Avi, I think these details are probably not of general interest, but we can continue separately.
Don On Wed, Mar 7, 2018 at 12:36 PM, Avi Koplovich <netbird.porta...@gmail.com> wrote: > 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> >> 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_EYoSl >>>> i1Orr/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. >>> >> >> >> >> -- >> Donald L Swiderski >> University of Michigan >> ph.(734) 763-9613 >> e-mail: dlsw...@umich.edu >> > -- > 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+unsubscr...@morphometrics.org. > -- Donald L Swiderski University of Michigan ph.(734) 763-9613 e-mail: dlswi...@umich.edu -- 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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