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,

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,
>> 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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> -- 
> Donald L Swiderski
> University of Michigan
> ph.(734) 763-9613
> e-mail: dlsw...@umich.edu <javascript:>

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