This course is entitled to teach the main concepts of shape analysis based on three-dimensional landmark coordinates. In this course we 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.
Dr. Melissa Tallman
(Grand Valley State University, United States of America).
Dr. Soledad De Esteban-Trivigno
(Transmitting Science, Spain).
Graduate or postgraduate degree in Biomedical, Life or Earth Sciences, basic knowledge of statistics and personal computers. All participants must bring their own personal laptop (Windows).
Monday 4th to Friday 8th May 2015.
Premises of the Centre de Restauració i Interpretació Paleontològic (CRIP), Av. dels Hostalets de Pierola, s/ nº, 08781 Els Hostalets de Pierola, Barcelona (Spain). How to arrive.
Using a microscribe.
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.
Processing Microscribe data:
- Using DVLR to merge two views.
- Using resample to resample a line.
Using Landmark Editor to collect data on surfaces.
Practice period with Landmark Editor:
- Each student should develop their own landmark protocol and landmark a series of scans using his/her own scans or ones that we provide.
Discussion and demonstration of sliding semi-landmarks (using Matlab).
How to do a precision test on 3D data.
Practice period testing the data collected from Landmark in the morning.
Data exploration: PCA analyses:
- Using Morphologika.
- Using MorphoJ.
Practice period: Formatting your data, performing PCAs on your data.
Visualizing shape change:
- Using MorphoJ in conjunction with Landmark Editor.
- Making calculations and visualizing vector displacements in Morpheus.
- GPAing with missing data using Morpheus.
|Data interpretations: Using mean configurations (PAST) and Procrustes distances:
- Minimum spanning trees.
- Variability within a sample (comparing fossil distributions to extant distributions).
Practice period: Visualizing changes in your data set along PC axes in Morpheus and Landmark Editor.
Data exploration: PLS analyses.
- Using MorphoJ to mean center (or not).
- Visualizing shape change in Landmark editor.
Data exploration: Phylogeny.
- Making a tree with mesquite.
- Visualizing shape changes in MorphoJ along a tree.
- Importing covariates and visualizing shape change associated with taxonomy (using MorphoJ).
Data exploration: Allometry.
- Using Procrustes form space.
- Visualizing change that is associated with size (MorphoJ).
- Removing change associated from size from your data (MorphoJ).
General practice period and time for questions and answers.
Programs that we will use:
- Stratovan Checkpoint.
- DVLR (free).
- Resample (free).
- Landmark Editor (free).
- Morphologika (free).
- MorphoJ (free).
- Morpheus (free, requires Windows XP).
- PAST (free).
- Microsoft Excel.
35 hours on-site. This course is equivalent to 3.5 ECTS (European Credit Transfer System). Participants who have completed the course will receive a certificate at the end of it.
Sunday 3rd May 2015:
19:00 Meeting point in Plaza Catalunya (Barcelona) to take the bus to Els Hostalets de Pierola. If you are planning to arrive later, you can find more information in How to arrive.
8:30 to 9:00 Breakfast.
Saturday 9th May 2015:
8:30 to 9:00 Breakfast.
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.
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 organisation, 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.”
You can read more in his blog here.
Jamie MacLaren, University of Antwerp, Belgium (4th Edition).
“The course was well run by the organisers, the meals were fantastic, the hostel was spotless, and Lisa was very helpful in the practical sessions. I am very pleased with this course.”
Participants’ comment in the course evaluation (3rd Edition).
Places are limited to 20 participants and will be occupied by strict registration order.
Reduced registration fee until January 31, 2015: 390 €. Full registration fee after January 31, 2015: 545 €. This includes course material, coffee breaks and lunches.
Former participants will have a 5 % discount* on the current course fee. Discounts are applied only on the fee, not to lodging or other options (see All Inclusive option below in Accommodation section).
We offer the possibility of paying in two instalments (contact us at firstname.lastname@example.org).
Please complete and submit your Registration Form (see below); we will confirm your acceptance by e-mail. If you do not receive any confirmation by e-mail after registration, please contact us at email@example.com.
If you wish to cancel your participation in this course, cancellations up to 20 days before the course start date will incur a 30 % cancellation fee. For later cancellations, or non-attendance, the full course fee will be charged.
If Transmitting Science must cancel this course due to unforeseen circumstances beyond the control of Transmitting Science, you will either be entitled to a full refund of the course fee, or your fee can be credited toward a future course / workshop. Transmitting Science is not responsible for travel fees, or any expenses incurred by you as a result of such cancellation. Every effort will be made to avoid the cancellation of any planned course / workshop.
The course will take place in the town of Els Hostalets de Pierola, Barcelona (Spain).
- All Inclusive option:
We offer this option that covers all of the expenses for the week; it includes transport to and from Barcelona city, lodging, breakfasts, dinners and a visit to a wine cellar. This costs 290 €.
Participants will be hosted in the Youth Hostel Can Roviralta, in shared dormitories (common bathrooms), although you will only share rooms with other classmates. The possibility exists that the dormitories will be mixed. Therefore, if this is an inconvenience for you, and you require staying in a dormitory with only women, or only men, please indicate so in the “Comments” field of the Registration Form (see below).
A supplemental charge will be added if you prefer to stay in a single room with private bathroom. The number of rooms is limited and if you prefer to have a single room, let us know it as soon as possible. If you want more information on this please contact us at firstname.lastname@example.org.
Please be aware that from the centre of Barcelona city it takes about one hour by car and one hour and a half by public transport to arrive to Els Hostalets de Pierola. Course attendees will find that staying in Els Hostalets de Pierola is more convenient.
- Other Options:
If you do not want the All Inclusive option, accommodation is available in places other than Els Hostalets de Pierola. You may stay in Barcelona city, Martorell or Igualada. You will find information about Hotels in Martorell here, and information about Hotels in Igualada here. Both Martorell and Igualada are located about 45 minutes by train from Els Hostalets de Pierola, while it takes about one hour and a half by public transport to arrive to Els Hostalets de Pierola from the centre of Barcelona city.
How to arrive to Els Hostalets de Pierola from Barcelona city, Martorell and Igualada.
Unfortunately there are no internal grants available for this course. However some discounts are offered to people belonging to some of the Associations, Institutions or Universities listed here. If you want to apply to this discount please state the name of your Association, Institution or University in the “Comments” field of the Registration Form (proof will be asked later).
Spanish unemployed scientists, as well as Spanish PhD students without any grant to develop their PhD, could benefit from a 40 % discount* on the course fee. If you want to ask for this discount, please contact us at email@example.com. That would apply for a maximum of 4 places and they will be covered by strict inscription order.
For further information contact: firstname.lastname@example.org.
* Discounts are not cumulative.