Re: [MORPHMET] Dennis Slice

2019-06-18 Thread Paolo Piras
Dear friends,
I want to join all of you in expressing my condolences for Dennis loss.
My grief goes to his family, friends and students.
I knew him in Isernia about ten years ago and I had the chance to speak
with him not only about morphometrics or science in general but also about
a great variety of arguments. I remember a very nice person, kind and
polite in any situation. As well as sharp and clever.
Our community will miss him so much...
Paolo


Il giorno mar 18 giu 2019 alle ore 00:00 Una Vidarsdottir <
una.vidarsdot...@gmail.com> ha scritto:

> Like so many I have struggled with words. I posted some on my Facebook and
> copy them here below. Oh I miss him.
>
>  I first met Dennis at the beginning of my PhD work in 1995. 24 years. We
> spent many an evening debating how best to do a certain analysis or how to
> test a certain theory. I remember a night... probably in 2006, when we
> walked the streets of Vienna through a long summernight talking the entire
> time.  Dennis was not a big ego although his mind, work and ideas might
> have merited it. In his own quiet and sometimes self-deprecating way, he
> inspired and influenced the work of the morphometrics community as a whole.
> Dennis believed his role as an academic lay in supporting this community
> to produce better and better science, from lending helpful pointers to
> fledgling researchers taking their first cautious steps in the field, to
> being a fountain of knowledge and ideas to those of us who have been
> involved much longer.
> First and foremost Dennis was my very dear friend, soul mate and entrusted
> colleague. I will miss him very much.
> (Some photos from another very warm evening in Vienna in 2008)
>
> On Mon, 17 Jun 2019, 18:27 K. James Soda,  wrote:
>
>> Sent on behalf of Dean Adams:
>>
>>
>> Colleagues,
>>
>>
>>
>> Like others I have spent the weekend grieving the passing of Dennis, and
>> trying to put my feelings of loss into words. Alas I cannot.
>>
>>
>>
>> I’ve known Dennis for 25 years, since we overlapped in Jim’s lab in the
>> 1990s. He was a constant fixture in our field, and his passing has left a
>> great hole. I will miss his positive attitude, his whit, his endless and
>> entertaining stories, and his life lessons. But mostly I will miss having
>> him in our community.
>>
>>
>>
>> I will miss you, Dennis.
>>
>>
>>
>> Dean
>>
>>
>>
>>
>>
>>
>>
>> Dr. Dean C. Adams
>>
>> Director of Graduate Education, EEB Program
>>
>> Professor
>>
>> Department of Ecology, Evolution, and Organismal Biology
>>
>> Iowa State University
>>
>> https://www.eeob.iastate.edu/faculty/adams/
>>
>> phone: 515-294-3834
>>
>> On Mon, Jun 17, 2019 at 3:53 AM K. James Soda 
>> wrote:
>>
>>> Hello Everyone,
>>>
>>> Since Friday afternoon, I have struggled to put into words the kind of
>>> adviser Dennis Slice was to his students to supplement the elegant
>>> testimonies to his abilities as a researcher, but words fail me. I do not
>>> know how I can properly portray the care and compassion that he afforded
>>> us. Despite his many accomplishments, he remained humble and never spoke
>>> down to us. He listened to our concerns with compassion and our ideas with
>>> an open mind. He treated us like family, and I know that I am not alone in
>>> saying that we felt the same way about him. Our weekly lab meetings and
>>> monthly lab dinners form some of my happiest memories of graduate school
>>> because he infused humor into our every interaction. He taught me so many
>>> things, both professionally (like people are more likely to read emails
>>> that are broken into smaller blocks) and personally (like a gentleman
>>> should always carry a handkerchief in case a lady cries). I can only hope
>>> that I as a professor will be able to foster curiosity and confidence in my
>>> students half as well as Dennis did in me.
>>>
>>> I deeply miss Dennis, and I suspect I always will.
>>>
>>> Thank you for your time,
>>>
>>> James Soda
>>>
>>> On Mon, Jun 17, 2019 at 3:19 AM Carmelo Fruciano 
>>> wrote:
>>>
 This is extremely sad news. He has made enormous contributions to our
 field and his figure will be greatly missed. I have had limited
 interactions with him but, based on the interactions I had the
 privilege
 to have, I also concur with Mauro Cavalcanti that he had a nice sense
 of
 humor.
 My most heartfelt condolences to his family, his friends, and all our
 field.
 Carmelo


 --


 ==
 Carmelo Fruciano
 Institute of Biology
 Ecole Normale Superieure - Paris
 CNRS
 http://www.fruciano.it/research/


 On 15/06/2019 16:55, mitte...@univie.ac.at wrote:
 >   Dear subscribers to morphmet,
 >
 >   With the deepest grief we must inform you of the sudden
 >   death on June 13 of Prof. Dennis E. Slice,
 >   holder of the fourth Rohlf Award for Excellence in Morphometrics
 >   and tireless founder and 

Re: [MORPHMET] digitizing very variable leaves

2018-03-15 Thread Paolo Piras
Not for fractal dimension but this can be done using user friendly free
softwares just google it

Il gio 15 mar 2018 15:17 Tina Klenovšek <tina.klenov...@um.si> ha scritto:

