Hi Helmi, I would concur with Murat. There aren't any satisfying options for 3D data. The 3D landmarks from one or more angles for each extremity is really your only option for publications. As for your final question, yes you can output LM 'warps' for CVA, regression, or pretty much any ordination you want, but your options on software that can do it are limited. Stephan Schlager's R packages are a good start as Murat already suggested and I'm happy to help work through some approaches in R if you want to shoot me an email.
Cheers, -Blake Blake Dickson PhD Candidate Museum of Comparative Zoology Harvard University 26 Oxford Street Cambridge, MA 02138 On Tue, 15 Jan 2019 at 21:28, Murat Maga <m...@uw.edu> wrote: > Dear Helmi, > > > > Visualizing deformation for 3D shapes is somewhat difficult, especially if > you are planning to put in a 2D medium like a paper. What you suggested are > your basic options. You can choose to do deformation grids independently > for each plane, that way it is a bit easier to see what’s going on, > especially on paper. > > > > I personally like animations, that is morphing from one (or more) PC > extreme to the other interactively as it brings out the full benefit of 3D. > You can do the same with regression coefficients (or CVs) as well. If you > still have access, those should be available in Landmark Editor as you > suggest. > > > > We have a working prototype that we are hoping to release in the few 6-8 > weeks that will let you do a bit more than what you can do in Landmark > editor, including GPA and PCA, visualizing landmark variability, and > plotting. I attached a screenshot to give you an idea. You can stack > multiple PCs to visualize simultaneously. > > > > If landmark editor doesn’t work for you and you really need something > shoot me an e-mail (off the list), I will try to help you. If you are > comfortable with R, you can also give a Stefan Schlager’s Morpho package a > try as well. > > > > M > > > > *From:* Helmi Hadi <helmih...@gmail.com> > *Sent:* Tuesday, January 15, 2019 5:30 PM > *To:* MORPHMET <morphmet@morphometrics.org> > *Subject:* [MORPHMET] Different types of 2D and 3D image when intepreting > PCA, CVA and other analysis. > > > > Dear Morphometricians, > > > > Which kind of graphical output would be better to place when interpreting > data output? I've made an imaginary PC graph with imaginary shape for 2D > analysis. Transformation grid/wireframe show almost the same thing, except > that transformation grid shows the bending energy. Wireframe removes the > bending energy, but in return you get a sort of view of the overall shape. > Wouldn't it be better for visualization to just find the raw data point > corresponding to the furthest ends of the PCs and just placing it there. > Then you get the fine details (curves) of the shape as well which you > cannot capture with landmarks, unless you are planning to fully landmark > the object. Example here is in the Leaf morphology article by Cardini. > <https://journals.plos.org/plosone/article/figure?id=10.1371/journal.pone.0025630.g004> > It shows all three leaf morphology visual representation side by side. > > > > For 3D, it will be harder to just use wireframe/transformational grid. > Then should I either: > > 1. find the raw data of the extremities of the PC1 vs PC2 graph and place > it in the graph or > > 2. take a raw specimen near the midpoint 0,0 value (in PC1 vs PC2) and > just use IDAV to morph it to whichever PC which is displayed? > > > > If the raw data output itself can be used, can it be used for CVA, or > Regression analysis as well? You can easily display the labels in MorphoJ > and identify which raw data it corresponds to and just place it there. > > > > Thanks > > > > Helmi > > -- > 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. > > -- > 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. > -- 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.
