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Tutorial: Image Acquisition and Processing

We will hold a 2 day image acquisition and image processing training data at Harwell to learn more about how we use the Bruker Skyscan 1172 and the Henkelman custom-build OPT instruments and the open source tools we use and have developed to do downstream processing, visualisation and analysis.

Image acquisition topics:

  • MicroCT: Harwell protocol, setting up Skyscan 1172
  • OPT: Harwell protocol, setting up OPT
  • Trainers: Lydia Teboul, Sara Johnson, James Cleak

Image processing topics:

  • Data creation with NRecon
  • Data management with the HARP (Harwell automated recon processor)
  • Visualisation of volume and iso-surface representations with 3D Slicer
  • Segmentation & Masking with Slicer, ITK-Snap, WASP (Watershed Annotation Segmentation Plugin ; Harwell plugin for 3D Slicer), and scripting
  • Registration and embryo phenotyping with elastix
  • Bring your own data
  • Trainers: Henrik Westerberg, Neil Horner, James Brown