1. Introduction

This is an R implementation of the automated three-dimensional geometric morphometric methods developed in the PhD thesis of Jesus Puente. The utility of the auto3dgm methods was illustrated in (Boyer et al., Anatomical Record) and the R code was written by Chris Glynn.

The R package can be downloaded here.

2. Instructions

To use auto3dgm the an an R distribution of at least version 3.0 is required in addition to the following R libraries installed: Matrix, clue, linprog, igraph, MASS.

Once these libraries are installed. Install auto3dgm.tar.gz

The following tutorial provides an example of how to use auto3dgm.

3. A Brief Tutorial

In this example the first five teeth taken from the set of fifteen teeth are aligned. The meshes to be aligned should be stored as off (object file format) files with an .off designation.

Install Matrix, clue, linprog, igraph, MASS, and auto3dgm.tar.gz

Download the following R code: Web_Example.R

Edit the following line in Web_Example.R
Output_dir = "/Users/sayanm/Desktop/Bones"
to
Output_dir = "YOUR_DIR"
where YOUR_DIR is the path to the directory you want the outputs of the program to be written.

Outputs

When you source/run Web_example.R you will get the following outputs in the Output_dir you specify:

Aligned_Shapes: the aligned meshes of the five teeth, for example the second tooth

MST.jpg: the jpg image of the minimum spanning tree of the five teeth

alignment.off: the mesh file of the five aligned teeth of the lower resolution images, in this case 64 points. There is a marker to designate the first shape and there are ten shapes to a row, see Figure 1 .The shapes are ordered according to the sequence of shape ids specified in Web_example.R

alignment_2.off: the mesh file of the five aligned teeth of the higher resolution images, in this case 128 points. There is a marker to designate the first shape and there are ten shapes to a row, see Figure 2.The shapes are ordered according to the sequence of shape ids specified in Web_example.R

map.off: a 3-dimensional representation of the minimum spanning tree, Figure 3

morphologika.txt: a morphologika file for the lower sampling resolution

morphologika_2.txt: a morphologika file for higher sampling resolution

morphologika_unscaled.txt: an unscaled morphologika file for the lower sampling resolution

morphologika_2_unscaled.txt: an unscaled morphologika file for higher sampling resolution

Inputs

The data used in this example consist of

001.off,...,015.off: fifteen teeth that are not aligned,an example tooth

lowres: a directory of low resolution files for the fifteen teeth

subsampled: a directory of subsampled files for the fifteen teeth