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

[andrea cardini]

I start with a "disclaimer" (and many apologies!): I read only the last 
two messages (by Jim and Carmelo), as I am stuck with teaching in this 
period.


I'd like only to suggest a reference on N vs the number of variables (in 
morphometrics but not necessarily only in this field). It's a difficult 
but very important and most interesting paper on this issue:
Bookstein, 2017, Evolutionary Biology: A Newly Noticed Formula Enforces 
Fundamental Limits on Geometric Morphometric Analyses

DOI 10.1007/s11692-017-9424-9

Cheers

Andrea

On 14/03/18 04:05, f.james.rohlf wrote:
Actually the rule is that the number of specimens should be larger than 
the number of variables 2p-4 not p landmarks in the case of 2D data.




__
F. James Rohlf, Distinguished Prof. Emeritus
Dept. Anthropology and Ecology & Evolution
Stonybrook University

 Original message 
From: Carmelo Fruciano <c.fruci...@unict.it>
Date: 3/12/18 9:51 PM (GMT-10:00)
To: MORPHMET <morphmet@morphometrics.org>
Subject: Re: ***SPAM*** [MORPHMET] Re: Digitizing landmarks on live larvae

Dear Avi,

I guess it's hard to formulate any rule of thumb.

Some analyses might not be defined if the number of variables exceed the 
number of observations. Some other analyses might be defined (there is 
many distance-based analyses nowadays which circumvent that problem).


However, whether a given analysis is defined doesn't mean that the 
inference is necessarily accurate. I guess it depends on what you plan 
to test/measure and the effect size you expect.



Andrea Cardini has some papers that can give you some hint on this, such as:

Cardini & Elton 2007 - Zoomorphology

Cardini et al. 2015 - Zoomorphology

Cardini & Elton 2017 - Hystrix

They should be downloadable from his website 
https://sites.google.com/site/alcardini/home/pubs




Obviously, having an idea of variation on your own data would be better.
I hope this helps.
Carmelo




On 3/12/2018 8:27 PM, Avi Koplovich wrote:

Hi Carmelo,
Thank you for those answers.
One more question please:
I know that the number of specimens should exceed the number of the 
total landmarks (fixed-landmarks + semi-landmarks). Is there a rule of 
thumb of by how much or what ratio between specimens to semi-landmarks 
one should keep?


Thank you,

Avi


On Sunday, March 11, 2018 at 5:15:24 PM UTC+2, Carmelo Fruciano wrote:



Il 6/03/2018 4:44 PM, Avi Koplovich ha scritto:
> Hi Carmelo,
> Thank you for your answer.
> My project tests for the influence of kairomones of a predator
fish on
> the morphology of Salamander larvae during its development. To
do this,
> I take pictures every other week of larvae spawned from six
different
> females and assigned to 3 treatments: No fish, 3 caged fish, 6
caged fish.

Hi Avi,
it sounds like an interesting experiment. I will try to answer to
your
questions but keeping in mind that I'm not very knowledgeable on
salamander development.

>  1. I intend to use landmark 1 (dorsal connection of the tail
fin) as a
>     fixed factor. But I thought I may be able to use the tail tip
>     (landmark 20) and head tip (landmark 48) as fixed landmarks
as well.
>     Do you think it's ok in an ontogeny experiment?

I guess it will depend on how long into ontogeny you will track the
larvae and whether or not that point will "disappear" over ontogeny
and/or slide unreasonably (depends also on your question). You, being
knowledgeable on their biology, are the best judge on that.

> If not, do you think
>     it's ok to slide all semi-landmarks of the tail on landmark
1, and
>     all head semi-landmarks on an eye landmark? Since the eye
isn't part
>     of the head contour, is it ok if I slide one semi-landmark
to the
>     eye and all rest semi-landmarks of the head one to each
other as a
>     closed shape?

The point(s) slid relative to the eye won't be sliding along the
direction tangent to the curve you want to approximate (i.e., the
curvature of the head). A good starting point on the method could be
Gunz & Mitteroecker 2013 - Hystrix

>  2. Is it ok if landmarks 1 and 39 slid relative to each other
as well
>     as 41 and 55, since both describe a closed shape?

It's not particularly desirable (see answer above).

>  3. Another worry I have is that landmark 40 which I used to
create the
>     comb fan for both the tail and the head is too far from both
of them
>     so it doesn't bypass the bending.
>  4. I'm affraid I don't fully understand why landmark 40 can not be
>     treated as a fixed landmark. In the book of Zelditch 2004,
she says
>     that one of the basic differences between fixed-landmark and
>     semi-landmark i

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

[Avi Koplovich]

Hi,
Thank you both!
I asked this question since I guess that deciding on how many 
semi-landmarks I can digitize isn't only a matter of how complex the 
specimen is, or my willing to estimate missing data (Gunz & Mitteroecker, 
2013), but also the number of specimens I posses. So just to clarify Jim's 
answer: 2p-4 means that having for instance 300 specimens I can use a total 
of 154 landmarks in 2D?
Thanks,
Avi

