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Advanced Courses in Life Sciences

8th Edition

3D Geometric Morphometrics

August 19th-23rd, 2019, Barcelona (Spain)

Geometric Morphometrics

Geometric Morphometrics Logo

3D Geometric MorphometricsThis course is entitled to teach the main concepts of shape analysis based on three-dimensional landmark coordinates. In this course, you will learn to manipulate 3D models and use them to collect landmark data, take measurements, and to quantify and visualize the main differences in shape.

LOCATION

Can Carol

C/ Font de la Reina, 5
08786 Capellades, Barcelona (Spain)

How to get there

DATE

August 19th-23rd, 2019

LANGUAGE

English

COURSE LENGTH & ECTS

35 hours on-site.

This course is equivalent to 2 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 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.

Instructor

Melissa Tallman instructor for Transmitting Science

Dr. Melissa Tallman
Grand Valley State University
United States of America

Coordinators

Ana Rosa Gómez-Cano coordinator at Transmitting Science

Dr. Ana Rosa Gómez-Cano
Transmitting Science
Spain

Soledad De Esteban-Trivigno instructor at Transmitting Science

Dr. Soledad De Esteban-Trivigno
Transmitting Science
Spain

Requirements

Graduate or postgraduate degree in Biomedical, Life or Earth Sciences, basic knowledge of statistics. Basic knowledge of Geometric Morphometric is recommended.

All participants must bring their own personal laptop (Windows).

Program

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).

Retrodeformation.


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.

Fees

  • Course Fee
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  • Early bird (until April 30th, 2019):
  • 545 *
  • Regular (after April 30th, 2019):
  • 690 *
  • 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
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  • Early bird (until April 30th, 2019):
  • 545 * + 350 = 895
  • Regular (after April 30th, 2019):
  • 690 * + 350 = 1,040
  • This includes course material, coffee breaks, transportation from and to Barcelona city, accommodation from Sunday to Friday, breakfasts, lunches and dinners (VAT included).
    * Participants from companies/industry will have an extra charge of 100 €.

We offer the possibility of paying in two instalments (contact the course coordinator). Discounts (see Funding below) are not cumulative and apply only on the fee, not to Accommodation Package or other options.

Accommodation

Accommodation Package

If you take the Accommodation Package you will be hosted in the Rural House Can Carol, in single-sex shared dormitories (2 – 4 people) with bathroom en-suite.

If the number of participants exceeds the available rooms at Can Carol, some of them could be accommodated in the Hotel Tall del Conill, by registration order. The hotel is at 10 minutes walking, although transport will be provided in the morning and after dinner. Lunches and dinners will be with the whole group.

A supplemental charge will be added if you prefer to stay in a single room.

Accommodation is included from Sunday (check-in) to Friday (check-out). Breakfast, lunch and dinner are also provided during the week, starting from the dinner of Sunday to lunch of Friday (included).

Other accommodation options

If you do not want the Accommodation Package, accommodation is available in places other than Can Carol: Where to stay near the Venue.

Rural House Can Carol

Rural House Can Carol (Capellades, Barcelona, Spain)

Rural House Can Carol

Rural House Can Carol (Capellades, Barcelona, Spain)

Rural House Can Carol

Rural House Can Carol (Capellades, Barcelona, Spain)

Schedule

Course Schedule
  • Monday to Friday:
    • 9:30 to 13:30 Lessons.
    • 13:30 to 15:00 Lunch (included).
    • 15:00 to 18:00 Lessons.
Accommodation Package Schedule
  • Sunday:
    • 19:00 Meeting point in Plaza Catalunya (Barcelona) to take the bus to Capellades. If you are planning to arrive later, you can find more information on How to get there.
    • 20:00 Registration in the Hotel.
    • 20:30 Dinner.
  • Monday to Thursday:
    • 8:00 to 9:00 Breakfast.
    • 20:00 Dinner.
  • Friday:
    • 8:00 to 9:00 Breakfast.
    • 18:00 Meeting point in the Hotel to take the bus to Barcelona city.
    • 19:30 Arrival at Plaza Catalunya (Barcelona).

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

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).

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

Discounts are not cumulative and apply only on the fee, not to Accommodation Package or other options.

