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Advanced Courses on Life Sciences

Course – 2nd Edition

Introduction to 3D Imaging Technologies: Photogrammetry, Laser, CT-scan and (µ)CT-scan for Life Sciences

June 26th-July 2nd, 2017, Barcelona (España)




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Course Introduction to 3D Imaging Technologies- Photogrammetry, Laser, CT-scan and micro CT-scan for Life SciencesCourse Overview

This course is addressed to life sciences researchers and technicians who routinely work with complex biological structures (specimens) and need to digitise their samples for different reasons, such as digital preservation, quantitative or biomechanics analyses, etc.

The goal of this course is to explain how you can work with a range of technologies with the aim of obtaining a 3D virtual models from different sources, such as laser imaging, photogrammetry and (micro) computed tomography (CT). By the end of the course participants should be able to obtain high quality digitalizations of samples with the most commonly used techniques and also be able to edit and manipulate the digital models that are produced.

Attendees will also learn to stain with Lugol’s iodine, a specific technique for specimen preparation for micro CT scanning which maximizes soft-tissue differentiation in CT imaging datasets. DiceCT Online.


Participants will be required to bring their own personal laptop with the following minimum requirements: Windows, CoreI5 or equivalent, 4 GB RAM, 1 GB memory dedicated to the graphic card, 20 GB of hard disk space available. If you wish to attend but do not have access to a laptop which meets these specifications, please contact the course coordinators.

During the course participants will use the following software:





May 21st-25th, 2018




46 hours on-site.

This course is equivalent to 3 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 18 participants and will be occupied by strict registration order.

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

Josep Fortuny instructor for Transmitting Science

Dr. Josep Fortuny
Institut Català de Paleontologia M. C. / Muséum National d’Histoire Naturelle
Spain / France

Sergio LLacer instructor for Transmitting Science

Sergio Llácer
Institut Català de Paleontologia Miquel Crusafont

Heinrich Mallison instructor for Transmitting Science

Dr. Heinrich Mallison

Paul Gignac instructor for Transmitting Science

Dr. Paul Gignac
Oklahoma State University Center for Health Sciences
United States of America


Types of data acquisition.
Collecting CT scans & Surface Scans.
– Demonstration of Stratovan Checkpoint.

Brief Review of Fundamentals of Morphometrics.
– How to choose landmarks.
– Generalized Procrustes Analysis.
– Other types of alignment.
– Thin plate spline warping.

Processing Microscribe data.
– Using DVLR to merge two views.
– Using resample to resample a line.

Using Landmark Editor to collect data on surfaces.
– Sliding semi-landmarks (using R geomorph package).

How to do a precision test on 3D data.

Data exploration: PCA analyses.
– Using Morphologika.
– Using MorphoJ.
– Between-group PCAs.
– PCAs in Procrustes form space.

Visualizing shape change.
– Using MorphoJ in conjunction with Landmark Editor.
– Making calculations and visualizing shape changes in PCA morphospace.
– Calculating PCA scores post hoc.

Data exploration: Regressions.
– Visualizing change that is associated with size (MorphoJ).
– Removing change associated from size from your data (MorphoJ).
– Common allometric trajectories.
– Comparing vector directions.
– Extracting linear dimensions from 3D data and using them as covariates.

Data exploration: PLS analyses.
– Using MorphoJ to mean center (or not).
– Visualizing shape change in Landmark editor.

Data exploration: Phylogeny.
– Visualizing shape changes in MorphoJ along a tree.
– Importing covariates and visualizing shape change associated with taxonomy (using MorphoJ).
– Creating a phyomorphospace.
– Correcting for phylogeny in PCA.

Data interpretations: Using mean configurations (PAST) and Procrustes distances.
– Minimum spanning trees.
– Variability within a sample (comparing fossil distributions to extant distributions).


Programs that we will use:

Stratovan Checkpoint (temporal licences will be provided during the course).
– DVLR (free).
– Resample (free).
Landmark Editor (free).
Morphologika (free).
MorphoJ (free).
PAST (free).
R (free, only for sliding semilandmarks, no previous knowledge is required).
– Microsoft Excel.


  • Course Fee
  • Early bird (until January 31st, 2020):
  • 535 € *
    (428 € for Ambassador Institutions)
  • Regular (after January 31st, 2020):
  • 644 € *
    (515.20 € for Ambassador Institutions)
  • This includes course material, coffee breaks and lunches (VAT included).
    * Participants from companies/industry will have an extra charge of 100 €.
  • Course Fee + Accommodation Package
  • Early bird (until January 31st, 2020):
  • 535 € * + 350 € = 885 €
    (778 € for Ambassador Institutions)
  • Regular (after January 31st, 2020):
  • 644 € * + 350 € = 994 €
    (865.20 € for Ambassador Institutions)
  • This includes course material, coffee breaks, transportation between the Venue and Barcelona, accommodation from Sunday to Friday, breakfasts, lunches and dinners (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


  • Monday to Thursday:
    • 9:30 to 13:30 Lessons.
    • 13:30 to 15:00 Lunch (included).
    • 15:00 to 18:00 Lessons.
  • Friday:
    • 9:30 to 13:30 Lessons.
    • 13:30 to 15:00 Lunch (included).

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@transmittingscience.com).

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 the country were the course will be held, as well as PhD students based in that country 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.