On Wednesday, March 14, 2018 at 5:06:03 AM UTC+2, f.james.rohlf wrote:
>
> Actually the rule is that the number of specimens should be larger than 
> the number of variables 2p-4 not p landmarks in the case of 2D data.
>
>
>
> __
> F. James Rohlf, Distinguished Prof. Emeritus 
> Dept. Anthropology and Ecology & Evolution 
> Stonybrook University
>
>  Original message 
> From: Carmelo Fruciano <c.fru...@unict.it > 
> Date: 3/12/18 9:51 PM (GMT-10:00) 
> To: MORPHMET <morp...@morphometrics.org > 
> Subject: Re: ***SPAM*** [MORPHMET] Re: Digitizing landmarks on live larvae 
>
> Dear Avi,
>
> I guess it's hard to formulate any rule of thumb.
>
> Some analyses might not be defined if the number of variables exceed the 
> number of observations. Some other analyses might be defined (there is many 
> distance-based analyses nowadays which circumvent that problem).
>
> However, whether a given analysis is defined doesn't mean that the 
> inference is necessarily accurate. I guess it depends on what you plan to 
> test/measure and the effect size you expect.
>
>
> Andrea Cardini has some papers that can give you some hint on this, such 
> as:
>
> Cardini & Elton 2007 - Zoomorphology
>
> Cardini et al. 2015 - Zoomorphology
>
> Cardini & Elton 2017 - Hystrix
>
> They should be downloadable from his website 
> https://sites.google.com/site/alcardini/home/pubs
>
>
> Obviously, having an idea of variation on your own data would be better.
> I hope this helps.
> Carmelo
>
>
>
>
> On 3/12/2018 8:27 PM, Avi Koplovich wrote:
>
> Hi Carmelo,
> Thank you for those answers.
> One more question please:
> I know that the number of specimens should exceed the number of the total 
> landmarks (fixed-landmarks + semi-landmarks). Is there a rule of thumb of 
> by how much or what ratio between specimens to semi-landmarks one should 
> keep? 
>
> Thank you,
>
> Avi
>
> On Sunday, March 11, 2018 at 5:15:24 PM UTC+2, Carmelo Fruciano wrote: 
>>
>>
>>
>> Il 6/03/2018 4:44 PM, Avi Koplovich ha scritto: 
>> > Hi Carmelo, 
>> > Thank you for your answer. 
>> > My project tests for the influence of kairomones of a predator fish on 
>> > the morphology of Salamander larvae during its development. To do this, 
>> > I take pictures every other week of larvae spawned from six different 
>> > females and assigned to 3 treatments: No fish, 3 caged fish, 6 caged 
>> fish. 
>>
>> Hi Avi, 
>> it sounds like an interesting experiment. I will try to answer to your 
>> questions but keeping in mind that I'm not very knowledgeable on 
>> salamander development. 
>>
>> >  1. I intend to use landmark 1 (dorsal connection of the tail fin) as a 
>> > fixed factor. But I thought I may be able to use the tail tip 
>> > (landmark 20) and head tip (landmark 48) as fixed landmarks as 
>> well. 
>> > Do you think it's ok in an ontogeny experiment? 
>>
>> I guess it will depend on how long into ontogeny you will track the 
>> larvae and whether or not that point will "disappear" over ontogeny 
>> and/or slide unreasonably (depends also on your question). You, being 
>> knowledgeable on their biology, are the best judge on that. 
>>
>> > If not, do you think 
>> > it's ok to slide all semi-landmarks of the tail on landmark 1, and 
>> > all head semi-landmarks on an eye landmark? Since the eye isn't 
>> part 
>> > of the head contour, is it ok if I slide one semi-landmark to the 
>> > eye and all rest semi-landmarks of the head one to each other as a 
>> > closed shape? 
>>
>> The point(s) slid relative to the eye won't be sliding along the 
>> direction tangent to the curve you want to approximate (i.e., the 
>> curvature of the head). A good starting point on the method could be 
>> Gunz & Mitteroecker 2013 - Hystrix 
>>
>> >  2. Is it ok if landmarks 1 and 39 slid relative to each other as well 
>> > as 41 and 55, since both describe a closed shape? 
>>
>> It's not particularly desirable (see answer above). 
>>
>> >

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

[f.james.rohlf]

Actually the rule is that the number of specimens should be larger than the 
number of variables 2p-4 not p landmarks in the case of 2D data.


__F. James Rohlf, Distinguished Prof. Emeritus Dept. 
Anthropology and Ecology & Evolution Stonybrook University
 Original message From: Carmelo Fruciano <c.fruci...@unict.it> 
Date: 3/12/18  9:51 PM  (GMT-10:00) To: MORPHMET <morphmet@morphometrics.org> 
Subject: Re: ***SPAM*** [MORPHMET] Re: Digitizing landmarks on live larvae 

Dear Avi,
I guess it's hard to formulate any rule of thumb.
Some analyses might not be defined if the number of variables
  exceed the number of observations. Some other analyses might be
  defined (there is many distance-based analyses nowadays which
  circumvent that problem).
However, whether a given analysis is defined doesn't mean that
  the inference is necessarily accurate. I guess it depends on what
  you plan to test/measure and the effect size you expect.



Andrea Cardini has some papers that can give you some hint on
  this, such as:
Cardini & Elton 2007 - Zoomorphology


Cardini et al. 2015 - Zoomorphology
Cardini & Elton 2017 - Hystrix


They should be downloadable from his website
  https://sites.google.com/site/alcardini/home/pubs






Obviously, having an idea of variation on your own data would be
better.

I hope this helps.

Carmelo









On 3/12/2018 8:27 PM, Avi Koplovich
  wrote:



  Hi Carmelo,

Thank you for those answers.

