• 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)




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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).


All participants must bring their own personal laptop.




Natural History Museum

Premises at Økern

Kabelgaten 40, Oslo, Norway


December 2nd-6th, 2019




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 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.

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

Soledad De Esteban-Trivigno Transmitting Science coordinator

Dr. Soledad De Esteban-Trivigno
Transmitting Science

Hugo de Boer

Dr. Hugo de Boer
University of Oslo



  • 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.


  • 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.


  • 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.


  • 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.


  • 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).


  • Course Fee
  • Early bird (until September 30th, 2019):
  • 630 € *
    (504 € for Ambassador Institutions)
  • Regular (after September 30th, 2019):
  • 750 € *
    (600 € for Ambassador Institutions)
  • This includes course material, coffee breaks and lunches (VAT included).
    * Participants from companies/industry will have an extra charge of 100 €.

You can check the list of Ambassador Institutions. If you want your institution to become a Transmitting Science Ambassador please contact us at communication@transmittingscience.com


Course Schedule
  • Monday to Friday:
    • 9:30 to 12:00 Lessons.
    • 12:00 to 13:00 Lunch.
    • 13:00 to 16:00 Lessons.

The class schedule is approximate; it is possible that the content of one day may run into the next and a working day may be longer than advertised.


Discounts are not cumulative and apply only on the Course Fee. We offer the possibility of paying in two instalments (contact courses.crete@transmittingscience.org).

Former participants will have a 5 % discount on the Course Fee.

20 % discount on the Course Fee is offered for members of some organizations (Ambassador Institutions). If you want to apply to this discount please indicate it in the Registration form (proof will be asked later).

Unemployed scientists living in Spain, as well as PhD students based in Greece without any grant or scholarship to develop their PhD, could benefit from a 40 % discount on the Course Fee. If you want to ask for this discount, please contact the course coordinator. That would apply for a maximum of 2 places and they will be covered by strict inscription order.


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