> Thank you very much, Paolo. I hope both can be done in NTSYSpc, because
> unfortunately I don't use R.
>
> Tina
>
>
>
> *From:* Paolo Piras [mailto:paolopir...@gmail.com]
> *Sent:* Thursday, March 15, 2018 2:14 PM
> *To:* Carmelo Fruciano
> *Cc:* MORPHMET
> *Subject:* Re: [MORPHMET] digitizing very variable leaves
>
>
>
> Hi Tina,
>
> if your colleagues are interested in the complexity of the leaves shapes
> more than in shape itself, it could be useful to compute the fractal
> dimension of the outlines of the leaves; it is very easy and it does not
> inform you about shape differences but about the "complexity" of the
> outlines that of course does not require landmark's digitization or
> homology. Shape Analysis and Fractal Diimension can be performed jointly
> (e.g. Fourier Analysis) in order to have a more complete picture of the
> phenomenon.
>
> Ciao
>
> Paolo
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> 2018-03-15 12:25 GMT+01:00 Carmelo Fruciano <c.fruci...@unict.it>:
>
> Hi Tina,
>
> The software Shape by Iwata & Ukai is an user friendly option for
> performing elliptic Fourier analysis.
>
> https://academic.oup.com/jhered/article/93/5/384/2187412
>
> http://lbm.ab.a.u-tokyo.ac.jp/~iwata/shape/
>
> Elliptic Fourier analysis is also implemented in NTSYSpc, which is also
> user-friendly.
>
> You probably want to read a bit on the methodology to see if it fits what
> you plan to do and its potential shortcomings.
>
> I hope this helps.
>
> Carmelo
>
>
>
> On 15/03/2018 12:14, 'Tina Klenovšek' via MORPHMET wrote:
>
> Thanks to all, Javier, Vincent, William, Joanna and Dr. Rohlf,
>
>
>
> my dilemma occurred because some botanists (I work with mammal skulls)
> have asked me to help them evaluate leaf variability of two tree species
> from different localities. So, variability within and among individual
> trees and species.
>
>
>
> In which user friendly program (like MorphoJ J) can I analyse outline
> data and visualize variability?
>
>
>
> Thank you again,
>
> Tina
>
>
>
> *From:* Joanna Lenarczyk [mailto:j.kowal...@botany.pl
> <j.kowal...@botany.pl>]
> *Sent:* Thursday, March 15, 2018 10:21 AM
> *To:* Tina Klenovšek
> *Subject:* Re: [MORPHMET] digitizing very variable leaves
>
>
>
> Hello Tina,
>
> You can try a program which does not need landmarks:
>
>
>
> http://www.eletel.p.lodz.pl/pms/SoftwareQmazda.html
>
>
>
> I hope it will help you :) I have not tried it yet by myself, but it can
> be useful when you cannot or do not want use landmarks :)
>
> Best,
>
> Joanna
>
>
>
> 2018-03-15 8:40 GMT+01:00 <f.james.ro...@stonybrook.edu>:
>
> One could do that computationally but I would worry about the homology it
> might imply for such variable leaf shapes. You might try it and then check
> to see if, for example, a lobe on one leaf might be 20% of the linear
> distance around the outline but in another it might be 30% of the way
> around. In such a case the lobe on one leaf would effectively be treated as
> homologous to a location between lobes on another leaf. If so, does that
> make biological sense for your study? If simple leaves were also included
> the implied homology of a point along its outline to that of one of the
> lobed leaves might be pretty arbitrary. Would be better if one knew
> something about the development of these leaves (which I do not!) and used
> that knowledge.
>
>
>
> An alternative would be to use outline methods to group shapes for the
> purpose of say identification with little implication that groups need be
> biologically meaningful. Sorry to be rather negative but I find highly
> variable leaf shapes difficult to put in a simple standard framework.
> Perhaps others will have better suggestions.
>
>
>
> 
>
> F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution
>
> Research Professor, Anthropology
>
> Stony Brook University
>
>
>
> *From:* Tina Klenovšek <tina.klenov...@um.si>
> *Sent:* Wednesday, March 14, 2018 12:28 AM
> *To:* f.james.rohlf <f.james.ro...@stonybrook.edu>
> *Cc:* morphmet@morphometrics.org
> *Subject:* RE: [MORPHMET] digitizing very variable leaves
>
>
>
> Thanks to everyone who answered.
>
>
>
> Dear Dr. Rohlf,
>
> I assumed great variability would be a pr

Re: [MORPHMET] digitizing very variable leaves

2018-03-15 Thread Paolo Piras
Hi Tina,
if your colleagues are interested in the complexity of the leaves shapes
more than in shape itself, it could be useful to compute the fractal
dimension of the outlines of the leaves; it is very easy and it does not
inform you about shape differences but about the "complexity" of the
outlines that of course does not require landmark's digitization or
homology. Shape Analysis and Fractal Diimension can be performed jointly
(e.g. Fourier Analysis) in order to have a more complete picture of the
phenomenon.
Ciao
Paolo










2018-03-15 12:25 GMT+01:00 Carmelo Fruciano :

