors.

2026

Watch Peter Bankhead discuss developing QuPath, an open-source digital pathology platform, in the March 2026 meeting of Edinburgh ReproducibiliTea:

2025

Peter Bankhead, co-author with Matthew Aquilina and others: GelGenie: an AI-powered framework for gel electrophoresis image analysis - article in Nature Communications

Aziz Sheikh, co-author with Samuel Cox and others: Conversion of Sensitive Data to the Observational Medical Outcomes Partnership Common Data Model: Protocol for the Development and Use of Carrot - protocol in JMIR Research Protocols

Kathy Harrison, co-author with Chuang Gao and others: A pipeline for harmonising NHS Scotland laboratory data to enable national-level analyses - article in Journal of Biomedical Informatics

Themis N. Efthimiou & Catherine J. Crompton: duet: An R package for dyadic analysis of motion data generated by OpenPose - article in Behavior Research Methods

2024

Jamie Burke, Samuel Gibbon, Justin Engelmann, Adam Threlfall, Ylenia Giarratano, Charlene Hamid, Stuart King, Ian J. C. MacCormick & Thomas J. MacGillivray: SLOctolyzer: Fully Automatic Analysis Toolkit for Segmentation and Feature Extracting in Scanning Laser Ophthalmoscopy Images - article in Translational Vision Science & Technology

Charlene Hamid, Megan Reid-Schachter, Neeraj Dhaun, Tom MacGillivray, Miguel O. Bernabeu and Ian J. C. MacCormick, co-authors with Justin Engelmann and others: Choroidalyzer: An Open-Source, End-to-End Pipeline for Choroidal Analysis in Optical Coherence Tomography - article in Investigative Ophthalmology & Visual Science

Aaron Yli-Hallila, Peter Bankhead, Mark J. Arends, Petri Lehenkari and Sanna Palosaari: QuPath Edu and OpenMicroanatomy: Open-source virtual microscopy tools for medical education - article in Journal of Anatomy

Alan O’Callaghan, Fiona Inglis & Peter Bankhead, co-authors with Jakub R. Kaczmarzyk and others: Open and reusable deep learning for pathology with WSInfer and QuPath – brief communication in NPJ Precision Oncology

Steven E. Williams, co-author with Zhouyang Xu and others: CardioXplorer: An Open-Source Modular Teleoperative Robotic Catheter Ablation System - article in Robotics

2023

Lucy Kershaw and Michael J Thrippleton, co-authors with Petra J van Houdt and others: Contrast-agent-based perfusion MRI code repository and testing framework: ISMRM Open Science Initiative for Perfusion Imaging (OSIPI) – article in Magnetic Resonance in Medicine

Michael J Thrippleton, co-author with Ben R. Dickie and others: A community-endorsed open-source lexicon for contrast agent–based perfusion MRI: A consensus guidelines report from the ISMRM Open Science Initiative for Perfusion Imaging (OSIPI) – article in Magnetic Resonance in Medicine

Steven Williams, co-author with José Alonso Solís-Lemus and others: Evaluation of an open-source pipeline to create patient-specific left atrial models: A reproducibility study – article in Computers in Biology and Medicine

Constantinos Eleftheriou, Thomas Clarke, V. Poon, Marie Zechner and Ian Duguid: Visiomode: An open-source platform for building rodent touchscreen-based behavioral assays – article in Journal of Neuroscience Methods

2022

Maria Valdés-Hermández, Roberto Duarte, Mark Bastin, Ian Deary, Michael Thrippleton and Joanna Wardlaw, co-authors with Jose Bernal and others: Assessment of perivascular space filtering methods using a three-dimensional computational model – article in Magnetic Resonance Imaging

Kevin Wing, co-author with Helen J. Curtis and others: OpenSAFELY NHS Service Restoration Observatory 1: primary care clinical activity in England during the first wave of COVID-19 – article in British Journal of General Practice

Peter Bankhead, co-author with Natalie C. Fisher and others: Development of a semi-automated method for tumour budding assessment in colorectal cancer and comparison with manual methods – article in Histopathology

Adrian Muwonge and others: Developing digital contact tracing tailored to haulage in East Africa to support COVID-19 surveillance: a protocol – article in BMJ Open

2021

Peter Bankhead, co-author with Justus Kaufmann and others: Using the R Package Spatstat to Assess Inhibitory Effects of Microregional Hypoxia on the Infiltration of Cancers of the Head and Neck Region by Cytotoxic T Lymphocytes – article in Cancers

Peter Bankhead, co-author with Florian Levet and others: Developing open-source software for bioimage analysis: opportunities and challenges – paper in F1000Research


If you are a CMVM-affiliated author and would like your publication on open-source software featured on this page, please get in touch at CMVMopenaccess@ed.ac.uk.

This article was published on