[MORPHMET] New publication on patterns of skull modularity and integration over postnatal ontogeny

2016-09-29 Thread 'Tina Klenovšek' via MORPHMET
Dear Morphometricians,

we wish to inform you about a publication on skull modularity and integration 
across ontogenetic stages in a long-lived vole with well-defined age stages 
conducted on wild and laboratory bred specimens from two phylogenetic groups:

Modularity and cranial integration across ontogenetic stages in Martino's vole, 
Dinaromys bogdanovi

Link: http://www.ctoz.nl/vol85/nr03/a02

Abstract: We explored modularity and morphological integration of the ventral 
cranium during postnatal ontogeny in Martino's vole (Dinaromys bogdanovi). Two 
closely related phylogenetic groups, originating from the Central and 
Southeastern part of the species range in the western Balkans, were considered. 
As expected, both phylogroups had similar patterns of ontogenetic changes in 
cranial size and shape variation, modularity and integration. At the level of 
within individual variation, the hypothesis that the viscerocranial and 
neurocranial regions are separate modules was rejected, indicating that the 
hypothesized modules are not developmental, but rather functional. At the level 
of among individual variation, the viscerocranium and the neurocranium could 
not be recognized as separate modules at the juvenile stage. The strength of 
association between the hypothesized modules becomes lower with age which 
finally results in a clear 2-module organization of the ventral cranium at the 
adult stage. On the other hand, patterns of morphological integration for the 
cranium as a whole, the viscerocranium and the neurocranium stay consistent 
across ontogenetic stages. The developmental mechanism producing integration of 
the cranium as a whole, as well as integration of the neurocranium, varies 
throughout postnatal ontogeny. In contrast, we detected the ontogenetic 
stability of the mechanism responsible for covariation of viscerocranial traits 
which could provide ongoing flexibility of the viscerocranial covariance 
structure for high functional demands during lifetime. Findings from our study 
most likely support the idea of the 'palimpsest-like' model of covariance 
structure. Moreover, similarity or dissimilarity in the patterns of within and 
among individual variation in different sets of analyzed traits and comparisons 
across ontogenetic stages demonstrate how studies on small mammals other than 
mice can give new insights into postnatal cranial development.

Kind regards,

Tina Klenovšek and Vida Jojić


doc. dr. Tina Klenovšek
Univerza v Mariboru | University of Maribor
Fakulteta za naravoslovje in matematiko
Faculty of Natural Sciences and Mathematics
Koroška cesta 160, 2000 Maribor, Slovenija
T: (00 386) 041 808 366
E: tina.klenov...@um.si,

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[MORPHMET] Three blocks PLS

2016-09-29 Thread Paolo Piras
Hi folks,
I write you in order to know if someone developed in R the Three blocks PLS
approach described in :

Bookstein, F. L., Gunz, P., & Ingeborg, H., et al. (2003). Cranial
integration in Homo: Singular warps analysis of the midsagittal plane in
ontogeny and evolution. Journal of Human Evolution, 44, 167 187.

Among the various ways to impement a three block pls they choose to adopt
the strategy described in:
Streissguth, A.P., Sampson, P., Barr, H., 1993. The Enduring Effects of
Prenatal Alcohol Exposure on Child Development. University of Michigan
Press, Michigan

Thanks in advance for any advice

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Re: [MORPHMET] Re: How to export .obj with textures as .ply with colours for morphometric analyses?

2016-09-29 Thread M. Viviana Toro Ibacache
Dear Patrick,

I apologise for the late reply. The software I used to do the procedure is
Geomagic Studio, version 2012, 64-bits.