> Hi Tina,
>
> The software Shape by Iwata & Ukai is an user friendly option for
> performing elliptic Fourier analysis.
>
> https://academic.oup.com/jhered/article/93/5/384/2187412
>
> http://lbm.ab.a.u-tokyo.ac.jp/~iwata/shape/
>
> Elliptic Fourier analysis is also implemented in NTSYSpc, which is also
> user-friendly.
>
> You probably want to read a bit on the methodology to see if it fits what
> you plan to do and its potential shortcomings.
>
> I hope this helps.
>
> Carmelo
>
>
>
> On 15/03/2018 12:14, 'Tina Klenovšek' via MORPHMET wrote:
>
> Thanks to all, Javier, Vincent, William, Joanna and Dr. Rohlf,
>
>
>
> my dilemma occurred because some botanists (I work with mammal skulls)
> have asked me to help them evaluate leaf variability of two tree species
> from different localities. So, variability within and among individual
> trees and species.
>
>
>
> In which user friendly program (like MorphoJ J) can I analyse outline
> data and visualize variability?
>
>
>
> Thank you again,
>
> Tina
>
>
>
> *From:* Joanna Lenarczyk [mailto:j.kowal...@botany.pl
> ]
> *Sent:* Thursday, March 15, 2018 10:21 AM
> *To:* Tina Klenovšek
> *Subject:* Re: [MORPHMET] digitizing very variable leaves
>
>
>
> Hello Tina,
>
> You can try a program which does not need landmarks:
>
>
>
> http://www.eletel.p.lodz.pl/pms/SoftwareQmazda.html
>
>
>
> I hope it will help you :) I have not tried it yet by myself, but it can
> be useful when you cannot or do not want use landmarks :)
>
> Best,
>
> Joanna
>
>
>
> 2018-03-15 8:40 GMT+01:00 :
>
> One could do that computationally but I would worry about the homology it
> might imply for such variable leaf shapes. You might try it and then check
> to see if, for example, a lobe on one leaf might be 20% of the linear
> distance around the outline but in another it might be 30% of the way
> around. In such a case the lobe on one leaf would effectively be treated as
> homologous to a location between lobes on another leaf. If so, does that
> make biological sense for your study? If simple leaves were also included
> the implied homology of a point along its outline to that of one of the
> lobed leaves might be pretty arbitrary. Would be better if one knew
> something about the development of these leaves (which I do not!) and used
> that knowledge.
>
>
>
> An alternative would be to use outline methods to group shapes for the
> purpose of say identification with little implication that groups need be
> biologically meaningful. Sorry to be rather negative but I find highly
> variable leaf shapes difficult to put in a simple standard framework.
> Perhaps others will have better suggestions.
>
>
>
> 
>
> F. James Rohlf, Distinguished Professor, Emeritus. Ecology & Evolution
>
> Research Professor, Anthropology
>
> Stony Brook University
>
>
>
> *From:* Tina Klenovšek 
> *Sent:* Wednesday, March 14, 2018 12:28 AM
> *To:* f.james.rohlf 
> *Cc:* morphmet@morphometrics.org
> *Subject:* RE: [MORPHMET] digitizing very variable leaves
>
>
>
> Thanks to everyone who answered.
>
>
>
> Dear Dr. Rohlf,
>
> I assumed great variability would be a problem.
>
> I was thinking the best way of digitizing would be to draw a curve on the
> outline of each leaf (simple and lobed leaves). Resample curves by length
> with approx. 40 landmarks. Then append curves to landmarks. Two landmarks,
> the leaf tip and base, would be fixed others could be defined as
> semi-landmarks. Is this sensible?
>
> Alternatively, we could analyse simple and lobed leaves separately.
>
> Thank you a lot for your help.
>
>
>
> Tina
>
>
>
>
>
> *From:* f.james.rohlf [mailto:f.james.ro...@stonybrook.edu
> ]
> *Sent:* Wednesday, March 14, 2018 3:59 AM
> *To:* Tina Klenovšek
> *Subject:* Re: [MORPHMET] digitizing very variable leaves
>
>
>
> An assumption of the usual GMM methods is that shape variation is "small".
> I think these leaves exceed this quite a bit! Another problem is landmarks.
> How to match leaves with and without lobes?
>
>
>
> __
>
> F. James Rohlf, Distinguished Prof. Emeritus
>
> Dept. Anthropology and Ecology & Evolution
>
> Stonybrook University
>
>
>
>  Original message 
>
> From: 'Tina Klenovšek' via MORPHMET 

[MORPHMET] New pub

2018-03-08 Thread Paolo Piras
Hi folks,

I want to signal you this new publication that just came out.

There we present a complete theory about the threefold decomposition of
deformation (homothetic, affine and non affine components) as well as new
methods to perform it in the Thin Plate Spline space (Varano et al 2017).
Moreover, some new efforts are present:

We unify in a unique formalism the Procrustes metric and the bending energy
metric (that is a pseudo-distance vanishing on affine transformations). We
also introduce two new types of energies: the stretching energy that deals
with affine transformations and the gamma energy (depending on two
source-dependent constants) that unifies affine and non affine energetics
in a given transformation. We also introduce the decay factor rho that
relates the strain energy (calculated on the body only) and the bending
energy (calculated on the whole R^m). We unify in a unique formalism the
Ordinary Procrustes Analysis and the Modified Ordinary Procrustes Analysis
(Varano et al., 2017). One key aspect is to consider the concept of
orthogonality between components non-strictly depending from the Euclidean
metric.

Our new methods deal also with the m-Volume size definition, that has a
more physical meaning ,in place of Centroid Size. We demonstrate the
usefulness of all of this using both simulated examples (in both 2D and 3D)
and using a real clinical example. This is inserted in a long term project
aimed at bridging Geometric Morphometrics and Continuum Mechanics.



Varano V., *Piras P.,* Gabriele S., Teresi L., Nardinocchi L., Dryden I.L.,
Torromeo C., Puddu P.E. 2018. The Decomposition of Deformation: new metrics
to enhance shape analysis in medical imaging. *Medical Image Analysis*, 46:
35-56.Doi:https://doi.org/10.1016/j.media.2018.02.005



A complete set of R functions for all of this is available upon request.

All the best

Paolo

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[MORPHMET] New pub

2018-02-02 Thread Paolo Piras
Hi folks,

I signal this new article that is in "online first" in Palaeogeography,
Palaeoclimatology, Palaeoecology. We analyzed mandible's phenotypes and
extinction rates starting from a new composite phylogeny that is an update
of a previous effort (Piras et al 2013) and that includes 157 valid taxa
(later pruned to include only those taxa for which mandible' phenotypes
were available).

Piras P.,  Silvestro D., Carotenuto, F., Castiglione S., Kotsakis T.,
Maiorino L., Melchionna M., Mondanaro A., Sansalone G., Serio C., Vero
V.A., Raia P. Evolution of the sabertooth mandible: a deadly
ecomorphological specialization. In press.  Palaeogeography,
Palaeoclimatology, Palaeoecology.
https://doi.org/10.1016/j.palaeo.2018.01.034

Regards
Paolo

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[MORPHMET] New Pub

2018-01-24 Thread Paolo Piras
Hi folks,
I would like to alert you about this new pub

Maiorino, L., Farke, A.A., Kotsakis, T., Raia, P., Piras, P. 2018. Who is
the most stressed? Morphological disparity and mechanical behavior of the
feeding apparatus of ceratopsian dinosaurs (Ornithischia, Marginocephalia).
Cretaceous Research, 84, pp. 483-500

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[MORPHMET] New pub

2017-12-07 Thread Paolo Piras
Hi folks,
I write to inform you about this new pub

Profico A., *Piras P.*, Buzi C., Di Vincenzo F., Lattarini F., Melchionna
M.A., Veneziano A., Raia P., Manzi G. 2017. The evolution of cranial base
and face in Cercopithecoidea and Hominoidea: modularity and morphological
integration. *American Journal of Primatology*, 79(12). DOI:
10.1002/ajp.22721

All the best
Paolo

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[MORPHMET] new pub

2017-08-02 Thread Paolo Piras
Hi folks,
I would like to signal you this paper where we tried to apply new
covariation/disintegration strategies to the interaction between human left
atrium and left ventricle
All the best
Paolo

https://www.nature.com/articles/s41598-017-06189-w

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Re: [MORPHMET] Question on Morpho

2017-07-13 Thread Paolo Piras
I think the problem is in the input:

 3.30e+08 -1.08e+08 5.22e+08

etc.

 are very strange coordinates; I suspect some trouble in the csv file with
comma symbol (, or .) ...

maybe you prepared it with excel?

