• Header of Imaging at Transmitting Science

Advanced Courses in Life Sciences

1st Edition

CTscan and Post-processing for Life and Geosciences

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

Imaging

Imaging Logo

CTscan and post-processing for life - and geosciencesCourse 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).

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 and ForBio.

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.

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

Instructors

Øyvind Hammer instructor for Transmitting Science

Dr. Øyvind Hammer
University of Oslo
Norway

Anna Nele Herdina instructor for Transmitting Science

Dr. Anna Nele Herdina
Medical University of Vienna
Austria

Coordinators

Soledad De Esteban-Trivigno instructor at Transmitting Science

Dr. Soledad De Esteban-Trivigno
Transmitting Science
Spain

Hugo de Boer

Dr. Hugo de Boer
University of Oslo
Norway

Requirements

All participants must bring their own personal laptop.

Program

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).

Fees

  • Course Fee
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  • 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 and coffee breaks (VAT included).
    * Participants from companies/industry will have an extra charge of 100 €.

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

Discounts (see Funding below) are not cumulative and apply only on the fee.

We offer the possibility of paying in two instalments (contact the course coordinator).

Schedule

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

The 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.

Funding

Discounts

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

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

Discounts are not cumulative and apply only on the fee.

Organizers

Transmitting Science Logo
Research School in Biosystematics (ForBio) Logo

Registration