ForBio and Transmitting Science jointly offer this course on CT scanning and data post-processing.
Content
The course gives a practical introduction to microfocus X-ray tomography (CT scanning) and post-processing of volume data, as used in zoology, botany, paleontology, geology and archaeology.
A Nikon Metrology XT H 225 ST instrument at the Natural History Museum in Oslo will be available to participants throughout the course. This flexible instrument can scan objects from about 2 mm to 20 cm across, with densities ranging from soft tissues to rocks, allowing demonstration of a range of applications and scanning parameters.
Visualization and post-processing of data will be based on the advanced software Avizo, available at most major research institutions.
We will also give a short overview to data analysis methods such as volumetric and texture analysis and geometric morphometrics.
Course instructor will be Dr. Øyvind Hammer at the Natural History Museum, University of Oslo. He has worked with microfocus X-ray tomography for many years and has produced many thousand scans for a wide variety of scientific applications. He has a background in computer science, physics and palaeontology. Dr Anna Nele Herdina will cover the use of contrasting agents (DiceCT).
Schedule
Monday, December 2nd, 2019.
- Introduction to X-rays, X-ray radiography and tomography. Medical CT, microfocus and nanofocus CT, synchrotron CT.
- Imaging parameters for digital radiography: Acceleration voltage, beam current, target type, spot size, exposure time, frame stacking, detector resolution and dynamic range, magnification, shading correction, scattering and filtering.
- X-ray density and X-ray contrast. Use of contrasting agents (DiceCT). Practical preparation of soft-tissue samples.
Tuesday, December 3rd, 2019.
- Practical radiography, working on the instrument. Maximizing image quality for different sample types, including DiceCT. Student samples are welcome.
- Principles and practice of X-ray tomography. Rotations, voxels, volumes, reconstruction. Beam hardening. Visualization: Slicing, volume rendering. We start making CT scans.
Wednesday, December 4th, 2019.
- Introduction to Avizo. Volume operations: Filtering (median, anisotropic Gaussian, non-local means).
- Transformations, merging, cropping, resampling. Volume file formats.
- Further visualization techniques: Colour maps, lighting, transparency, surface rendering, composite rendering.
- We continue making CT scans.
Thursday, December 5th, 2019.
- Basic segmentation and labelling techniques: Thresholding, morphological image processing (erosion, dilation, opening, closing), separation.
- Advanced segmentation and labelling. The watershed algorithm. Manual segmentation techniques.
- Measuring tools, placement of landmarks. Label (volumetric) analysis.
- Animation.
Friday, December 6th, 2019.
- Downstream analysis: 3D morphometrics, surface and mesh generation for biomechanics and 3D printing, texture analysis (distributions of sizes and orientations), slice registration (thin sections, SEM images).
Instructors
Øyvind Hammer (Natural History Museum, University of Oslo) and Anna Nele Herdina (Medical University of Vienna
Austria)
Coordinators: Soledad De Esteban-Trivigno - Transmitting Science, and Hugo de Boer – ForBio
Fee: There is no fee for ForBio members based in Norway. A 20% reduction applies to all other ForBio members. Travel and accommodation: Expenses for travel and accommodation will be reimbursed for ForBio members based in Norway. Registration: Everyone should register through Transmitting Science here. For more information about ForBio and membership please see here. Registration deadline is September 30th 2019.