There could be the problem.

best

paolio




2017-07-13 10:30 GMT+02:00 Antonio Profico :

> Dear Pablo,
>
> try:  proc <- ProcGPA(a$arr).
>
> The object "a" is a list, the array is an element (arr) of the list.
>
> Let me know if works,
>
> Antonio
>
> 2017-07-13 4:59 GMT+01:00 Pablo Fisichella :
>
>> Dear All
>>
>> I am using the package Morpho in order to make some GM analyses but I
>> obtained some errors. Now I am trying to use the function read.csv.folder
>>
>> I ran this command
>>
>> a<-read.csv.folder("E:/Documents/Zan2", x = 2:44, y = 2:4, rownames =
>> NULL, header = TRUE, dec = ",", sep = ";", pattern = "csv", addSpec = NULL,
>> back = TRUE)
>>
>> In the r console appeared my 5 files .csv (see below) with 43
>> landmarks/semilandmark in 3 dimensions for 5 individuals (0093, 0137, 0377,
>> 1865, 1880)
>>
>> Then I tried perform a Procrustes Analysis using this function: proc <-
>> ProcGPA(a) however this error appear: Error in addo(a3) : please provide
>> 3D numeric array
>>
>> I feel that this error is related to my data array but I dont know how I
>> can solve this in order to run a GPA
>>
>> thanks in advance, I appreciate any help you can give me.
>>
>> cheers,
>>
>> Pablo
>>
>> $arr
>> , , 0093
>>
>>   X YZ
>> 1  3.30e+08 -1.08e+08 5.22e+08
>> 2  2.94e+08 -5.35e+07 5.12e+08
>> 3  2.76e+08 -7.79e+07 5.59e+08
>> 4  3.13e+08 -1.37e+08 5.48e+08
>> 5  3.21e+08 -1.35e+08 5.45e+08
>> 6  3.27e+08 -1.33e+08 5.42e+08
>> 7  3.32e+08 -1.30e+08 5.39e+08
>> 8  3.36e+08 -1.28e+08 5.36e+08
>> 9  3.38e+08 -1.25e+08 5.34e+08
>> 10 3.39e+08 -1.23e+08 5.32e+08
>> 11 3.39e+08 -1.20e+08 5.30e+08
>> 12 3.37e+08 -1.17e+08 5.29e+08
>> 13 3.33e+08 -1.14e+08 5.27e+08
>> 14 3.29e+08 -9.43e+07 5.21e+08
>> 15 3.30e+08 -9.20e+07 5.19e+08
>> 16 3.31e+08 -8.92e+07 5.17e+08
>> 17 3.31e+08 -8.59e+07 5.16e+08
>> 18 3.30e+08 -8.20e+07 5.15e+08
>> 19 3.28e+08 -7.77e+07 5.14e+08
>> 20 3.24e+08 -7.33e+07 5.13e+08
>> 21 3.19e+08 -6.86e+07 5.11e+08
>> 22 3.12e+08 -6.36e+07 5.10e+08
>> 23 3.04e+08 -5.84e+07 5.08e+08
>> 24 2.84e+08 -4.42e+07 5.20e+08
>> 25 2.81e+08 -4.40e+07 5.27e+08
>> 26 2.79e+08 -4.37e+07 5.32e+08
>> 27 2.78e+08 -4.28e+07 5.38e+08
>> 28 2.77e+08 -4.35e+07 5.43e+08
>> 29 2.76e+08 -4.60e+07 5.47e+08
>> 30 2.76e+08 -4.93e+07 5.50e+08
>> 31 2.75e+08 -5.34e+07 5.53e+08
>> 32 2.76e+08 -5.83e+07 5.55e+08
>> 33 2.76e+08 -6.43e+07 5.56e+08
>> 34 2.83e+08 -8.41e+07 5.67e+08
>> 35 2.85e+08 -8.59e+07 5.69e+08
>> 36 2.87e+08 -8.77e+07 5.70e+08
>> 37 2.89e+08 -8.99e+07 5.72e+08
>> 38 2.91e+08 -9.27e+07 5.73e+08
>> 39 2.93e+08 -9.67e+07 5.74e+08
>> 40 2.96e+08 -1.02e+08 5.74e+08
>> 41 2.97e+08 -1.09e+08 5.73e+08
>> 42 2.97e+08 -1.17e+08 5.69e+08
>> 43 2.96e+08 -1.26e+08 5.65e+08
>>
>> , , 0137
>>
>>   XYZ
>> 1  5.31e+08 5660 1.45e+08
>> 2  5.64e+08 -330 1.47e+08
>> 3  5.85e+08 2190 1.03e+08
>> 4  5.35e+08 7310 9.86e+07
>> 5  5.35e+08 7580 1.07e+08
>> 6  5.34e+08 7780 1.14e+08
>> 7  5.35e+08 7940 1.20e+08
>> 8  5.34e+08 7990 1.26e+08
>> 9  5.34e+08 7910 1.31e+08
>> 10 5.33e+08 7750 1.35e+08
>> 11 5.33e+08 7490 1.38e+08
>> 12 5.31e+08 7090 1.40e+08
>> 13 5.30e+08 6620 1.41e+08
>> 14 5.39e+08 5470 1.50e+08
>> 15 5.42e+08 5320 1.53e+08
>> 16 5.44e+08 5160 1.55e+08
>> 17 5.47e+08 4940 1.57e+08
>> 18 5.49e+08 4610 1.59e+08
>> 19 5.52e+08 4120 1.61e+08
>> 20 5.54e+08 3400 1.61e+08
>> 21 5.56e+08 2490 1.59e+08
>> 22 5.57e+08 1450 1.57e+08
>> 23 5.58e+08  291 1.54e+08
>> 24 5.77e+08 -654 1.40e+08
>> 25 5.82e+08 -335 1.34e+08
>> 26 5.88e+08   632000 1.31e+08
>> 27 5.92e+08  417 1.27e+08
>> 28 5.94e+08  687 1.23e+08
>> 29 5.95e+08  931 1.19e+08
>> 30 5.94e+08 1150 1.16e+08
>> 31 5.93e+08 1340 1.13e+08
>> 32 5.92e+08 1530 1.11e+08
>> 33 5.90e+08 1730 1.09e+08
>> 34 5.85e+08 3280 9.65e+07
>> 35 5.85e+08 3610 9.61e+07
>> 36 5.84e+08 3930 9.58e+07
>> 37 5.84e+08 4270 9.54e+07
>> 38 5.83e+08 4650 9.45e+07
>> 39 5.81e+08 5040 9.30e+07
>> 40 5.76e+08 5420 9.10e+07
>> 41 5.70e+08 5830 8.85e+07
>> 42 5.62e+08 6080 8.60e+07
>> 43 5.52e+08 6310 8.31e+07
>>
>> , , 0377
>>
>>   XYZ
>> 1  5.48e+08 7410 1.08e+08
>> 2  5.79e+08 1400 1.01e+08
>> 3  6.04e+08 4710 5.61e+07
>> 4  5.56e+08 9770 5.76e+07
>> 5  5.57e+08 9850 6.97e+07
>> 6  5.56e+08 9740 8.03e+07
>> 7  5.55e+08 9630 8.91e+07
>> 8  5.54e+08 9440 9.59e+07
>> 9  5.52e+08 9190 1.01e+08
>> 10 5.50e+08 8850 1.03e+08
>> 11 5.49e+08 8580 1.04e+08
>> 12 5.49e+08 8350 1.04e+08
>> 13 5.49e+08 8060 1.04e+08
>> 14 5.56e+08 6830 1.14e+08
>> 15 

