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 2016]

Overview of Wolfram's Mathematica.
[Download slides] [Assignment 1 (PDF) (NB)] 

Basics of programming using Mathematica.
[Download slides] [Assignment 2 (PDF) (NB)] 

Basics of performing a Geometric Morphometric Analysis from start to finish.
[Download slides] [Assignment 3 on Faces(PDF) (NB)] 

Results of analysis of face photographs and explanation of morphospace.
[Download slides] 

Explanation of Procrustes superimposition and principal components analysis (morphospace construction).
[Download slides] [Assignment 4 (PDF) (NB)] 

Introduction to statistical analyses commonly used in geometric morphometrics.
[Download slides] 

Overview of designing bootstrapping and randomization tests, plus twoblock partial least squares.
[Download slides] [Assignment 5 (PDF) (NB)] ; 

Introduction to semilandmarks and outlines analysis, plus EDMA for localizing which part of a shape varies.
[Download slides] [Assignment 6 (PDF) (NB)] 

A little about making graphics in Mathematica.
[Download slides] ; 

Building trees from morphometrics and comments on the relationship between morphometric variation and phylogenetic history.
[Download slides]
[Assignment 7 simulating evolution (PDF) (NB)]


Models of phenotypic evolution, simulating evolution, adaptive landscapes, and independent contrasts.
[Download slides]
[Assignment 8 phylogeny and morphometrics (PDF) (NB)]
[Assignment 9 phylogenetic correlations (PDF) (NB)]


Manipulating images in Mathematica, collecting landmarks, and morphing images.
[Assignment 10 image morphing (PDF)]


Mathematica Morphometrics Package
Download Geometric Morphometrics for Mathematica and other Mathematica packages here
Handouts
Mathematica Quick Guide
Manipulating Data In Mathematica
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
Mammal tree [Newick format]
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
