-------- Original Message --------
Subject: Re: Outlines
Date: Fri, 24 Oct 2008 17:35:21 +0200
From: [EMAIL PROTECTED]
To: morphmet <[EMAIL PROTECTED]>
References: <[EMAIL PROTECTED]>
Check out George P.Lohmann's use of the Zahn-Rosskies algorithm for
outline coordinates on a closed curve. Lohmann studied planktic
foraminifers using an application of the extraction of latent roots
and vectors (he called his technique eigenshape analysis).
Lohmann, G. P. and Schweitzer, P. N. 1989. On eigenshape analysis-
Morphometrics in Systematic Biology Workshop (Ann Arbor, 1988). F. J.
Rohlf and F. L. Bookstein
Lohmann, G. P. 1983 Eigenshape analysis of microfossils. A general
morphometric procedure for describing changes in shape. Mathematical
Geology, 15, 659-672.
Quoting morphmet <[EMAIL PROTECTED]>:
-------- Original Message --------
Subject: Re: Outlines in tpsDig
Date: Thu, 23 Oct 2008 13:24:04 -0700 (PDT)
From: Matthew Burton-Kelly <[EMAIL PROTECTED]>
To: [email protected]
References: <[EMAIL PROTECTED]>
Have you tried using ImageJ to do automatic digitization? I've heard
that it works well for that.
Matt
On 23 Oct, 2008, at 1:51 PM, morphmet wrote:
-------- Original Message --------
Subject: Outlines in tpsDig
Date: Thu, 23 Oct 2008 11:39:20 -0700 (PDT)
From: Sarah Degroot <[EMAIL PROTECTED]>
To: <[email protected]>
I am trying to make my tps files multitask-- I have black & white
images and want to digitize outlines such that I can use the points
in both EFA and a sliding landmark analysis. However, some of
the specimens are fairly complex, such that I need at least 220
points to capture the outline adequately. I don't want to place
220 points by hand, especially since my preliminary analysis
involves over 570 specimens. I tried drawing a curve with
tpsdig, but that took 28 points (minimally), and it captured the
outline poorly (even though I resampled the curve with more
points). I'm also not eager to place even 28 points on each of
570+ specimens--there has to be a faster way.
It seems the easiest thing to do would be to use the outline tool
in tpsdig, but this tool appears to be inconsistent about where it
places the starting point. I click just to the right of where I
want the starting point, but when I look at the tps file, the
starting point is clearly somewhere else around the outline, and
usually nowhere near where I clicked. This is the case for both
tpsdig 2.09 and 1.40 (1.40 has given me a few other outline
anomalies, too, such as negative coordinates).
I need the starting position of the x-y coordinates for the outline
to be in the same place on all specimens because (1) I am not
correcting for starting position in EFA because I do not want the
outline rotated (they are all oriented the same way, but the long
axis is not necessarily the same), and (2) I want one fixed
"landmark" as a reference point for the sliding landmark analysis.
I'd like something similar to Perez et al.'s (2006; J. Anat. 208:
769-784) placement of semilandmarks around molars, although I'm not
quite sure how they did it. I can't imagine they placed all 80
points by hand (p. 772).
Suggestions are appreciated.
Sarah
sarah.degroot at cgu.edu
Graduate Student
Rancho Santa Ana Botanic Garden / Claremont Graduate University
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-----------------------------
Matthew Burton-Kelly
Graduate Student
Department of Geology and Geological Engineering
University of North Dakota
(802) 922-3696
[EMAIL PROTECTED]
http://uweb.und.nodak.edu/~matthew.burton.kelly/
--------------------------------------------
"About thirty years ago there was much talk that geologists ought only
to observe and not theorize; and I well remember someone saying that
at this rate a man might as well go into a gravelpit and count the
pebbles and describe the colors. How odd it is that anyone should not
see that all observation must be for or against some view if it is to
be of any service!"
-Charles Darwin, in an 1861 letter to Henry Fawcett.
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