I am delighted to announce that as of 15th September, I will be taking up my new position as Lecturer in Zoology at the University of New England, New South Wales Australia. I am going to be a part of the The Function, Evolution and Anatomy Research (FEAR) lab, bringing my expertise in Geometric Morphometrics and large-scale 3D datasets to the team of Functional Morphologists. I will also be teaching the Principals of Zoology course. I can't wait!
I've been hard at work these past few months on improving the 3D visualisation capabilities of geomorph, our R package for analysis of geometric morphometric data. Of note is the implementation of 3D Warping.
Version 2.0 of geomorph brings new developments in how shape deformations from 3D coordinate shape data can be viewed. I have implemented a set of neat functions for warping of 3D surface files (e.g., .ply files), which allows the user to visualise the shape deformations along Principal Component axes, Multivariate Regression slopes, Partial Least Squares axes and group differences, to name a few.
The new function warpRefMesh reads in a .ply ﬁle and landmark coordinates associated with this specimen, and uses the thin-plate spline method (Bookstein 1989) to warp the mesh into the shape deﬁned by a second set of landmark coordinates, usually those of the mean shape for a set of aligned specimens. When using this function for warping, it is highly recommended that the mean shape (derived from the users sample using mshape) is used as the reference for warping (see Rohlf 1998).
See my blog on geomorph.net for the workflow. But most importantly, lets look at some eyecandy!
My new postdoctoral position at Iowa State University is already being very fruitful.
I am now a co-author to the geometric morphometrics digitizing and analysis software in R, called geomorph. For a detailed look at what the software does, take a look at the CRAN pdf or this paper. In brief, the software package is designed to be used for digitizing 2D and 3D landmarks, and implementing many of the common (and some not so common) procedures and statistical analyses with these data.
Digitizing of landmarks and sliding surface semi-landmarks on three-dimensional structures was already implemented by my co-authors, using the vertices of 3D surface models (e.g. ply models). I have improved these existing functions to take full advantage of the enhanced plotting capabilities of PLY files with rgl (the ply files are read in and stored as objects of class Mesh3d) . Now the digitizing experience is more user friendly; the color detail of the meshes and the plotted faces allow better visualization of complex meshes, and the software is now compatible with functions in the Morpho R package. We welcome users to try out the new digitizing functions and tell us what they think! You can send me a message here (right) or visit the geomorph blog page.