Developing an interactive neuroimaging education resource with Neurodesk

Neuroimaging education presents both conceptual and technical challenges: one must master complex foundational principles while navigating technical requirements including software installation, dependency management, and cross-platform compatibility. These tasks are valuable learning opportunities, but they can be time-consuming, which may shift focus away from learning about core neuroimaging concepts. While neuroimaging education benefits from many established resources, interactive notebooks can further integrate instruction with execution, providing a hands-on complement to existing educational materials. Here, we showcase NeurodeskEDU, an emerging learning resource developed using Neurodesk, an open-source, containerised neuroimaging platform, which enables neuroimaging workflows to be executed in a fully reproducible fashion through interactive Jupyter Notebooks. The notebooks integrate code, visualisations, narrative documentation, and direct access to open datasets into analysis workflows. Containerised software delivery reduces installation overhead while ensuring consistent execution across computing platforms. Community contributions undergo automated testing via GitHub Actions to ensure notebook quality and functionality, while persistent DOIs establish notebooks as formally citable scholarly outputs. This new community learning resource provides multiple deployment modes: zero-install cloud execution, downloadable notebooks for local use, static HTML documentation, and interactive slideshows for teaching scenarios. Through three use cases, we demonstrate how such interactive notebooks consolidate fragmented educational workflows, enable seamless multi-tool integration, and support scalable deployment from workshops to self-directed learning. By establishing educational materials as scholarly outputs with systematic quality assurance and version control, this work addresses ongoing challenges in computational publishing: maintaining reproducibility as software evolves, facilitating community contributions, and providing formal academic recognition for educational scholarship.

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Publication Details

Journal
Aperture Neuro
Published
2026-05-21
DOI
https://doi.org/10.52294/001c.160858
Primary Topic
Scientific Computing and Data Management
Type
article
Field-Weighted Citation Impact
0.00

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article

Developing an interactive neuroimaging education resource with Neurodesk

Thomas B. Shaw, Aswin Narayanan, Michal Toth, Michèle Masson‐Trottier et al.
Aperture Neuro
Scientific Computing and Data Management
article

Developing an interactive neuroimaging education resource with Neurodesk

Thomas B. Shaw, Aswin Narayanan, Michal Toth, Michèle Masson‐Trottier, Giulia Baracchini, Monika Dörig, Kyle Mapue, Marla Pinkert, Paul A. Taylor, Christopher Rorden, Fernanda L. Ribeiro, Andrew Jahn, Angela Renton, Thuy T. Dao, Daniel Handwerker, Steffen Bollmann, Ashley Stewart
article en

Abstract

Neuroimaging education presents both conceptual and technical challenges: one must master complex foundational principles while navigating technical requirements including software installation, dependency management, and cross-platform compatibility. These tasks are valuable learning opportunities, but they can be time-consuming, which may shift focus away from learning about core neuroimaging concepts. While neuroimaging education benefits from many established resources, interactive notebooks can further integrate instruction with execution, providing a hands-on complement to existing educational materials. Here, we showcase NeurodeskEDU, an emerging learning resource developed using Neurodesk, an open-source, containerised neuroimaging platform, which enables neuroimaging workflows to be executed in a fully reproducible fashion through interactive Jupyter Notebooks. The notebooks integrate code, visualisations, narrative documentation, and direct access to open datasets into analysis workflows. Containerised software delivery reduces installation overhead while ensuring consistent execution across computing platforms. Community contributions undergo automated testing via GitHub Actions to ensure notebook quality and functionality, while persistent DOIs establish notebooks as formally citable scholarly outputs. This new community learning resource provides multiple deployment modes: zero-install cloud execution, downloadable notebooks for local use, static HTML documentation, and interactive slideshows for teaching scenarios. Through three use cases, we demonstrate how such interactive notebooks consolidate fragmented educational workflows, enable seamless multi-tool integration, and support scalable deployment from workshops to self-directed learning. By establishing educational materials as scholarly outputs with systematic quality assurance and version control, this work addresses ongoing challenges in computational publishing: maintaining reproducibility as software evolves, facilitating community contributions, and providing formal academic recognition for educational scholarship.

Aperture NeuroVol. 6(SI 2)
The University of Sydney (AU), University of South Carolina (US), The University of Queensland (AU), Justus-Liebig-Universität Gießen (DE), University of Zurich (CH), University of Michigan (US), Universitätsklinik Balgrist (CH), Max Planck Institute for Human Cognitive and Brain Sciences (DE), National Institute of Mental Health (US), École Polytechnique Fédérale de Lausanne (CH)
National Science Foundation, U.S. Department of Health and Human Services, Kavli Foundation, Wellcome Trust, National Imaging Facility, Motor Neurone Disease Research Australia, European Commission, Australian Research Data Commons, National Institutes of Health, HORIZON EUROPE Framework Programme, National Health and Medical Research Council, National Institute of Mental Health, H2020 Marie Skłodowska-Curie Actions, HORIZON EUROPE Marie Sklodowska-Curie Actions
Quality Education
Openalex Percentile: Top 3%
Scientific Computing and Data Management
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