Testimonials

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

“Throughout the course, we dabbled in Landmark editor, Morphologika, MorphoJ, PAST, Meshlab, Checkpoint, … the list goes on. It can safely be said that much knowledge was gleaned from our excellent instructor, Dr. Melissa Tallman, and that no matter what organisms we are planning to study, we will now know how to apply the programs to answer our question…well, for the most part! All in all, the course was a roaring success in my eyes, and I hope for the rest of the participants also. Both Zebo and I would like to thank Sole, Lissa and Juanvi for their organization, their patience, their culinary expertise respectively…and, of course, their coffee. It has been a memorable trip, I have made many good contacts and hopefully some good friends, all of whom I hope to see on the academic circuit in the near future.” (4th Edition)

You can read more in his blog here.

Jamie MacLarenUniversity of Antwerp, Belgium

Previous editions of this course

6th Edition, May 23rd-27th, 2016

Course 3D Geometric Morphometrics - 6th Edition, May 23rd-27th, 2016Ten people belonging to the following countries and institutions participated in this edition:

  • Germany: Eberhard Karls University Tübingen.
  • Spain: Universidad de Granada, Universidad Complutense de Madrid, Institut Català de Paleontogia Miquel Crusafont.
  • Czech Republic: Masaryk University.
  • United Kingdom: University of Bristol.
  • Switzerland: University of Vienna.
  • United States of America: Arizona State University.

5th Edition, May 4th-8th, 2015

Course 3D Geometric Morphometrics - 5th Edition, May 4th-8th, 2015Eight people belonging to the following countries and institutions participated in this edition:

  • Spain: Institut Català de Paleontologia Miquel Crusafont, University of Girona.
  • France: Muséum national d’Histoire naturelle.
  • Switzerland: University of Bern.
  • United Kingdom: University of Durham.
  • Finland: University of Helsinki.

4th Edition, May 20th-24th, 2014

Course 3D Geometric Morphometrics - 4th Edition, May 20th-24th, 2014Nineteen people belonging to the following countries and institutions participated in this edition:

  • United States of America: Appalachian State University, Texas A&M University, University of New Mexico.
  • Spain: Centre for Genomic Regulation.
  • Greece: Hellenic Centre for Marine Research, National and Κapodistrian University of Athens.
  • The Netherlands: Leiden University, Naturalis Biodiversity Center.
  • Mexico: National Autonomous University of Mexico.
  • United Kingdom: Plymouth University.
  • Italy: Second University of Naples.
  • Germany: Senckenberg Gesellschaft für Naturforschung.
  • People’s Republic of China: University of Hong Kong.
  • Belgium: University of Antwerp.
  • Switzerland: University of Zurich.

3rd Edition, May 15th-17th, 2013

Course 3D Geometric Morphometrics - 3rd Edition, May 15th-17th, 2013Fourteen people belonging to the following countries and institutions participated in this edition:

  • Slovenia: University of Maribor.
  • United States of America: Texas A&M University, Virginia Institute of Marine Science, University of Louisiana at Lafayette.
  • People’s Republic of China: Chinese Academy of Sciences.
  • The Netherlands: Leiden University.
  • Switzerland: University of Basel, University of Zurich.
  • Colombia: Universidad Nacional de Colombia.
  • Germany: Friedrich-Schiller-Universität Jena.
  • Italy: Università degli Studi di Milano.
  • Spain: Universitat de València.

2nd Edition, July 17th-20th, 2012

Course 3D Geometric Morphometrics - 2nd Edition, July 17th-20th, 2012Fourteen people belonging to the following countries and institutions participated in this edition:

  • United Kingdom: University College London.
  • Germany: Bayerische Staatssammlung für Paläontologie und Geologie, Ludwig Maximilians Universität Munich.
  • France: University of Poitiers.
  • Portugal: University of Coimbra.
  • United States of America: Texas A&M University, University of Pennsylvania.
  • Sweden: Uppsala University.
  • The Netherlands: Leiden University.
  • Spain: Universidad Complutense de Madrid, Institut Català de Paleontologia Miquel Crusafont, Universitat de Barcelona.
  • Poland: Wroclaw University.

Organizers

Transmitting Science Logo

Collaborators

Logo Ajuntament Capellades
Colegio Oficial de Biólogos de Castilla y León Logo
Colegio Oficial de Biólogos de Euskadi Logo
Colexio Oficial de Biólogos de Galicia Logo
Col·legi Oficial de Biòlegs de la Comunitat Valenciana Logo
European Association of Vertebrate Palaeontologists (EAVP) Logo
Sociedade Brasileira de Paleontologia (SBP) Logo

Sponsor

Stratovan Logo

Registration