Re: [MORPHMET] Curve sliding semilandmarks

2016-12-06 Thread Emma Sherratt
Dear Lawrence, You can use geomorph's gpagen function for sliding semilandmarks during Procrustes superimposition, by minimising bending energy or by minimising Procrustes distance. I would say that it is better to sample the curve in IDAV Landmark Editorwith many semilandmarks, in order to

Re: [MORPHMET] RE: micro-CT suggestions

2016-12-06 Thread Murat Maga
Dear Angelo, 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

Re: [MORPHMET] micro-CT suggestions

2016-12-06 Thread Joseph Kunkel
Angela, 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

Re: [MORPHMET] RE: micro-CT suggestions

2016-12-06 Thread Thomas O'Mahoney
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

Re: [MORPHMET] Curve sliding semilandmarks

2016-12-06 Thread Thomas O'Mahoney
Dear Lawrence, 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.). Best, Tom On

Re: [MORPHMET] RE: micro-CT suggestions

2016-12-06 Thread Angela Roggero
dear Luci, 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 is the

[MORPHMET] Curve sliding semilandmarks

2016-12-06 Thread Lawrence Fatica
Hi all, 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

[MORPHMET] problem fixed

2016-12-06 Thread andrea cardini
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. Cheers Andrea -- Dr. Andrea Cardini Researcher, Dipartimento di Scienze Chimiche e Geologiche,

Re: [MORPHMET] geiger rescale error

2016-12-06 Thread marko.djurakic via MORPHMET
Hi Andrea, The code you provided works for me and I am using R 3.2.2, geiger 2.0.6 and ape_4.0. 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:

Re: [MORPHMET] geiger rescale error

2016-12-06 Thread Carmelo Fruciano
Hi Andrea, 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

[MORPHMET] geiger rescale error

2016-12-06 Thread andrea cardini
Dear All, 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. Thanks