Visualisation and quantification of tomographic datasets

General course information

Lab/synchrotron X-ray tomography has emerged as one of the most important techniques for research in a wide range of applications including healthcare, energy, food and geology. Advances in the quality of X-ray beams, optics, high speed data acquisition and in-situ environments have made significant improvements to non-destructive imaging of a specimen structure in 3D and over a wide range of length scales (micron-and nanoscales). Although the direct benefit of X-ray tomography is the 3D visualisation of the internal structure of specimens, which is very valuable to understand the structure/function relationships, the technique has however a lot more to offer. The information is hidden in the data and robust methods and workflows are needed to extract it in a relevant and accurate way, and make it readily available for decision making.


The training is organised in two parts: theory (0.5 day) and computer-based practical works using the Thermo Scientific™ Amira-Avizo Software 3D (1.5 day). At the end of the second day, the users are invited to practise on their own dataset with the help of the trainers. The attendees are invited to bring their own laptop (an Avizo license will be provided for the training).

Who should attend?

This course is aimed at both beginners with no prior experience in 3D imaging and image processing, and intermediate-level researchers who want to know more about it and explore different ways of analysing 3D datasets.

Learning outcomes

  • Basics of image processing (voxel, structuring element, neighbouring, etc.)

  •  Import/manipulate tomographic dataset

  • Surface/volume renderings

  • Filtering

  • Mathematical Morphology: dilation, erosion, opening, closing, geodesic reconstruction

  • Basic/advanced segmentation

  • Quantification

  • Registration/stitching of 3D datasets

  • Animation/movies