----- Forwarded message from andrea cardini <[email protected]> -----
Date: Fri, 4 Oct 2013 06:51:34 -0400
From: andrea cardini <[email protected]>
Reply-To: andrea cardini <[email protected]>
Subject: Re: 3D semilandmark software pipeline
To: [email protected]
Will, I've little experience with 3D sliding but
in 2D I slide the points in TPSRelw, restore size
and then import them in MorphoJ (or other GMM software) for specific analyses.
With 3D data, I only played with semilandmarks on
curves, slid them in R, rescaled (so that when
they are re-superimposed I get also centroid size
- CS - in MorphoJ or Morphologika) and imported them (in MorphoJ/Morphologika).
Maybe, check that shape distances are unchanged
when you resuperimpose the data in, say, MorphoJ,
compared to the shape data after the
superimposition and sliding in another software.
The way CS was computed by the software you used
for sliding could, possibly, lead to small
differences when you use it to restore scale and
then redo a simple GPA in a 'non-sliding
software'. However, I would expect such differences to be very small.
The other option is to import the 'slid shape
coordinates' and import CS as a covariate. Then,
be careful not to think that what MorphoJ or
Morphologika call CS is the actual CS: it will be
a series of numbers which are all 1 (except for
decimal approx.). The real CS will be the covariate.
Also, be careful as the real dimensionality of
the data will be less than # of landmarks by 2
(or 3) minus 4 (or 7). If you do a PCA and
discard PCs with zero variance, you should have less issues.
Good luck
Andrea
At 03:41 03/10/2013, you wrote:
>----- Forwarded message from William Ary <[email protected]> -----
>
>Date: Mon, 30 Sep 2013 01:28:40 -0400
>From: William Ary <[email protected]>
>Reply-To: William Ary <[email protected]>
>Subject: 3D semilandmark software pipeline
>To: [email protected]
>
>Hello all-
>
>I am using a 3D morphometrics software pipeline
>that begins with UC Davis Landmark and ends with
>MorphoJ and I want to adapt it for use with
>semilandmarks. Are there any other softwares I
>need to slide my semilandmarks as assigned with
>Landmark software before importing them for a
>procrustes fit and PCA? If so, are they
>compatible with MorphoJ or must it be done in
>another package? I am considering using Shapes
>or Geomorph in R, but I don't know if it is necessary to switch over.
>
>Thanks!
>
>Will Ary
>MS Candidate, Berta Lab
>Department of Biology
>San Diego State University
><mailto:[email protected]>[email protected]
>
>
>
>----- End forwarded message -----
>
>
Dr. Andrea Cardini
Researcher in Animal Biology, Dipartimento di
Scienze Chimiche e Geologiche, Università di
Modena e Reggio Emilia, l.go S. Eufemia 19, 41121 Modena, Italy
Honorary Fellow, Centre for Anatomical and Human
Sciences, University of Hull, Cottingham Road,
Hull, HU6 7RX, UK & University of York, Heslington, York YO10 5DD, UK
Adjunct Associate Professor, Centre for Forensic
Science , The University of Western Australia, 35
Stirling Highway, Crawley WA 6009, Australia
E-mail address: [email protected], [email protected]
WEBPAGE: http://sites.google.com/site/hymsfme/drandreacardini
FREE Yellow BOOK on Geometric Morphometrics:
http://www.italian-journal-of-mammalogy.it/issue/view/405
or full volume at:
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf
Editorial board for:
Zoomorphology:
http://www.springer.com/life+sciences/animal+sciences/journal/435
Journal of Zoological Systematics and
Evolutionary Research: http://www.wiley.com/bw/journal.asp?ref=0947-5745&site=1
Hystrix, the Italian Journal of
Mammalogy: http://www.italian-journal-of-mammalogy.it/
----- End forwarded message -----
