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,

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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