One more question please:

I know that the number of specimens should exceed the number of
the total landmarks (fixed-landmarks + semi-landmarks). Is there
a rule of thumb of by how much or what ratio between specimens
to semi-landmarks one should keep?
Thank you,
Avi




On Sunday, March 11, 2018 at 5:15:24 PM UTC+2, Carmelo Fruciano
wrote:

  

  

  Il 6/03/2018 4:44 PM, Avi Koplovich ha scritto:
  

  > Hi Carmelo,
  

  > Thank you for your answer.
  

  > My project tests for the influence of kairomones of a
  predator fish on 

  > the morphology of Salamander larvae during its
  development. To do this, 

  > I take pictures every other week of larvae spawned from
  six different 

  > females and assigned to 3 treatments: No fish, 3 caged
  fish, 6 caged fish.
  

  

  Hi Avi,
  

  it sounds like an interesting experiment. I will try to answer
  to your 

  questions but keeping in mind that I'm not very knowledgeable
  on 

  salamander development.
  

  

  >  1. I intend to use landmark 1 (dorsal connection of the
  tail fin) as a
  

  >     fixed factor. But I thought I may be able to use the
  tail tip
  

  >     (landmark 20) and head tip (landmark 48) as fixed
  landmarks as well.
  

  >     Do you think it's ok in an ontogeny experiment?
  

  

  I guess it will depend on how long into ontogeny you will
  track the 

  larvae and whether or not that point will "disappear" over
  ontogeny 

  and/or slide unreasonably (depends also on your question).
  You, being 

  knowledgeable on their biology, are the best judge on that.
  

  

  > If not, do you think
  

  >     it's ok to slide all semi-landmarks of the tail on
  landmark 1, and
  

  >     all head semi-landmarks on an eye landmark? Since the
  eye isn't part
  

  >     of the head contour, is it ok if I slide one
  semi-landmark to the
  

  >     eye and all rest semi-landmarks of the head one to
  each other as a
  

  >     closed shape?
  

  

  The point(s) slid relative to the eye won't be sliding along
  the 

  direction tangent to the curve you want to approximate (i.e.,
  the 

  curvature of the head). A good starting point on the method
  could be
  

  Gunz & Mitteroecker 2013 - Hystrix
  

  

  >  2. Is it ok if landmarks 1 and 39 slid relative to each
  other as well
  

  >     as 41 and 55, since both describe a closed shape?
  

  

  It's not particularly desirable (see answer above).
  

  

  >  3. Another worry I have is that landmark 40 which I u

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

[Carmelo Fruciano]

Dear Avi,

I guess it's hard to formulate any rule of thumb.

Some analyses might not be defined if the number of variables exceed the 
number of observations. Some other analyses might be defined (there is 
many distance-based analyses nowadays which circumvent that problem).


However, whether a given analysis is defined doesn't mean that the 
inference is necessarily accurate. I guess it depends on what you plan 
to test/measure and the effect size you expect.



Andrea Cardini has some papers that can give you some hint on this, such as:

Cardini & Elton 2007 - Zoomorphology

Cardini et al. 2015 - Zoomorphology

Cardini & Elton 2017 - Hystrix

They should be downloadable from his website 
https://sites.google.com/site/alcardini/home/pubs




Obviously, having an idea of variation on your own data would be better.
I hope this helps.
Carmelo




On 3/12/2018 8:27 PM, Avi Koplovich wrote:

Hi Carmelo,
Thank you for those answers.
One more question please:
I know that the number of specimens should exceed the number of the 
total landmarks (fixed-landmarks + semi-landmarks). Is there a rule of 
thumb of by how much or what ratio between specimens to semi-landmarks 
one should keep?


Thank you,

Avi


On Sunday, March 11, 2018 at 5:15:24 PM UTC+2, Carmelo Fruciano wrote:



Il 6/03/2018 4:44 PM, Avi Koplovich ha scritto:
> Hi Carmelo,
> Thank you for your answer.
> My project tests for the influence of kairomones of a predator
fish on
> the morphology of Salamander larvae during its development. To
do this,
> I take pictures every other week of larvae spawned from six
different
> females and assigned to 3 treatments: No fish, 3 caged fish, 6
caged fish.

Hi Avi,
it sounds like an interesting experiment. I will try to answer to
your
questions but keeping in mind that I'm not very knowledgeable on
salamander development.

>  1. I intend to use landmark 1 (dorsal connection of the tail
fin) as a
>     fixed factor. But I thought I may be able to use the tail tip
>     (landmark 20) and head tip (landmark 48) as fixed landmarks
as well.
>     Do you think it's ok in an ontogeny experiment?

I guess it will depend on how long into ontogeny you will track the
larvae and whether or not that point will "disappear" over ontogeny
and/or slide unreasonably (depends also on your question). You, being
knowledgeable on their biology, are the best judge on that.

> If not, do you think
>     it's ok to slide all semi-landmarks of the tail on landmark
1, and
>     all head semi-landmarks on an eye landmark? Since the eye
isn't part
>     of the head contour, is it ok if I slide one semi-landmark
to the
>     eye and all rest semi-landmarks of the head one to each
other as a
>     closed shape?

The point(s) slid relative to the eye won't be sliding along the
direction tangent to the curve you want to approximate (i.e., the
curvature of the head). A good starting point on the method could be
Gunz & Mitteroecker 2013 - Hystrix

>  2. Is it ok if landmarks 1 and 39 slid relative to each other
as well
>     as 41 and 55, since both describe a closed shape?