Best wishes,

2016-09-19 5:19 GMT-03:00 lv xiao :

> Hi Dr. Viviana, thank you very much for your exposition. I noted that
> there are several softwares in Geomagic, such as Geomagic Design, Geomagic
> Freeform, and Geomagic Wrap. May I know which Geomagic software did you
> use? Thank you very much!
> Best regards,
> Patrick WEN
> On Wednesday, 14 September 2016 18:11:12 UTC+8, mtoroibacache wrote:
>> Dear Colleagues,
>> I really appreciate your help with this. Indeed, there is a bit of
>> everything you mentioned in both the problem and the solution. I will try
>> to summarise it in case it can help someone else:
>> - File names: Indeed I had problems in the past with .obj files whose
>> names had spaces, as Thomas mentioned. This was not the case though (I
>> learned my lesson), but it could happen to someone else.
>> - Lack of software to do this in a very reliable way: as Bill mentioned,
>> there might be issues with accuracy by transforming an .obj with texture to
>> a coloured .ply. I will explore the use of Blender directly in .obj files
>> for landmark placing. I am not too worried about my data as the landmark
>> configuration corresponds to human faces (the texture will guide me in
>> placing landmarks in some curved places), where in my experience geometry
>> dimensions exceed small inaccuracies. But it is definitely something to
>> bear in  mind. Of course, I shall run tests to assess the effect of
>> measurement error on my data.
>> - The .obj texture files: a big problem seemed to be that the original
>> data had three .jpg files depicting texture. As Pablo mentioned, the
>> "standard" texture should be one file. So...
>> - ... Geomagic comes to rescue (maybe Blender does this too?): Anneke
>> suggested to use Geomagic, which indeed helps a lot. Antonio took my files
>> and helped me to generate in Geomagic the single-.png-file texture, which
>> can then be used to produce coloured .ply and .wrl files in Meshlab that
>> can be opened in Avizo (.wrl, for which an extra step in Geomagic is
>> needed), and in the R packages Geomorph and Morpho for landmark placing.
>> About Joes's comment, I do not believe .stl can hold colours, but I do
>> not have too much experience with the .stl format. The .obj format (as well
>> as .ply) has a relatively simple structure that describes the position in
>> space of faces and vertices plus other stuff and can be created "by hand"
>> using a text editor such as Notepad (I am sure you might have checked this
>> but just in case https://en.wikipedia.org/wiki/Wavefront_.obj_file). I
>> have written .ply files in the past that worked very well for doing
>> morphometric analyses in R.
>> So, again thanks everyone for all the help!
>> Best wishes,
>> Viviana
>> 2016-09-07 21:35 GMT+02:00 pablo.diaz.jarufe :
>>> Hello Viviana
>>> Working with DAVID I noticed that the textures of the OBJ files. are
>>> saved in PNG format, not in JPG; and all the views are in the same
>>> file. There is any way to create this kind of PNG. file with your
>>> pictures?. May be this correction could work fine in meshlab.
>>> I hope this information will be useful
>>> Best
>>> El jueves, 1 de septiembre de 2016, 8:31:47 (UTC-3), mtoroibacache
>>> escribió:

 Deal Morphometricians,

 I have .obj files with textures from three .jpg photos. I can load and
 see the textures very nicely in Meshlab, but I need the textures to be
 transformed into a coloured .ply file to do geometric morphometric analyses
 (the landmarks are represented in the textures). So far it has not worked
 doing it from Meshlab, so my questions are:

 - I know I can place landmarks in Meshlab using the .obj file, but when
 I do it, the software crashes. any thoughts? the .obj file is 16 Mb big. Is
 there a limit to files size in Meshlab? I would rather not to downsample
 the mesh to not lose anatomical details.

 - When using the Transfer Texture to Vertex Color function, the texture
 gets messed. It seems from web forums that Mshlab takes only one of the (in
 this case) three .jpg files to do the colouring of the .ply mesh. Does
 anybody know how to fix this? Another freeware software?

 - Is there any landmark acquisition software that loads .obj files with
 textures? So far, I have not been able to do it in Landmark Editor, Evan
 toolbox, Avizo, Morpho nor Geomorph.

 Any help is greatly appreciated.

 Best (y saludos),


 *Viviana Toro-Ibacache DDS MSc PhD*
 Profesora Asistente *(Assistant Professor)*
 Centro de Análisis Cuantitativo en Antropología Dental (CA2)
 Unidad de Anatomía, Instituto de Investigación en Ciencias Odontológicas