Re: Re: [MORPHMET] Digitizing landmarks on live larvae

[Carmelo Fruciano]

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 ]
Sent: Tuesday, February 27, 2018 3:09 AM
To: MORPHMET 
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)?

Re: [MORPHMET] Digitizing landmarks on live larvae

[Avi Koplovich]

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 ] 
> Sent: Tuesday, February 27, 2018 3:09 AM 
> To: MORPHMET  
> 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
>  
> I'll be happy if you can advise on that. 
> Thank you, 
> Avi 
>
> -- 
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org 
> --- 
> You received this message because you are subscribed to the Google Groups 
> "MORPHMET" group. 
> To unsubscribe from this group and stop receiving emails from it, send an 
> email to morphmet+u...@morphometrics.org . 
>
>

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RE: [MORPHMET] Digitizing landmarks on live larvae

[f.james.rohlf]

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.porta...@gmail.com] 
Sent: Tuesday, February 27, 2018 3:09 AM
To: MORPHMET 
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
I'll be happy if you can advise on that.
Thank you,
Avi

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MORPHMET may be accessed via its webpage at http://www.morphometrics.org
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to morphmet+unsubscr...@morphometrics.org.

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--- 
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To unsubscribe from this group and stop receiving emails from it, send an email 
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