It's not particularly desirable (see answer above).

>  3. Another worry I have is that landmark 40 which I used to
create the
>     comb fan for both the tail and the head is too far from both
of them
>     so it doesn't bypass the bending.
>  4. I'm affraid I don't fully understand why landmark 40 can not be
>     treated as a fixed landmark. In the book of Zelditch 2004,
she says
>     that one of the basic differences between fixed-landmark and
>     semi-landmark is the degree of freedom, while fixed has two
because
>     it is docked on both X and Y axes while semi only on one of
them
>     (depending on the nature of the specific fan). Please
correct me if
>     I'm wrong, but what if I use the side line of the larvae
(which is
>     an anatomical/homologous feature) as my X axis and use the Y
>     component of landmark 1 (dorsal connection of the tail fin)
to dock
>     landmark 40 on the Y axis? Is it wrong because of the
dependency of
>     landmark 40 on landmark 1 regarding the Y coordinate?

I think Don has covered these two very well.

>  5. Emma Sherratt told me she straightened the bent tail-body
using TPS
>     software in her paper Sherratt et al. 2017 - Nature ecology &
>     evolution. In the supplementary material of her paper she
wrote:
>     "To correct for dorso-ventral bending in the landmark
configurations
>     (caused by the joint of the tail with the head/body), we
used the
>     ‘unbend specimens’ function of tpsUtil v.1.86 (Rohlf 2015). The
>     landmark configurations for each specimen were transformed
using the
>     

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

[Avi Koplovich]

Hi Carmelo,
Thank you for those answers.
One more question please:
I know that the number of specimens should exceed the number of the total 
landmarks (fixed-landmarks + semi-landmarks). Is there a rule of thumb of 
by how much or what ratio between specimens to semi-landmarks one should 
keep?

Thank you,

Avi

On Sunday, March 11, 2018 at 5:15:24 PM UTC+2, Carmelo Fruciano wrote:
>
>
>
> Il 6/03/2018 4:44 PM, Avi Koplovich ha scritto: 
> > Hi Carmelo, 
> > Thank you for your answer. 
> > My project tests for the influence of kairomones of a predator fish on 
> > the morphology of Salamander larvae during its development. To do this, 
> > I take pictures every other week of larvae spawned from six different 
> > females and assigned to 3 treatments: No fish, 3 caged fish, 6 caged 
> fish. 
>
> Hi Avi, 
> it sounds like an interesting experiment. I will try to answer to your 
> questions but keeping in mind that I'm not very knowledgeable on 
> salamander development. 
>
> >  1. I intend to use landmark 1 (dorsal connection of the tail fin) as a 
> > fixed factor. But I thought I may be able to use the tail tip 
> > (landmark 20) and head tip (landmark 48) as fixed landmarks as well. 
> > Do you think it's ok in an ontogeny experiment? 
>
> I guess it will depend on how long into ontogeny you will track the 
> larvae and whether or not that point will "disappear" over ontogeny 
> and/or slide unreasonably (depends also on your question). You, being 
> knowledgeable on their biology, are the best judge on that. 
>
> > If not, do you think 
> > it's ok to slide all semi-landmarks of the tail on landmark 1, and 
> > all head semi-landmarks on an eye landmark? Since the eye isn't part 
> > of the head contour, is it ok if I slide one semi-landmark to the 
> > eye and all rest semi-landmarks of the head one to each other as a 
> > closed shape? 
>
> The point(s) slid relative to the eye won't be sliding along the 
> direction tangent to the curve you want to approximate (i.e., the 
> curvature of the head). A good starting point on the method could be 
> Gunz & Mitteroecker 2013 - Hystrix 
>
> >  2. Is it ok if landmarks 1 and 39 slid relative to each other as well 
> > as 41 and 55, since both describe a closed shape? 
>
> It's not particularly desirable (see answer above). 
>
> >  3. Another worry I have is that landmark 40 which I used to create the 
> > comb fan for both the tail and the head is too far from both of them 
> > so it doesn't bypass the bending. 
> >  4. I'm affraid I don't fully understand why landmark 40 can not be 
> > treated as a fixed landmark. In the book of Zelditch 2004, she says 
> > that one of the basic differences between fixed-landmark and 
> > semi-landmark is the degree of freedom, while fixed has two because 
> > it is docked on both X and Y axes while semi only on one of them 
> > (depending on the nature of the specific fan). Please correct me if 
> > I'm wrong, but what if I use the side line of the larvae (which is 
> > an anatomical/homologous feature) as my X axis and use the Y 
> > component of landmark 1 (dorsal connection of the tail fin) to dock 
> > landmark 40 on the Y axis? Is it wrong because of the dependency of 
> > landmark 40 on landmark 1 regarding the Y coordinate? 
>
> I think Don has covered these two very well. 
>
> >  5. Emma Sherratt told me she straightened the bent tail-body using TPS 
> > software in her paper Sherratt et al. 2017 - Nature ecology & 
> > evolution. In the supplementary material of her paper she wrote: 
> > "To correct for dorso-ventral bending in the landmark configurations 
> > (caused by the joint of the tail with the head/body), we used the 
> > ‘unbend specimens’ function of tpsUtil v.1.86 (Rohlf 2015). The 
> > landmark configurations for each specimen were transformed using the 
> > quadratic approach, straightening from the eye (1) along the 
> > notochord landmarks (46 to 55) to the tip of the tail (8)." 
> > Jim mentioned this unbending function here before. I read the help 
> > about unbending specimens and thought I can use landmarks 20 (tail 
> > tip), 48 (head tip) and several semi-landmarks I can digitize using 
> > the comb fan (equally spaced) along the side line of the larvae, in 
> > order to create the quadratic curve (while the side line "helper" 
> > semi-landmarks can be later omitted from the dataset - I saw 
> > Fruciano et al. 2016). Does this sound good? 
> > I bet that this can basically solve the problems I mentioned in 3 & 
> > 4, since then I can digitized the whole body contour. 
>
> That function is great but, as everything, relies on a set of 
> assumptions (see also Fruciano 2016 - Development Genes and Evolution 
> for a brief discussion). In your case: 
> - that you can consistently identify those points along an hypothetical 
> line (which you 