Re: [MORPHMET] mirror-relabeling R function

2017-07-03 Thread Paolo Piras
Hi Andrea

Morpho package does the job:



among the othe functions you can find:

mirror mirror landmarks or triangular mesh in place
mirror.matrix mirror landmarks or triangular mesh in place
mirror.mesh3d mirror landmarks or triangular mesh in place
mirror2plane mirror points or mesh on an arbitrary plane
mirror2plane.matrix mirror points or mesh on an arbitrary plane
mirror2plane.mesh3d mirror points or mesh on an arbitrary plane

ciao

paolo

2017-07-03 11:19 GMT+02:00 andrea cardini :

> Dear All,
> please, is there an R function that I could use to mirror-relabel a 3D
> landmark configuration?
> Thanks in advance.
> Cheers
>
> Andrea
>
>
> --
>
> Dr. Andrea Cardini
> Researcher, Dipartimento di Scienze Chimiche e Geologiche, Università di
> Modena e Reggio Emilia, Via Campi, 103 - 41125 Modena - Italy
> tel. 0039 059 2058472
>
> Adjunct Associate Professor, School of Anatomy, Physiology and Human
> Biology, The University of Western Australia, 35 Stirling Highway, Crawley
> WA 6009, Australia
>
> E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
> WEBPAGE: https://sites.google.com/site/alcardini/home/main
>
> FREE Yellow BOOK on Geometric Morphometrics:
> http://www.italian-journal-of-mammalogy.it/public/journals/3
> /issue_241_complete_100.pdf
>
> ESTIMATE YOUR GLOBAL FOOTPRINT: http://www.footprintnetwork.or
> g/en/index.php/GFN/page/calculators/
>
> --
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[MORPHMET] Thematic session VIP image conference

2017-03-01 Thread Paolo Piras
Hi folks,
probably this does not fully intercept your interest; however, I would be
grateful if you can forward this announcement  to any colleague you think
could be interested
Thankyou very much for your help in doing this
All the best
Paolo


The thematic session “Shape Analysis in Medical Imaging: From Math to
Clinics”
for the International Conference VipIMAGE 2017 - VI ECCOMAS THEMATIC
CONFERENCE ON COMPUTATIONAL VISION AND MEDICAL IMAGE PROCESSING
is open for registration at

https://web.fe.up.pt/~vipimage/nav/conference/sessions.html

We kindly invite you to  participate; we also request you to forward this
mail to your
colleagues, research scholars and students as well as encourage them
to participate in the Conference.

With our very best regards.
Luciano Teresi
Valerio Varano
Paolo Piras
Paolo Emilio Puddu

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[MORPHMET] New pub

2017-02-17 Thread Paolo Piras
Hi folks
I would like to signal this new pub that is now on Evolutionary Ecology
Research.

Maiorino L., Farke A.A., Kotsakis T., Piras P*.* 2017. Macroevolutionary
patterns in cranial and lower jaw shape of ceratopsian dinosaurs
(Dinosauria, Ornithischia): phylogeny, morphological integration and
evolutionary rates. *Evolutionary Ecology Research*, 18: 123-167.

Best
Paolo

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[MORPHMET] New publication

2017-01-09 Thread Paolo Piras
Hi folks,
I write to signal this new publication available as online first

Sansalone G., Colangelo P., Kotsakis T., Loy A, Castiglia R., Bannikova
A.A., Zemlemerova E.D., Piras P. 2017. Influence of evolutionary allometry
on rates of morphological evolution and disparity in strictly subterranean
moles (Talpinae, Talpidae, Eulipotyphla, Mammalia). *Journal of Mammalian
Evolution. **doi:10.1007/s10914-016-9370-9*

Regards
Paolo

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Re: [MORPHMET] Trying to trace a quote

2016-10-19 Thread Paolo Piras
Hi Bill,
did you try to google it?

