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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).
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.
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 organizers, 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).
For further information contact: email@example.com.
|We accept donations, which would be entirely devoted to support students without financial resources so that theymay offset the cost of participating in our courses and workshops.|