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

[Carmelo Fruciano]

Il 6/03/2018 4:44 PM, Avi Koplovich ha scritto:

Hi Carmelo,
Thank you for your answer.
My project tests for the influence of kairomones of a predator fish on 
the morphology of Salamander larvae during its development. To do this, 
I take pictures every other week of larvae spawned from six different 
females and assigned to 3 treatments: No fish, 3 caged fish, 6 caged fish.


Hi Avi,
it sounds like an interesting experiment. I will try to answer to your 
questions but keeping in mind that I'm not very knowledgeable on 
salamander development.



 1. I intend to use landmark 1 (dorsal connection of the tail fin) as a
fixed factor. But I thought I may be able to use the tail tip
(landmark 20) and head tip (landmark 48) as fixed landmarks as well.
Do you think it's ok in an ontogeny experiment?


I guess it will depend on how long into ontogeny you will track the 
larvae and whether or not that point will "disappear" over ontogeny 
and/or slide unreasonably (depends also on your question). You, being 
knowledgeable on their biology, are the best judge on that.



If not, do you think
it's ok to slide all semi-landmarks of the tail on landmark 1, and
all head semi-landmarks on an eye landmark? Since the eye isn't part
of the head contour, is it ok if I slide one semi-landmark to the
eye and all rest semi-landmarks of the head one to each other as a
closed shape?


The point(s) slid relative to the eye won't be sliding along the 
direction tangent to the curve you want to approximate (i.e., the 
curvature of the head). A good starting point on the method could be

Gunz & Mitteroecker 2013 - Hystrix


 2. Is it ok if landmarks 1 and 39 slid relative to each other as well
as 41 and 55, since both describe a closed shape?


It's not particularly desirable (see answer above).


 3. Another worry I have is that landmark 40 which I used to create the
comb fan for both the tail and the head is too far from both of them
so it doesn't bypass the bending.
 4. I'm affraid I don't fully understand why landmark 40 can not be
treated as a fixed landmark. In the book of Zelditch 2004, she says
that one of the basic differences between fixed-landmark and
semi-landmark is the degree of freedom, while fixed has two because
it is docked on both X and Y axes while semi only on one of them
(depending on the nature of the specific fan). Please correct me if
I'm wrong, but what if I use the side line of the larvae (which is
an anatomical/homologous feature) as my X axis and use the Y
component of landmark 1 (dorsal connection of the tail fin) to dock
landmark 40 on the Y axis? Is it wrong because of the dependency of
landmark 40 on landmark 1 regarding the Y coordinate?


I think Don has covered these two very well.


 5. Emma Sherratt told me she straightened the bent tail-body using TPS
software in her paper Sherratt et al. 2017 - Nature ecology &
evolution. In the supplementary material of her paper she wrote:
"To correct for dorso-ventral bending in the landmark configurations
(caused by the joint of the tail with the head/body), we used the
‘unbend specimens’ function of tpsUtil v.1.86 (Rohlf 2015). The
landmark configurations for each specimen were transformed using the
quadratic approach, straightening from the eye (1) along the
notochord landmarks (46 to 55) to the tip of the tail (8)."
Jim mentioned this unbending function here before. I read the help
about unbending specimens and thought I can use landmarks 20 (tail
tip), 48 (head tip) and several semi-landmarks I can digitize using
the comb fan (equally spaced) along the side line of the larvae, in
order to create the quadratic curve (while the side line "helper"
semi-landmarks can be later omitted from the dataset - I saw
Fruciano et al. 2016). Does this sound good?
I bet that this can basically solve the problems I mentioned in 3 &
4, since then I can digitized the whole body contour.


That function is great but, as everything, relies on a set of 
assumptions (see also Fruciano 2016 - Development Genes and Evolution 
for a brief discussion). In your case:
- that you can consistently identify those points along an hypothetical 
line (which you would remove after the unbending)

- that your arching is well represented by the chosen function

You are the best judge on whether these assumptions are satisfied in 
your case or not.
I suggested the Valentin et al. (2008 - Journal of Fish Biology) 
approach because it's more flexible (less stringent assumptions, which 
obviously doesn't mean assumption-free) and therefore more generally 
applicable. But, of course, the approach in tpsUtil can be a great 
solution if it's appropriate to your data.


Best,
Carmelo

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

[Donald Swiderski]

Avi,

I think these details are probably not of general interest, but we can
continue separately.