It seems it is from John von Neumann
https://stevengoddard.wordpress.com/2011/04/18/with-four-parameters-i-can-fit-an-elephant-and-with-five-i-can-make-him-wiggle-his-trunk/
http://www.johndcook.com/blog/2011/06/21/how-to-fit-an-elephant/

ciao
paolo

2016-10-19 19:10 GMT+02:00 Bill Sellers :

> Dear All,
>
> I wonder if anyone can help me. I'm trying to trace a quotation that a now
> long retired colleague of mine used to use. He doesn't remember where he
> got it from but it is very apt, and since it relates to animal shape I'm
> hoping someone on this mailing list will recognise it (particularly since
> I'm probably not remembering it quite properly and google is being
> unhelpful). The quote as best I remember it is:
>
> "Give me 4 parameters and I can build you an elephant. Give me 5 and I can
> make it wag its tail."
>
> I've always imagined it was something that a 1930s developmental biologist
> or mathematician would have said when discussing the utility of
> developmental models at the time.
>
> Can anyone help?
>
> Cheers
> Bill
> --
> Bill Sellers, Tel: 01612751719, Mobile: 07857655786,
> http://www.animalsimulation.org
> University of Manchester, D1239 Michael Smith Building, Manchester, M13
> 9PT.
>
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>

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[MORPHMET] New publication

2016-10-07 Thread Paolo Piras
Hi folks
This new pub just appeared

*Piras P.,* Torromeo C., Re F., Evangelista A., Gabriele S., Esposito G.,
Nardinocchi P., Teresi L., Madeo A., Chialastri C., Schiariti M., Varano
V., Uguccioni M., Puddu P.E. (2016). Left Atrial trajectory impairment in
Hypertrophic Cardiomyopathy disclosed by Geometric Morphometrics and
Parallel Transport. *Scientific Report*. Article number: 34906. doi:
10.1038/srep34906



All the best

paolo

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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
Paolo

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[MORPHMET] Nuew paper on ontogenetic trajectories

2016-05-10 Thread Paolo Piras
Hi folks,
I would like to signal you this new paper:
*Piras P.,* Teresi L., Traversetti L., Varano V, Gabriele S., Kotsakis T.,
Raia P., Puddu P.E., Scalici M. (2016). The conceptual framework of
ontogenetic trajectories: Parallel Transport allows the recognition and
visualization of pure deformation patterns. *Evolution and Development* 18:
182:200. DOI: 10./ede.12186
Here we argue that looking at pure deformations, by separating intra-and
inter- individual trajectories is very effective in interpreting
morphological consequences of ontogenetic allometry. In this case the
deformation, rather than shape difference, should be the focus of
investigations. Albeit not directly discussed here, possible inferences on
the abused concept of heterochrony could emerge from this approach.

Best
Paolo

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[MORPHMET] Nuew pub

2016-04-29 Thread Paolo Piras
Hi folks,
I just want to signal you this new pub:

Goffredo M., Piras P., Varano V., Gabriele S., D’Anna C., Conforto S.
(2016). Shape analysis of bicipital contraction by means of RGB-D Sensor,
parallel transport and trajectory analysis. In: Kyriacou, E., Christofides,
S., Pattichis, C.S. (Eds.): Proceedings of XIV Mediterranean Conference on
Medical and Biological Engineering and Computing 2016: MEDICON 2016, March
31st–April 2nd 2016, Paphos, Cyprus, 57: 628-633. Springer International
Publishing. http://dx.doi.org/10.1007/978-3-319-32703-7_121.

The pdf is available on request
best
paolo

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Re: [MORPHMET] testing for convergence in 3D shape space

2016-01-27 Thread Paolo Piras
Hi!
maybe these are inherent


*Piras P.,* Sansalone G., Teresi L., Kotsakis T., Colangelo P. & Loy A.
(2012) - Testing convergent and parallel adaptations of talpids humerus
mechanical performance by means of Geometric Morphometrics and Finite
Element Analysis. *Journal of Morphology*, 273: 696-711.
*Piras P.,* Sansalone G., Teresi L., Moscato M., Profico A., Eng R., Cox T.
C., Loy A., Colangelo P. & Kotsakis T. (2015) - Digging adaptation in
insectivorous subterranean eutherians. The enigma of *Mesoscalops
montanensis* unveiled by geometric morphometrics and finite element
analysis. *Journal of Morphology*, 276: 1157–1171.

ciao
paolo

2016-01-27 6:40 GMT+01:00 Christy Hipsley :

> Dear All,
>
> I'm working with a 3D GM data set and am looking for a specific test of
> convergence that also accounts for phylogeny. After some searching it's
> still not clear to me what is appropriate - so far I only see programs that
> use reduced PC axes as continuous characters, but nothing that uses the
> full Procrustes coordinates. I've applied a phylogenetic ANOVA in Geomorph
> to at least show that after accounting for phylogeny, morphological shape
> is significantly different among ecological groups (in this clade several
> unrelated lineages occur in the same ecological niche).
>
> Does anyone know of a method for testing for convergence across a
> phylogeny using the full shape data or is it always using PC scores? What
> about using scores from a CVA instead, since they are specifically
> addressing the question of differences among the a priori ecological groups
> (and PCA does not)? Could those be mapped onto a phylogeny and modelled in
> terms of BM vs OU, to test if that morphological change is adaptive?
>
> Any advice on these analyses would be appreciated. I'm aware of the
> package Surface but I'm not convinced that is right for my system.
>
> My shape data has a significant phylogenetic signal and I suspect that one
> ecological group in particular is highly convergent.
>
>
> Thanks for any help!
>
> Christy
>
> School of BioSciences
> University of Melbourne
> Parkville VIC 3010, Australia
> Email: chips...@unimelb.edu.au
>
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[MORPHMET] New pub Geometric Morphometrics in cardiology

2016-01-19 Thread Paolo Piras
Hi folks,
for those that could be interested I signal this publication

*Piras P.*, Teresi L., Gabriele S., Evangelista A., Esposito G., Varano V.,
Torromeo C., Nardinocchi P. & Puddu P.E. (2016) - Systo–diastolic LV shape
analysis by geometric morphometrics and parallel transport highly
discriminates myocardial infarction. In: Camara O., et. al. (Eds), STACOM
2015, Lecture Notes in Computer Science, vol. 9534, Springer International,
pp. 119-129.

