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Advanced Courses in Life Sciences

2nd Edition

3D Model Generation in Life Sciences

October 3rd-7th, 2016, Barcelona (Spain)

Cruzado-Caballero P, Fortuny J, Llacer S, Canudo J. (2015) Paleoneuroanatomy of the European
lambeosaurine dinosaur Arenysaurus ardevoli. PeerJ 3:e802. DOI: 10.7717/peerj.802/supp-1.

This course is addressed to life sciences researchers and technicians who routinely work with complex biological structures and need to analyze them in three dimensions, and who digitise their samples for any reason, such as digital preservation or retrospective analysis of a previously scanned sample. You may arrive at this course from a diversity of different backgrounds (laser, photogrammetry, CT, etc.) and use it as a basis to move on to further analyses.

The course is designed to enable participants to arrive at a three-dimensional image solution by concentrating on not just one methodology or technology but by considering the range that is available. This range is now quite extensive, including such things as 3D imaging, 3D printing, image processing, image filtering, laser imaging, photogrammetry, computed tomography (CT), and more. Images resulting from one methodology or technology should not be the end of the road but a starting point from which you can gain much more by performing other analyses, applying other methodologies or using different technologies, even with existing data.

Despite it is easy to become satisfied by one methodology that you know well, yet there may be much more you can achieve. And there are other advantages. Not only will your final result be more precise and accurate, you also have the potential of finding a more efficient approach than the one originally chosen, even though a multi-solution approach might seem inefficient at the outset.

The goal of this course is to explain how you can work with a range of technologies with the aim of obtaining a 3D model from different sources. By the end of the course participants should be able to work in an autonomous way to develop 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.


Institut Català de Paleontologia Miquel Crusafont

Edificio Z, ICTA-ICP
C/ de les Columnes, s/ nº
Campus de la Universitat Autònoma de Barcelona
08193 Bellaterra (Cerdanyola del Vallès), Barcelona.




35 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 20 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 LLácer instructor for Transmitting Science

Sergio Llácer
Institut Català de Paleontologia Miquel Crusafont


Soledad De Esteban-Trivigno instructor at Transmitting Science

Dr. Soledad De Esteban-Trivigno
Transmitting Science

Judit Marigó coordinator at Transmitting Science

Dr. Judit Marigó
Muséum national d’Histoire naturelle / Institut Català de Paleontologia Miquel Crusafont
France / Spain


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:

– Free: Meshlab, Visual SFM, CVMS, VSDC Free video Editor, ImageJ.

– Not free: Avizo, Rhinoceros, Geomagic. Temporal licences will be provided for these softwares.


Monday, October 3rd, 2016.

Course presentation. Start up the software. What is digital modelling? What is this technology used for? The pros, cons and limitations of modelling. Introduction to CAD. The common file formats in the world of 3D visualisation (.ply, .stl, .wrp, …). Laser tech and photogrammetry: Theory. Laser tech practice (Next Engine).

Tuesday, October 4th, 2016.

Pros and cons of Laser and Photogrammetry and a consideration of how to use both techniques properly. Photogrammetry practice – How to generate 3D models – Visual SFM and Photoscan. Advantages and limitations.

Wednesday, October 5th, 2016.

Computed Tomography (CT): Theory and practice I. Image improvement. Radiographic images. Segmentation. Thresholding. Surface generation.

Thursday, October 6th, 2016.

Computed Tomography (CT): Practice II. Advanced segmentation. Measurements. 3D model edition: Geomagics and general applications of 3D modelling. Visit to the 3D Virtual Lab of the ICP.

Friday, October 7th, 2016.

Generation and editing of videos. 3D printing. Demonstration of practical examples from the students’ data and group discussion.


You will find below some testimonials from former participants to previous editions of this course:

Dr. Stefano Schiaparelli

“It was a great course which has fulfilled all my expectations. There was a high level of organization and a pleasant atmosphere during the whole course.” (1st Edition)

Dr. Stefano SchiaparelliUniversity of Genova, Italy


  • Course Fee
  • Early bird (until May 31st, 2016)
  • 460
  • Regular (after May 31st, 2016)
  • 645
  • This includes course material, coffee breaks and lunches.

This course will be held if at least 50 % of the places are filled.

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


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

Unfortunately there are no scholarships available for this course. However 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).

Spanish unemployed scientists, as well as Spanish PhD students 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 coordinators. That would apply for a maximum of 2 places and they will be covered by strict inscription order.

Discounts are not cumulative.


Course Schedule
Monday, October 3rd through Friday, October 7th, 2016
9:30 to 13:30 Lessons.
13:30 to 15:00 Lunch.
15:00 to 18:00 Lessons.

There will be two coffee breaks each day, halfway through each lesson session.

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.


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