Don


On Wed, Mar 7, 2018 at 12:36 PM, Avi Koplovich 
wrote:

> Hi Don,
> This surely solves my problem with considering landmark 40 as a fixed one
> (it's not!). So I tried what you offered but I have a few questions:
>
>1. While digitizing according to a fan one should follow the
>intersections of the contour with the fan lines and repeat the same lines
>in all individuals (which consequently, gives the exact same number of
>semi-landmarks). Is this required also while drawing a background curve -
>should I try to repeat more or less the same locations (and number of
>points), or while resampling the curve by length I can change the number of
>semi-landmarks to space evenly and as long I set the same number for all
>specimens, then it's ok?
>I played with it a bit, and realized that as long as the length of the
>curve is fixed, resampling it by length using a fixed number of points (for
>all specimens) will locate them in the same relative locations. Please
>correct me if I'm wrong.
>2. Just to make sure I understood the benefit of the background curve
>over the fan: With the background curve I can digitize semi-landmarks in
>different densities along the curve and then divide them into a fixed
>number of curve points, so I don't have to decide on a specific density for
>the whole curve?
>3. And I bet I sill need to use the unbending tool in specimens that
>have non-natural postures, right? I mean, using the background curve
>doesn't solve the bending specimen as well, right?
>4. Can the head-tip and tail-tip be treated as fixed landmarks (each
>with two degrees of freedom and homologous)?
>
> Thanks again,
> Avi
>
>
> On Wednesday, March 7, 2018 at 12:10:56 AM UTC+2, dlswider wrote:
>>
>> Avi,
>>
>> The reason landmark 40 is not a landmark is related to you definition of
>> it as a point between two others.  If it were simply the midpoint on a
>> line connecting two other points, it would not represent any data that was
>> not captured by the coordinates of the points used in the definition (it
>> therefore would have no degrees of freedom).  The coordinates of a
>> landmark, as an anatomically defined point, cannot be inferred from the
>> coordinates of other digitized points, so it has 2 degrees of freedom.  A
>> semilandmark is defined to be on an anatomical edge between two other
>> points;  the condition of the definition that it be between other points
>> takes away a degree of freedom, but the potential for that edge to vary in
>> curvature leaves a degree of freedom (a dimension of variation) to be
>> captured in the coordinates of the point.  Your definition of the point
>> as an intersection the line between two landmarks and a line on the side of
>> the body (a line pigment or lateral line?) is similar to the definition of
>> a semilandmark – it is constrained to be along the segment, but free to
>> vary in how close it is to one end of the segment, leaving only one degree
>> of freedom.
>>
>> There is at least one reason for not using landmark 40 to anchor both
>> combs: doing so induces a correlation between them because they share an
>> end point.  Using the same comb for multiple curves will cause similar
>> problems.
>>
>> Finally, the fan and comb were attempts to do something that can now be
>> done better in tpsDig.  You can use the “Draw background curves” tool in
>> tpsDig to place points along the curve, then use the.  “resample curve”
>> (choose “by length”) to easily get even spacing along the length (and
>> independently for each curve).  Then, in tpsUtil, use “Append tps curves
>> to landmarks” to have the curve points included in the list of landmarks
>> (you also have to designate which ‘landmarks’ are really semilandmarks).
>>
>> Hope this helps
>>
>> Don
>>
>>
>> On Tue, Mar 6, 2018 at 10:44 AM, Avi Koplovich 
>> wrote:
>>
>>> Hi Carmelo,
>>> Thank you for your answer.
>>> My project tests for the influence of kairomones of a predator fish on
>>> the morphology of Salamander larvae during its development. To do this, I
>>> take pictures every other week of larvae spawned from six different females
>>> and assigned to 3 treatments: No fish, 3 caged fish, 6 caged fish.
>>>
>>>1. I intend to use landmark 1 (dorsal connection of the tail fin) as
>>>a fixed factor. But I thought I may be able to use the tail tip (landmark
>>>20) and head tip (landmark 48) as fixed landmarks as well. Do you think
>>>it's ok in an ontogeny experiment? If not, do you think it's ok to slide
>>>all semi-landmarks of the tail on landmark 1, and all head semi-landmarks
>>>on an eye landmark? Since the eye isn't part of the head contour, is it 
>>> ok
>>>if I slide one semi-landmark to the eye and all rest semi-landmarks of 
>>> the
>>>

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

[Avi Koplovich]

 Hi Don,
This surely solves my problem with considering landmark 40 as a fixed one 
(it's not!). So I tried what you offered but I have a few questions:

   1. While digitizing according to a fan one should follow the 
   intersections of the contour with the fan lines and repeat the same lines 
   in all individuals (which consequently, gives the exact same number of 
   semi-landmarks). Is this required also while drawing a background curve - 
   should I try to repeat more or less the same locations (and number of 
   points), or while resampling the curve by length I can change the number of 
   semi-landmarks to space evenly and as long I set the same number for all 
   specimens, then it's ok?
   I played with it a bit, and realized that as long as the length of the 
   curve is fixed, resampling it by length using a fixed number of points (for 
   all specimens) will locate them in the same relative locations. Please 
   correct me if I'm wrong.
   2. Just to make sure I understood the benefit of the background curve 
   over the fan: With the background curve I can digitize semi-landmarks in 
   different densities along the curve and then divide them into a fixed 
   number of curve points, so I don't have to decide on a specific density for 
   the whole curve?
   3. And I bet I sill need to use the unbending tool in specimens that 
   have non-natural postures, right? I mean, using the background curve 
   doesn't solve the bending specimen as well, right?
   4. Can the head-tip and tail-tip be treated as fixed landmarks (each 
   with two degrees of freedom and homologous)?