PDF available on request
Best
paolo

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[MORPHMET] R functions and working examples Varano et al., 2015

2015-10-12 Thread Paolo Piras
Hi folks,
given that I received many requests for R functions associated to
Varano, V., Gabriele, S., Teresi, L., Dryden, I., Puddu, P., Torromeo, C.,
& Piras, P. 2015. Comparing shape trajectories of biological soft tissues
in the size-and-shape space. In Biomat 2014: International Symposium on
Mathematical and Computational Biology (pp. 351-365), I decided to share
them here with some fully working examples.
I invite those to which I already sent the functions to re-download this
updated material.
I then attach R functions (including ancyllaries), the main function help,
a workspace and the R script for running the examples. These examples are
very easy and more complex designs could be set.
As wrote at the begin of the R script, I stress that, in order to recover
perfectly deformations, there is the need to go beyond Levi Civita
connection. I hope to update you soon on this issue.
Best
paolo

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The arguments of the pt2dvar() function are :


array = an input array of n shapes represented by k landmarks in 
2-dimensions, i.e. k x 2 x n; these are the input data subjected to the entire 
procedure; If you want to use this for studying allometry your input data 
should be predictions coming from separate regressions between size+shape and 
size or shape and size. This because estimating hierarchically the deformations 
within each group relatively to a local reference assumes that a reasonably 
"clean deformational direction" exists. Using real data there is too much 
noise. It is also *mandatory* that these shapes are ordered, within each group, 
according to the direction of deformation. For example, in the case of 
allometry, when using predictions, be sure that these predictions are ordered 
by group and, within each group, by size at which predictions were calculated. 
The best should be to do such ordination before running regression and 
claculating predictions to be inputted here. Scale them at unit size if the 
analysis in the shape space is desired.

group = a factor corresponding to group affiliation of each shape in the 
array
doopa= F   leave this default
tol=0.01 the value to manage possible reflections in deformation vector 
differences; leave it as is if you do not have reflections in the output. 

CR=NULL   a kx2 matrix; this is the shape towards which you transport 
deformations hierarchically estimated within each group; if NULL the GRAND mean 
of the entire sample is used. In case of allometry-oriented investigations CR 
should be the consensus of smallest per-group predictions. Scale it at unit 
size if the analysis in the shape space is desired.

locs=NULL  an array k x 2 x n追evels(group) these are the local references, one 
for each group, relatively to which you will estimate the within-group 
deformations. If NULL per-group means are used. In case of allometry-oriented 
investigations locs should be smallest (in terms of size at which predictions 
were calculated) per-group predictions. Scale them at unit size if the analysis 
in the shape space is desired.

sss=T  Data are assumed to be analyzed in the Size and Shape Space. The Shape 
Space is now implemented (sss=F). In this case array, CR and locs should be 
scaled at unit size. Rotation is not mandatory in input as all objects are 
properly aligned internally at the various steps.

OUTPUT is a list that includes:

final=the data that have been transported.

epsilons= error relative to an euclidean approximattion in the size and shape 
space
epsilons2= error relative to an euclidean approximattion in the shape space

THESE RESULTS ARE ROTATION DIAGNOSTICS FOR INNER STEPS useful TO DETECT 
POSSIBLE REFLECTIONS. HOPEFULLY YOU SHOULD IGNORE THEM
trasprotsmua= vectors deriving from the Parallel Transport. For diagnostics 
only.
trasprotsva= rotations deriving from the Parallel Transport. For diagnostics 
only.
locsop= locs rotated on CR via OPA
locsrot= rotation matrices corresponding to locsop
specop= input specimens rotated on their proper loc via OPA
specrots= rotation matrices corresponding to specop





R script with examples.R
Description: Binary data


Data example for running pt2dvar.RData
Description: Binary data


pt2dvar and necessary ancillaries.r
Description: Binary data


[MORPHMET] New contribution aimed at studying morphological trajectories

2015-09-28 Thread Paolo Piras
Hi folks,
I signal you this new contribution presenting a new 2D explicit formula for
Parallel Transport in the Size and Shape Space for the analysis of
morphological trajectories.

Varano, V., Gabriele, S., Teresi, L., Dryden, I., Puddu, P., Torromeo, C.,
& Piras, P. 2015. Comparing shape trajectories of biological soft tissues
in the size-and-shape space. In Biomat 2014: International Symposium on
Mathematical and Computational Biology (pp. 351-365).

Our approach is suited for 2D-configurations only (as we exploit the
potential of complex notation) constituted by homologous landmarks and
identifying very different initial shapes that experience any kind of
deformation (such as in allometry).
The aim is to look at pure deformation patterns occurring within groups by
filtering out initial inter-group differences.This is achieved by properly
setting the Levi Civita Parallel Transport in the Riemannian  Size and
Shape Space.
Albeit it is not cited in the text, a R function exists to perform the
analyses described in the paper.
In the case you cannot download the paper here

http://www.worldscientific.com/worldscibooks/10.1142/9566

please email me to have the article and/or the R function.
Any advice and/or function testing is welcome.
Best
Paolo

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[MORPHMET] new publication

2015-09-17 Thread Paolo Piras
Hi folks,
This new publication is available as online early view

Maiorino, L., Farke, A. A., Kotsakis, T., Teresi, L. and Piras, P. (2015),
Variation in the shape and mechanical performance of the lower jaws in
ceratopsid dinosaurs (Ornithischia, Ceratopsia). Journal of Anatomy.
doi: 10./joa.12374
http://onlinelibrary.wiley.com/doi/10./joa.12374/abstract

best
paolo

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Re: [MORPHMET] Suggestions for geomorph

2015-06-18 Thread Paolo Piras
http://home.uchicago.edu/~aolsen/software.shtml

Is awesome!

