General course information
Correlative imaging combines data from multiple acquisition techniques and length scales to build a more complete picture of a specimen than any single modality can provide on its own. This is particularly powerful when combining 3D X-ray or neutron tomography with high-resolution 2D or 3D techniques such as FIB-SEM, allowing researchers to link bulk-scale structural context with fine, local microstructural detail. However, correlating datasets acquired at different resolutions, on different instruments, and sometimes with different contrast mechanisms, introduces a range of practical challenges: alignment, registration, normalisation, and interpretation. This course covers the acquisition principles and the practical Avizo-based workflows needed to bring these datasets together reliably.
Organisation
The training is organised in two parts: theory (0.5 day), covering an introduction to acquisition techniques and the principles of correlative workflows, and computer-based practical work using the Thermo Scientific™ Amira-Avizo Software 3D (1.5 day). At the end of the course, 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).
Prerequisites
Prior attendance of a foundational tomography/image processing course (e.g. “Visualisation, AI-Assisted Analysis and Quantification of Tomographic Datasets”) is recommended, or equivalent working experience with 3D image processing.
Who should attend?
This course is aimed at researchers who already have some familiarity with 3D image processing and who want to combine multiple imaging modalities and/or resolutions in their analysis workflow. It is particularly relevant to those working with FIB-SEM, multi-scale tomography, neutron/X-ray correlative studies, or any workflow requiring registration of datasets from different instruments.
Learning outcomes
Introduction to acquisition techniques
• Overview of X-ray tomography (lab and synchrotron) and its resolution/field-of-view trade-offs
• Overview of neutron tomography: complementary contrast mechanisms to X-ray (e.g. sensitivity to light elements/hydrogenous materials), typical facilities, and where it adds value in a correlative study
• Overview of FIB-SEM acquisition: serial sectioning principles, imaging modes, and typical artefacts
• Other correlative modalities (e.g. SEM/EDS, confocal, other 2D imaging) and where they fit into a correlative workflow
• Understanding contrast mechanisms across modalities and their implications for registration and interpretation
FIB-SEM data processing
• Import and inspection of FIB-SEM image stacks
• Alignment correction of serial sections (drift, curtaining, and misalignment between slices)
• Tilt correction
• Grayscale normalisation across slices and datasets
Working with multi-resolution and multi-modality data
• Handling datasets of different resolutions within the same project
• Resampling strategies and their impact on data fidelity
• Registration of datasets from different modalities (rigid and non-rigid approaches), including X-ray/neutron tomography pairs and tomography/FIB-SEM pairs
• Defining and extracting regions of interest for correlative analysis (e.g. locating a FIB-SEM ROI within a lower-resolution tomography volume)
• Quality-checking and visualising correlative results
Practical workflows
• End-to-end example: from lower-resolution tomography to FIB-SEM ROI, aligned and registered
• Illustration of quantification from multiple modalities
• Working on your own dataset with trainer support
How to register:
Please contact Sarah Batts if you wish to sign up for this course (sarah.batts@manchester.ac.uk). Places are limited to 10 attendees per course. Courses generally fill up very quickly and places are allocated on a first come first serve basis. If there is low attendance, a course may be cancelled with a month’s notice.
