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Neurodesk

Run your imaging analyses anywhere

Stop wrestling with dependencies, version conflicts, and platform incompatibilities. Neurodesk gives you consistent, reproducible biomedical imaging tools across any system.
Try Neurodesk now Install locally
100+ neuroimaging and biomedical imaging toolsPublished in Nature Methods2025 iAwards — Best Tech Platform
One environmentRun tools consistently across operating systems.Choose your interfaceSupports graphical desktops, command line and computational notebooks.Work in the cloudDeploy anywhere without installation overhead.Contribute learning resourcesShare your knowledge with the community.

See Neurodesk in action

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From data to analysis to visualisation — all in one reproducible environment.

Neurodesk components

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Flexible tools that work together or independently. Neurodesk makes it easy for beginners and experts to use biomedical imaging tools on desktop, HPC, web, and cloud.

Neurodesktop

Complete virtual desktop environment with GUI applications, ready to use in your browser or locally.

  • 100+ pre-installed neuroimaging tools
  • Familiar desktop interface for graphical applications
  • Install Neurodesk once, all tools are ready to use
Neurodesktop

Neurocontainers

Individual containerised tools you can use in your own pipelines and workflows.

  • Transparent, version-controlled builds
  • Use via Docker or Singularity
  • Perfect for HPC and cloud
Neurocontainer

Neurocommand

Command-line tool manager that fetches and runs containers seamlessly.

  • Simple module-based interface
  • Integrates with existing workflows
  • Accessible through Neurodesk for command-line workflows
$ pip3 install -r neurodesk/requirements.txt --user
$ bash build.sh --cli
$ bash containers.sh
$ module use $PWD/local/containers/modules

Trusted by researchers worldwide

3,800+monthly users
100+countries
$2.5M+AUD in research grants

Community

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Neurodesk is a community project. Our active community provides transparency and inclusion — we encourage you to engage and contribute.

Support usHelp sustain Neurodesk with a donation to support development and infrastructure.FAQAnswers to common questions about installing, running, and contributing to Neurodesk.DiscussionsAsk questions, suggest new features or raise any issues you have (GitHub account required).ContributorsMeet the researchers, developers, and community members building Neurodesk.Contribution guideLearn how you can contribute to Neurodesk code and documentation.Learning resourcesTutorials, examples, and educational material for getting the most out of Neurodesk.
Independently evaluated

“Neurodesk offers an extensive container repository, with the versatility of a command-line interface for technical users and a GUI that lowers barriers for non-technical users.”

— Imaging Neuroscience (MIT Press), accessibility and usability studyRead the paper →

Ready to run Neurodesk anywhere?

Join researchers worldwide using Neurodesk for transparent, reproducible neuroimaging.

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