Geometric Morphometrics is the analysis of shape using Cartesian geometric coordinates rather than linear, areal, or volumetric variables. Geometric morphometric methods (GMM) include 2D and 3D points representing landmarks, curves, outlines, or surfaces. This course is a practical, applied introduction to GMM. Students learn to collect, analyze, and interpret geometric morphometric data. Shape theory and methods are covered, including Procrustes superimposition and its statistical implications, analysis of curves and outlines, and Monte Carlo modeling of shape.

[Course Syllabus]

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	Lecture 1 - Introduction to Geometric Morphometrics Overview of principles of geometric morphometric methods (GMM), including definitions of landmarks, outlines and surfaces, differentiation between traditional morphometrics and GMM, short history of morphometrics, components of a morphometric study, and examples of equipment needed for GMM studies. [Download slides]
	Lecture 2 - Introduction to Mathematica Mathematica interface, functions, variables, and graphics [Download slides] [sample data set] [Assignment 1]
	Lecture 3 - First GMM analysis Review of data manipulation commands in Mathematica, getting rows, getting columns, general steps GMM analysis, specific steps in Mathematica, tpsImport[], Procrustes[], PrincipalComponentsOfShape[]. [Download slides] [Answer to Assignment 1]
	Lecture 4 - First GMM Analysis followup Review data manipulation, review installing Mathematica package, review steps for analysis of faces, interpret results of analysis of faces, including discussion of biases in the data. [Download slides]
	Lecture 5 - Procrustes, PCA and shape modelling Procrustes, Procrustes distances (including calculation in Mathematica), details of Principal Components Analysis, shape modelling [Download slides] [Assignment 2]
	Lecture 6 - Statistical tests Review, Introduction to Regression and ANOVA using PC scores, Performing Regression and ANOVA in Mathematica, Applications of Regression and ANOVA, Introduction to tarsal problem for Assignment 3. [Download slides] [Collecting 3D landmarks] [Assignment 3 - Carnivore tarsals]
	Lecture 7 - Analysis of outlines Introduction to outline data. Fourier analysis, Eigenshape analysis, semilandmark analysis. Issues with semilandmark positions, solutions with extended eigenshape and sliding semilandmarks. [Download slides] [Assignment 4 - outlines] [Marmot molar tps file] [Turtle image file]
	Lecture 8 - EDMA Issues with Procrustes and introduction to Euclidean Distance Matrix Analsysis [Download slides]
	Lecture 9 - Graphics Principles of design for quantitative data graphics, advanced functions in Mathematica for their creation. [Download slides]
	Lecture 10 - Review of Mathematica, GMM, and Graphics Commands Review of basic syntax and procedures in Mathematica, review of the basic steps in GMM and how to do them in Mathematica, advanced discussion of creating customized graphics in Mathematica. [Download slides] [Download Mathematica Notebook] (right click and save notebook as a file, then open in Mathematica)
	Lecture 11 - Trees and Clustering Introduction to phylogenetics in the context of geometric morphometrics, discussion of phylogenetic signal in morphometrics, introduction to tree building. [Download slides]
	Lecture 12 - Evolution and Ancestors Phenotypic evolution, random walks (Brownian motion), reconstructing ancesrtral shapes [Download slides] [mammal tree]
	Lecture 13 - 2B PLS and Bootstrapping Review, multivariate regression, two-block partial least squares analysis, Boostrapping statistics [Download slides]

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Mathematica Morphometrics Package

Download Geometric Morphometrics for Mathematica and other Mathematica packages here

Handouts

How to collect landmarks from photos
Collecting 3D landmarks with MicroScribe
Collecting outline points in ImageJ

Sample Data Files

Associated data from Caumul and Polly, 2005 [Excel format]
Onyx turtle images for outlines
Marmot molar TPS file

Morphometrics Resources

Jim Rohlf's morphometrics site
MorphoJ software from Klingenberg
GMM tools for Mathematica and R
EVAN toolbox

Online Morphometric, Image, and Scan Data

Digital Morphology Site (DigiMorph)
MorphoBrowser
Virtual Zooarchaeology of the Arctic

IU Natural History Collections

IU Paleontology Collection
Adams Zooarchaeological Collection
Glenn Black Lab of Archaeology
IU Herbarium

IU Paleo Collection on
FaceBook

Online Phylogenetic Data

CladeStore
TreeBase
MorphoBank
NCBI Taxonomy
Molecular Data from Extinct Species