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

``` 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 <netbird....@gmail.com
> <javascript:>> wrote:
>
>> Hi Carmelo,
>> 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.
>>
>>
>> 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:
>>>
>>>
>>> I'll be happy if you can advise on that.
>>> Thank you,
>>> Avi
>>
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>
>
>
> --
> Donald L Swiderski
> University of Michigan
> ph.(734) 763-9613
> e-mail: dlsw...@umich.edu <javascript:>
>

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