Hi! I have a 3D-GMM data set of carnivore skulls and I would like to calculate the Procrustes distance of every individual specimen to a predefined shape after the Procrustes superimposition. In which (open source) software can I do that relatively straightforward and how? Thanks in advance!
Hi Stefan,
I guess the most straightforward way would be to take a look at the available R-packages: Shapes, Geomorph, Morpho. It includes a little bit of programming but has the big advantage of flexibility, including the computation of Procustes distance between any given pair of shapes. If you need some help with the code let me now, but generally R is really easy to use.
Othewise you could play around with various standalone freeware solutions. Take a look at this summary, you´ll find a lot of good programs: http://life.bio.sunysb.edu/morph/
Most of the programs are updated regularly. For detailed question you could also consider subscribing to morphmet. People are always very helpful: http://www.morphometrics.org/home/morphmet
Viele Grüße, Sascha
Hello Stefan,
The free software Morphologika (https://sites.google.com/site/hymsfme/downloadmorphologica) offers to save results including Procrustes mean, distances with and without tangent projection and other for 3D data. It works with files in Morphologika format (which MorphoJ also takes, so you might know it). If you are not familiar with the format, let me know and I can help you with it.
Best,
Viviana
Check out the EVAN toolkit (http://www.evan-society.org) This is the latest edition of morphologika and some other morpho packages put together in one package. by the people who wrote the other packages. There are workshops on how to use the software and lots of tutorials if you need help, a discussion board and sample data sets. What makes it unique is that it takes in true 3D volumetric data instead of just 3D coordinates (which it can do as well). Between this and MorphoJ which does similar things, I think you should have everything you need to do your analyses.
Thanks to all of you! I've tried Vivianas way to solve the problem and it worked very well.
Hi Stefan,
Even that you got answers that helped you to solve the problem, here I provided a R code that can help you to do the same stuff in R statistical environment. R is in a pure sense an open source (not only freeware software).
As Sascha said, doing this in R you will be able to enjoy a power of R's flexibility and advanced analyses. Even more, it provides an intuitive way how Procrustes distance is actually calculated (and programmed).
Code is in the attachment.
Hope this will help.
Marko
Our Checkpoint software (below) can help you collect landmark points as well as perform some 3D shape analysis on the collected points, including PCA and Procrustes.
https://www.stratovan.com/products/checkpoint?utm_source=rg&utm_medium=ans&utm_campaign=gmm2
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