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, >> 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 >> >> -- >> MORPHMET may be accessed via its webpage at http://www.morphometrics.org >> --- >> You received this message because you are subscribed to the Google Groups >> "MORPHMET" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to morphmet+u...@morphometrics.org <javascript:>. >> > > > > -- > Donald L Swiderski > University of Michigan > ph.(734) 763-9613 > e-mail: dlsw...@umich.edu <javascript:> > -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. 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