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

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


On Tue, Mar 6, 2018 at 10:44 AM, Avi Koplovich <netbird.porta...@gmail.com>

> 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_EYoSl
>> i1Orr/view?usp=sharing
>> I'll be happy if you can advise on that.
>> Thank you,
>> Avi
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University of Michigan
ph.(734) 763-9613
e-mail: dlswi...@umich.edu

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