Thanks again,
Avi


On Wednesday, March 7, 2018 at 12:10:56 AM UTC+2, dlswider wrote:
>
> Avi,
>
> The reason landmark 40 is not a landmark is related to you definition of 
> it as a point between two others.  If it were simply the midpoint on a 
> line connecting two other points, it would not represent any data that was 
> not captured by the coordinates of the points used in the definition (it 
> therefore would have no degrees of freedom).  The coordinates of a 
> landmark, as an anatomically defined point, cannot be inferred from the 
> coordinates of other digitized points, so it has 2 degrees of freedom.  A 
> semilandmark is defined to be on an anatomical edge between two other 
> points;  the condition of the definition that it be between other points 
> takes away a degree of freedom, but the potential for that edge to vary in 
> curvature leaves a degree of freedom (a dimension of variation) to be 
> captured in the coordinates of the point.  Your definition of the point 
> as an intersection the line between two landmarks and a line on the side of 
> the body (a line pigment or lateral line?) is similar to the definition of 
> a semilandmark – it is constrained to be along the segment, but free to 
> vary in how close it is to one end of the segment, leaving only one degree 
> of freedom.
>
> There is at least one reason for not using landmark 40 to anchor both 
> combs: doing so induces a correlation between them because they share an 
> end point.  Using the same comb for multiple curves will cause similar 
> problems.
>
> Finally, the fan and comb were attempts to do something that can now be 
> done better in tpsDig.  You can use the “Draw background curves” tool in 
> tpsDig to place points along the curve, then use the.  “resample curve” 
> (choose “by length”) to easily get even spacing along the length (and 
> independently for each curve).  Then, in tpsUtil, use “Append tps curves 
> to landmarks” to have the curve points included in the list of landmarks 
> (you also have to designate which ‘landmarks’ are really semilandmarks).
>
> Hope this helps
>
> Don
>
>
> On Tue, Mar 6, 2018 at 10:44 AM, Avi Koplovich  > wrote:
>
>> Hi Carmelo,
>> Thank you for your answer.
>> My project tests for the influence of kairomones of a predator fish on 
>> the morphology of Salamander larvae during its development. To do this, I 
>> take pictures every other week of larvae spawned from six different females 
>> and assigned to 3 treatments: No fish, 3 caged fish, 6 caged fish.
>>
>>1. I intend to use landmark 1 (dorsal connection of the tail fin) as 
>>a fixed factor. But I thought I may be able to use the tail tip (landmark 
>>20) and head tip (landmark 48) as fixed landmarks as well. Do you think 
>>it's ok in an ontogeny experiment? If not, do you think it's ok to slide 
>>all semi-landmarks of the tail on landmark 1, and all head semi-landmarks 
>>on an eye landmark? Since the eye isn't part of the head contour, is it 
>> ok 
>>if I slide one semi-landmark to the eye and all rest semi-landmarks of 
>> the 
>>head one to each other as a closed shape?
>>2. Is it ok if landmarks 1 and 39 slid relative to each other as well 
>>as 41 and 55, since both describe a closed shape?
>>3. Another worry I have is that landmark 40 which I used to create 
>>   

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

[Donald Swiderski]

Avi,

The reason landmark 40 is not a landmark is related to you definition of it
as a point between two others.  If it were simply the midpoint on a line
connecting two other points, it would not represent any data that was not
captured by the coordinates of the points used in the definition (it
therefore would have no degrees of freedom).  The coordinates of a
landmark, as an anatomically defined point, cannot be inferred from the
coordinates of other digitized points, so it has 2 degrees of freedom.  A
semilandmark is defined to be on an anatomical edge between two other
points;  the condition of the definition that it be between other points
takes away a degree of freedom, but the potential for that edge to vary in
curvature leaves a degree of freedom (a dimension of variation) to be
captured in the coordinates of the point.  Your definition of the point as
an intersection the line between two landmarks and a line on the side of
the body (a line pigment or lateral line?) is similar to the definition of
a semilandmark – it is constrained to be along the segment, but free to
vary in how close it is to one end of the segment, leaving only one degree
of freedom.

There is at least one reason for not using landmark 40 to anchor both
combs: doing so induces a correlation between them because they share an
end point.  Using the same comb for multiple curves will cause similar
problems.

Finally, the fan and comb were attempts to do something that can now be
done better in tpsDig.  You can use the “Draw background curves” tool in
tpsDig to place points along the curve, then use the.  “resample curve”
(choose “by length”) to easily get even spacing along the length (and
independently for each curve).  Then, in tpsUtil, use “Append tps curves to
landmarks” to have the curve points included in the list of landmarks (you
also have to designate which ‘landmarks’ are really semilandmarks).

