You can use geomorph's gpagen function for sliding semilandmarks during
Procrustes superimposition, by minimising bending energy or by minimising
I would say that it is better to sample the curve in IDAV Landmark
Editorwith many semilandmarks, in order to
I would stay 1172 as far away possible as I can. It is the $30 inkjet
equivalent of the mCT world. Cheap to buy, very frustrating to operate. Also
signal to noise (SNR) on that machines leaves much to be desired. They are also
phasing it out (due to these constraints). Unless
We are studying lobster cuticle with the SkyScan 1272 (which has a carousel
sampler that holds 18 samples). My regular sized object is a 6mm medallion of
cuticle which can be scanned entirely at at 2.5 um resolution. Smaller regions
of interest can be analyzed but the size of the
Dera Luci and Angela Roggero,
Nikon and Northstar imaging are also manufacturers that are worth looking
into. The Nikon XTH225 is extremely popular in the UK for digitising
objects from ~2cm up to ~50cm. Resolution varies between 3-5 microns and
100 microns, depending on sample size etc. If you
Stefan Schlager's excellent Morpho package for R has the option to slide
semilandmarks without the mesh. I have had some success with this myself,
but you can of course include your mesh with these protocols in either
Morpho or Geomorph (written by Dean Adams et al.).
we too are interested in buying a microCT, and are examining some
instruments just now. Essentially, we want to scan hundreds of similar,
small and low-density objects (insects), and recently tested both
SkyScan 1174, and 1172 (Brucker). Besides, I will be glad to know what
I am working on a project examining shape variation in the pelvis. I used
IDAV Landmark to place four curves of five semilandmarks each (as well as
several fixed landmarks) along the major contours of the pelvis. I plan on
doing the analysis in R, but I am unsure what my options are
Thanks to Marko Djurakic for finding the problem with the geiger
function, and to all others who answered with suggestions: the issue was
that another package had a function with the same name.
Dr. Andrea Cardini
Researcher, Dipartimento di Scienze Chimiche e Geologiche,
The code you provided works for me and I am using R 3.2.2, geiger 2.0.6
However, ensure that the gegier is loaded in the R environment or ensure
that other packages with the same function name do not possibly
interfere with geiger (see this post:
I have run the code you posted without problems.
In this moment, I'm using R 3.3.2 x64 on a Windows machine.
The geiger version I tried this on is geiger_2.0.6.
You might wanna try also posting the question on the list R-sig-phylo
as a lot of people developing R packages for
I've just tried the rescale function in geiger on my data and got an
error message. As I have no experience with it, I tried the first
example for this function in the help: same error message (see below).
Has anyone had similar issues? Probably I made some silly mistake.
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