----- Forwarded message from "Otarola-Castillo, Erik"
<[email protected]> -----
Date: Thu, 14 Mar 2013 11:14:32 -0400
From: "Otarola-Castillo, Erik" <[email protected]>
Reply-To: "Otarola-Castillo, Erik" <[email protected]>
Subject: RE: Software for landmarks
To: "[email protected]" <[email protected]>
Will,
The R package geomorph might solve both your problems. First, geomorph includes
functions to digitize points, curves, and surface landmarks from imported 3D
surface scans. The surface scans can be formatted as .ply, .wrl, or text files
formatted using various delimiter-separated values (e.g., comma, tab, etc.).
Second, the “gpagen()” function conducts GPA of 2 and 3-dimensional landmarks
(points) and semilandmarks (curve and surface points) through either Procrustes
distance or bending energy minimization.
You can download geomorph and page through the manual (geomorph.pdf) from the
Comprehensive R Archive Network (CRAN):
http://cran.r-project.org/web/packages/geomorph/index.html
We also created a blog: www.geomorph.net, where you might be able to find
helpful updates, current problems, solutions, etc.
Cheers,
Erik
_____________________________________________
Erik Otárola-Castillo
Department of Human Evolutionary Biology
Department of Statistics
Harvard University
11 Divinity Ave, Cambridge, MA 02138
Phone: 631-796-7331
R package ‘geomorph’ blog: http://www.geomorph.net/
Website: www.people.fas.harvard.edu/~eotarolacastillo
______________________________________________
-----Original Message-----
From: [email protected]
[mailto:[email protected]]
Sent: Wednesday, March 13, 2013 11:44 PM
To: [email protected]
Subject: Software for landmarks
----- Forwarded message from William Ary <[email protected]> -----
Date: Wed, 13 Mar 2013 17:25:31 -0400
From: William Ary <[email protected]>
Reply-To: William Ary <[email protected]>
Subject: Software for landmarks
To: [email protected]
Hello, everyone-
My lab is using segmented high-resolution CT images to generate models for
geometric morphometrics. I am having problems doing the following:
1. Finding homologous landmarks for smooth bones that have no intersections
with other bones. This forces us to use less repeatable things like ridges and
prominences that are harder to place landmarks on in a consistent manner. I
plan to use a sliding semilandmark method to solve this problem, possibly a 3-D
version as I have heard that the Geomorph package in R handles 3D
semilandmarks. Other packages like SPHARM, MorphoJ, Morphologika etc. are in
the running if they can solve my landmark issue.
2. Picking a software for placing landmarks that works with our large
high-resolution models with millions of elements. I have sampled the vast array
of programs to some degree, having tried Paraview, Meshlab, MiniMagics, and our
segmentation software, Analyze. I have encountered problems with all of them as
follows:
Paraview- Doesn't record points, cannot find way to place multiple points,
doesn't record Cartesian 3-space coordinates.
Meshlab- Looked great but bogs down or crashes when placing points, likely due
to model complexity
MiniMagics- Could not figure out how to place multiple landmarks/model size
issues. Investigating if MIMICS is better.
Analyze- Points disappear on the topology of the model and are hard to see once
the model is moved.
After all this, I welcome any suggestions you may have on which programs allow
picking landmarks/semilandmarks on high resolution models and how to generate
landmarks on our smooth bones. We are hoping there is an alternative to
coarsening our models. I would be especially grateful to know how to go about
placing a series of sliding semilandmarks. I have read some papers on this, but
suggested reading is always appreciated!
Many thanks!
Will Ary
Master's candidate
San Diego State University
[email protected]
----- End forwarded message -----
----- End forwarded message -----
