Dear Avi,
elaborating further also based on Jim's answer, some open
questions/considerations that you might entertain are:
- if you intend to use sliding semilandmarks (which in general sounds
like a good idea), how are certain points such as 1,39,41,55 going to be
slid? (i.e., relative to which other points?) - Notice that in the paper
you cited the points on the tail are bounded by fixed landmarks. In that
respect, I wonder if maybe your point 1 could be characterized as a
fixed homologous point (you define it as "dorsal connection of the tail
fin")
- I guess that whether the relative position of the eye is useful
depends on your particular biological question; as Jim said, it might
actually be interesting; an alternative to using a fixed landmark in the
eye (at the center of it, I assume) would be to use sliding
semilandmarks along the contour of the eye. These can be slid relative
to each other and can give you information on the relative size of the
eye (which may or may not be of interest for your specific question).
This seems the solution adopted by Levis et al. (at least looking at
their figure). Another option with respect to that would also be
removing the extra semilandmarks after sliding considering them "helper
points" (see, for instance, fig. 1a in Fruciano et al. 2016 - Ecology
and Evolution)
- If you can model variation due to arching with a relatively simple
model, there are methods to account for it, including the one
implemented in tpsUtil and the one developed by Valentin et al. 2008 -
Journal of Fish Biology (you can find a discussion of these also in my
review on measurement error Fruciano 2016 - Development Genes and
Evolution). Collecting data as accurately as possible in the first place
is the best idea (and you're doing that), but substantial artifactual
variation might be still present in your data despite of your best
efforts (if at all possible, consider also quantifying how similar
repeated pictures of the same specimens are; you can read about this
also in the review I mentioned above)
I hope this helps.
Best,
Carmelo
Il 28/02/2018 9:30 PM, Avi Koplovich ha scritto:
Hi James,
Thank you for your fast answer.
I'll continue to mark the landmarks as separated sublets, i.e. head and
tail.
1. Is it ok to use landmark 40 (intersection of the side line and the
dorsal connection of the tail fin) as a common mark point to create
a comb fan for both tail and head?
2. Another question: Is this landmark 40 can be treated as fixed
landmark as it is restricted by both x and y axis?
3. Can I use landmarks 20 (tail tip) and 48 (head tip) as fixed
landmarks in an ontogenetic experiment?
4. Last question: Can/Should I use the eye as a fixed landmark for the
head (i.e. can it interfere with interpreting the head contour)?
p.s. I saw your forum message here on updating tpsdig 2.31 and already
updated it.
Many thanks,
Avi
On Wednesday, February 28, 2018 at 8:51:39 PM UTC+2, f.james.rohlf wrote:
Bending of long slender organisms (or other structures) can be an
important practical problem. Changes due to bending could dominate
the results. Separating sets of landmarks into more rigid sublets
can help as long as the endpoints of the subsets are homologous and
not arbitrary or dependent on the bending of a particular specimen.
The tpsUtil program has an "unending" option if one has a subset of
points that one knows should be in a straight line. That would be
difficult for larvae.
Note: I see you are using ver. 2.30 of tpsDig. Version 2.31 is
current. I do try to keep fixing bugs so It can be useful to stay
current.
____________________________________________
F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution
Research Professor, Anthropology
Stony Brook University
-----Original Message-----
From: Avi Koplovich [mailto:netbird....@gmail.com <javascript:>]
Sent: Tuesday, February 27, 2018 3:09 AM
To: MORPHMET <morp...@morphometrics.org <javascript:>>
Subject: [MORPHMET] Digitizing landmarks on live larvae
Hi,
I've started a new project and came to the point of marking fixed
and semi landmarks.
Not all pictures are satisfying, mostly because of the posture of
the larvae during photographing (sometimes raising it's tail). So in
order to reduce the noise by the animal posture, I thought it would
be helpful to separate head and tail as was done in Levis et. al.
2016, Biol. J. Linn. Soc.
I'm using the landmarks 1, 20 and 48 as fixed landmarks, and all the
rest are semi landmarks. I'm not sure of using 20 and 48 as fixed
landmarks, and I wonder if I can use landmark 40 as fixed landmark
since it is restricted by both x (side line) and y (dorsal
connection of the tail fin). Can/Should I use the eye as a fixed
landmark for the head (i.e. can it interfere with interpreting the
head contour)?
Here is an example to show what I mean:
https://drive.google.com/file/d/1iO7lCN3ZCtV7DF9vsczkb_EYoSli1Orr/view?usp=sharing
<https://drive.google.com/file/d/1iO7lCN3ZCtV7DF9vsczkb_EYoSli1Orr/view?usp=sharing>
I'll be happy if you can advise on that.
Thank you,
Avi
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