Hope this helps

Don


On Tue, Mar 6, 2018 at 10:44 AM, Avi Koplovich 
wrote:

> Hi Carmelo,
> Thank you for your answer.
> My project tests for the influence of kairomones of a predator fish on the
> morphology of Salamander larvae during its development. To do this, I take
> pictures every other week of larvae spawned from six different females and
> assigned to 3 treatments: No fish, 3 caged fish, 6 caged fish.
>
>1. I intend to use landmark 1 (dorsal connection of the tail fin) as a
>fixed factor. But I thought I may be able to use the tail tip (landmark 20)
>and head tip (landmark 48) as fixed landmarks as well. Do you think it's ok
>in an ontogeny experiment? If not, do you think it's ok to slide all
>semi-landmarks of the tail on landmark 1, and all head semi-landmarks on an
>eye landmark? Since the eye isn't part of the head contour, is it ok if I
>slide one semi-landmark to the eye and all rest semi-landmarks of the head
>one to each other as a closed shape?
>2. Is it ok if landmarks 1 and 39 slid relative to each other as well
>as 41 and 55, since both describe a closed shape?
>3. Another worry I have is that landmark 40 which I used to create the
>comb fan for both the tail and the head is too far from both of them so it
>doesn't bypass the bending.
>4. I'm affraid I don't fully understand why landmark 40 can not be
>treated as a fixed landmark. In the book of Zelditch 2004, she says that
>one of the basic differences between fixed-landmark and semi-landmark is
>the degree of freedom, while fixed has two because it is docked on both X
>and Y axes while semi only on one of them (depending on the nature of the
>specific fan). Please correct me if I'm wrong, but what if I use the side
>line of the larvae (which is an anatomical/homologous feature) as my X axis
>and use the Y component of landmark 1 (dorsal connection of the tail fin)
>to dock landmark 40 on the Y axis? Is it wrong because of the dependency of
>landmark 40 on landmark 1 regarding the Y coordinate?
>5. Emma Sherratt told me she straightened the bent tail-body using TPS
>software in her paper Sherratt et al. 2017 - Nature ecology & evolution. In
>the supplementary material of her paper she wrote:
>"To correct for dorso-ventral bending in the landmark configurations
>(caused by the joint of the tail with the head/body), we used the ‘unbend
>specimens’ function of tpsUtil v.1.86 (Rohlf 2015). The landmark
>configurations for each specimen were transformed using the quadratic
>approach, straightening from the eye (1) along the notochord landmarks (46
>to 55) to the tip of the tail (8)."
>Jim mentioned this unbending function here before. I read the help
>about unbending specimens and thought I can use landmarks 20 (tail tip), 48
>(head tip) and several semi-landmarks I can digitize using the comb fan
>(equally spaced) along the side line of the larvae, in order to create the
>quadratic 

[MORPHMET] Re: Digitizing landmarks on live larvae

[Avi Koplovich]

 Hi Carmelo,
Thank you for your answer.
My project tests for the influence of kairomones of a predator fish on the 
morphology of Salamander larvae during its development. To do this, I take 
pictures every other week of larvae spawned from six different females and 
assigned to 3 treatments: No fish, 3 caged fish, 6 caged fish.

   1. I intend to use landmark 1 (dorsal connection of the tail fin) as a 
   fixed factor. But I thought I may be able to use the tail tip (landmark 20) 
   and head tip (landmark 48) as fixed landmarks as well. Do you think it's ok 
   in an ontogeny experiment? If not, do you think it's ok to slide all 
   semi-landmarks of the tail on landmark 1, and all head semi-landmarks on an 
   eye landmark? Since the eye isn't part of the head contour, is it ok if I 
   slide one semi-landmark to the eye and all rest semi-landmarks of the head 
   one to each other as a closed shape?
   2. Is it ok if landmarks 1 and 39 slid relative to each other as well as 
   41 and 55, since both describe a closed shape?
   3. Another worry I have is that landmark 40 which I used to create the 
   comb fan for both the tail and the head is too far from both of them so it 
   doesn't bypass the bending.
   4. I'm affraid I don't fully understand why landmark 40 can not be 
   treated as a fixed landmark. In the book of Zelditch 2004, she says that 
   one of the basic differences between fixed-landmark and semi-landmark is 
   the degree of freedom, while fixed has two because it is docked on both X 
   and Y axes while semi only on one of them (depending on the nature of the 
   specific fan). Please correct me if I'm wrong, but what if I use the side 
   line of the larvae (which is an anatomical/homologous feature) as my X axis 
   and use the Y component of landmark 1 (dorsal connection of the tail fin) 
   to dock landmark 40 on the Y axis? Is it wrong because of the dependency of 
   landmark 40 on landmark 1 regarding the Y coordinate?
   5. Emma Sherratt told me she straightened the bent tail-body using TPS 
   software in her paper Sherratt et al. 2017 - Nature ecology & evolution. In 
   the supplementary material of her paper she wrote:
   "To correct for dorso-ventral bending in the landmark configurations 
   (caused by the joint of the tail with the head/body), we used the ‘unbend 
   specimens’ function of tpsUtil v.1.86 (Rohlf 2015). The landmark 
   configurations for each specimen were transformed using the quadratic 
   approach, straightening from the eye (1) along the notochord landmarks (46 
   to 55) to the tip of the tail (8)."
   Jim mentioned this unbending function here before. I read the help about 
   unbending specimens and thought I can use landmarks 20 (tail tip), 48 (head 
   tip) and several semi-landmarks I can digitize using the comb fan (equally 
   spaced) along the side line of the larvae, in order to create the quadratic 
   curve (while the side line "helper" semi-landmarks can be later omitted 
   from the dataset - I saw Fruciano et al. 2016). Does this sound good?
   I bet that this can basically solve the problems I mentioned in 3 & 4, 
   since then I can digitized the whole body contour.
   

Many thanks in advance,
Avi


On Wednesday, February 28, 2018 at 7:38:22 PM UTC+2, Avi Koplovich wrote:
>
> 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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