Imaging tools on UKB-RAP

Working with UK Biobank’s imaging data? UK Biobank's Research Analysis Platform includes powerful tools to help you view, annotate and analyse images at scale within our secure, cloud-based environment.

AI-assisted annotation

Learn how to use open-source AI framework MONAI to to support annotation, segmentation and interactive analysis. MONAI is able to streamline the annotation and analysis of medical images, enabling faster, more consistent results across large datasets.

Read the guide: Using MONAI on UKB-RAP

Image visualisation

Discover how to view and interact with images using 3D Slicer, a fully featured volume-visualisation and annotation tool integrated into UKB-RAP. The guide covers both DICOM and NIFTI formats and shows how to mount your files and start the session.

Read the guide: Viewing images on UKB RAP with 3D Slicer

Deploying your own tools

Learn how to combine Docker and the Swiss Army Knife tool to deploy your own custom-built analysis tools on UKB-RAP.

Read the guide: UKB-RAP Imaging ML on our Github notebooks page

Brain imaging analysis

How to access and use JupyterLab with FSL and FreeSurfer to perform neuroimaging workflows - including brain extraction, registration and segmentation - via command-line tools and Python.

Read the guide: JupyterLab with FSL and FreeSurfer

MATLAB analysis

See how to run imaging workflows using a graphical user interface (GUI) version of MATLAB on UKB-RAP, including how to start an instance, pull a Docker image, and start a container.

Read the guide: Working with MATLAB