-------- Original Message --------
Subject: RE: error in digitising landmarks
Date: Thu, 3 Feb 2011 15:00:52 -0500
From: Garrido-Varas, Claudia <[email protected]>
To: [email protected] <[email protected]>
Dear Carmelo,
Thank you very much for your email. I will try what you say.
Yes, I said reliable because the landmarks that I am using have been
chosen by myself, so, I want to test them and want to test my personal
error, and see that maybe I should use only the ones that have the least
error.
Once that I know I have picked up the proper landmarks I will compare
the shape change in different individuals, see if sex has an impact and
look at bilateral asymmetry.
Another thing that I would like to ask is if I need to have a scale,
because in the morhoJ program one never needs to input which pair of
landmarks are the ones of the scale, I get very confused in how centroid
size can be computed if I don't give the scale.
I will start with what you said, and hopefully I will understand.
Thanks again,
Claudia
________________________________________
From: morphmet [[email protected]]
Sent: 03 February 2011 19:36
To: morphmet
Subject: Re: error in digitising landmarks
-------- Original Message --------
Subject: Re: error in digitising landmarks
Date: Thu, 3 Feb 2011 13:59:52 -0500
From: Carmelo Fruciano <[email protected]>
To: [email protected]
Dear you,
I am new to GM, I am working with a hand bone (third metacarpal) and
I have chosen 9 landmarks, I also included a ruler on the pictures a
scale and gave 2 landmarks more to mark 10mm.
I took one picture and copied this file 29 times, digitised the
landmarks with TPSdig, made one file with the 30 observations. Then
I used MorphoJ and did a procrustes fit then find outliers and the
maximum distance was 0.00011.
What I really want to do is to calculate de error after digitising
30 times the next image, to see if my landmarks are reliable, and I
am not sure how to do it, I tried to run a procrustes ANOVA, but
don't understand why I need to do this, and it asks me for
classifiers and I am not sure what classifier to include since they
are all the same image.
Dear Claudia,
first of all I have to say I'm really impressed that you took the time
and made the effort of digitizing 30 times the same bone: I would
stick to just a few repetitions but, if you can make the same thing
with a reasonable number of different specimens that would be great
(other than impressive due to the effort that it requires, even if
I've been obsessed with error I never took it to this level!).
I think that the idea behind many procedures to evaluate error is to
relate the variation within specimens (that is, variation associated
with digitization) to variation between specimens (that is, probably
the real biological variation you're interested in)...the basic idea
being that if variation due to digitization is small relative to
biological signal you can be pretty confident about the analysis of
biological variation...
So you would need to carry out this procedure (or a less stressing one
with less repetitions) on more specimens to relate the two sources of
variation.
With MorphoJ I think you would have to put a classifier for the
specimen and a classifier for repetition (but it's ages I don't do
this in MorphoJ so I'm not sure I remember right)...
However, these procedures calculate how reliable is "overall" your
digitization. In your particular case, you might have higher error at
certain landmarks, lower error at other landmarks (and you might
decide that, in your opinion, landmarks with higher
digitization-induced variation must be discarded). For this, you
probably want to check variation at each landmark. A simple and
"exploratory" approach might be to check plots of your digitized
landmarks after Procustes superimposition to see if variation at
certain landmarks is too large or biased. Ideally, points would be
clustered tightly together and form a "circle" (not an ellipse).
With your one specimen-30 repetitions dataset you could use TPSRelw,
carry out a Procustes superimposition, then click to display the
consensus and choose, in the new window, the menu "Options" turning
"on" the option "Points".
Of course, you're not guaranteed that patterns of error do not vary
among specimens, so I would redo it with a few other specimens to
check...
I'm saying this because you talk about seeing "if my landmarks are
reliable" so probably you are more concerned about choice of landmarks
other than "overall error"...
I hope this helps
Carmelo
--
Carmelo Fruciano
Dipartimento di Biologia
University of Catania
Tel. +39 095 7306023
Cell. +39 349 5822831
e-mail [email protected]
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