• Advanced Courses in Life Sciences

    Header of Palaeontology and Archaeology at Transmitting Science

1st Edition

CTscan and post-processing for life and geosciences

December 2nd-6th, 2019, Oslo (Norway)

Imaging

Imaging

Registration

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Course overview

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).

Requirements

All participants must bring their own personal laptop.

Contact

courses@transmittingscience.org

LOCATION

Natural History Museum

Premises at Økern

Kabelgaten 40, Oslo, Norway

DATE

December 2nd-6th, 2019

LANGUAGE

English

COURSE LENGTH & ECTS

30 hours on-site.

This course is equivalent to 1 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School.

The recognition of ECTS by other institutions depends on each university or school.

PLACES

Places are limited to 15 participants and will be occupied by strict registration order. If the course fills up there will be an assistant instructor to help during the practise time.

Participants who have completed the course will receive a certificate at the end of it.

Instructors

Oyvind Hammer instructor for Transmitting Science

Dr. Øyvind Hammer
University of Oslo
NorwayUniversity of Exeter
United Kingdom

Anna Nele Herdina instructor for Transmitting Science

Dr. Anna Nele Herdina
Medical University of Vienna
Austria

Coordinators

Soledad De Esteban-Trivigno Transmitting Science coordinator

Dr. Soledad De Esteban-Trivigno
Transmitting Science
Spain

Hugo de Boer

Dr. Hugo de Boer
University of Oslo
Norway

Contact: courses@transmittingscience.org

Program

Monday

  • 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

  • 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

  • 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

  • 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

  • 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).