Thanks for sharing!

Paolo

2015-06-09 11:51 GMT+02:00 Vincent Bonhomme bonhomme.vinc...@gmail.com:

 Hi Mauro and all,

 StereoMorph
 http://cran.r-project.org/web/packages/StereoMorph/index.html is a
 brand new alternative, shiny-powered to cope with common weaknesses of R in
 terms of graphical/interactions

 hth

 v


 2015-06-08 22:58 GMT+02:00 Mauro Cavalcanti mauro...@gmail.com:

 Dear members of the geomorph Development Team,

 I have been using the digitize2d() function of the geomorph R package to
 obtain landmark coordinates from my fish specimens.It works fine, but I
 respectfully have two suggestions for its improvement.

 First one is quite simple: when end of file is reached and the last
 specimen has been digitized, the function stops with one of those ugly and
 arcane error messages (well, all programming languages generate ugly and
 arcane error messages! ;-)). This should not happen; instead, the function
 should issue a user-friendly warning, like End of file, Last specimen
 (or perhaps something less friendly, like Can't you see you have reached
 the end of file, you moron? ;-))

 Second suggestion may be more difficult to implement, but if it can be
 done, it would provide a great improvement: the ability to edit a
 previoulsly created file. Currently, the function detects the specimens
 without landmark coordinates and starts digitizing from this specimen on;
 if all specimens have already landmark coordinates, then the function stops
 with the same ugly error messages referred to above. It would be really
 great if one could see each specimen with the superimposed digitized
 landmarks, one by one, so that landmarks could be checked, added, or
 deleted.

 Hope this helps!

 With warmest regards,

 --
 Dr. Mauro J. Cavalcanti
 E-mail: mauro...@gmail.com
 Web: http://sites.google.com/site/maurobio

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 --
 vincentbonhomme.fr http://www.vincentbonhomme.fr

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[MORPHMET] New pubs on deformation

2015-04-17 Thread Paolo Piras
Hi folks 
I would like to signal this contribution just published 

A New 4D Trajectory-Based Approach Unveils Abnormal LV Revolution Dynamics 
in Hypertrophic Cardiomyopathy
Andrea Madeo, Paolo Piras, Federica Re, Stefano Gabriele, Paola 
Nardinocchi, Luciano Teresi, Concetta Torromeo, Claudia Chialastri, Michele 
Schiariti, Geltrude Giura, Antonietta Evangelista, Tania Dominici, Valerio 
Varano, Elisabetta Zachara, Paolo Emilio Puddu
Research Article | published 13 Apr 2015 | PLOS ONE
10.1371/journal.pone.0122376

Here we use a strategy named Parallel Transport in its simplest euclidean 
fashion in order to evaluate the pure deformation thus filtering out 
between groups differences in order to evaluate the process per-se.It was 
previously already preliminary applied in

4D-Analysis of Left Ventricular Heart Cycle Using Procrustes Motion Analysis
Paolo Piras, Antonietta Evangelista, Stefano Gabriele, Paola Nardinocchi, 
Luciano Teresi, Concetta Torromeo, Michele Schiariti, Valerio Varano, Paolo 
Emilio Puddu
Research Article | published 23 Jan 2014 | PLOS ONE
10.1371/journal.pone.0086896


A fully Riemannian approach is in
Comparing shape trajectories of biological soft  tissues in the 
size-and-shape”- V. Varano, S. Gabriele, Luciano Teresi, I. Dryden, P.E. 
Puddu, C. Torromeo, Paolo Piras. In press. BIOMAT 2014 Congress Book. 

and in

Teresi, L,V. Varano, S. Gabriele, P. Piras, I. L. Dryden. Discovering 
deformation: a new method for studying shape change trajectories. World 
Congress on Biomechanics, Boston, USA, 2014

These approaches have relevant implications for studying allometric  change.
Best
paolo


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Re: [MORPHMET] Abridged summary of morp...@morphometrics.org - 1 update in 1 topic

2015-01-29 Thread Paolo Piras

Dear Rollo,
thankyou very much for your message; actually these data are very close to 
what I was looking for and surely I will play with them.
best regards
paolo piras





Il giorno giovedì 29 gennaio 2015 15:54:02 UTC+1, Rollo Moore ha scritto:

 I don't know if this meets your needs, but the R package [1] by Stanfill 
 et al includes a data set called 'drill' that acts as an example in 
 arm/body movement in a drilling task (created for study in Rancourt[2] et 
 al).

 rotations: An R Package for SO(3) Data by Bryan Stanfill, Heike Hofmann, 
 Ulrike Genschel

 B. Stanfill, H. Hofmann, and U. Genschel. rotations: Tools for Working 
 with Rotation Data, 2014a. URL
 http://CRAN.R-project.org/package=rotations. R package version 1.2. [p1]

 D. Rancourt, L.-P. Rivest, and J. Asselin. Using orientation statistics to 
 investigate variations in human
 kinematics. Journal of the Royal Statistical Society. Series C (Applied 
 Statistics), 49(1):81–94, 2000.

 http://www.ece.uvic.ca/~bctill/papers/mocap/Rancourt_etal_2000.pdf


  

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   Paolo Piras paolo...@gmail.com javascript:: Jan 21 11:40AM -0800 

 Hi folks,
  
 I write you in order if someone knows the existence of some free to 
 download database of anatomically homologous landmarks-based human 
 movement 
 data(i.e. gait).
  
 Thanks in advance ...more 
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[MORPHMET] HUMAN MOVEMENT

2015-01-21 Thread Paolo Piras


Hi folks,

I write you in order if someone knows the existence of some free to 
download database of anatomically homologous landmarks-based human movement 
data(i.e. gait).

Thanks in advance

paolo piras

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[MORPHMET] Re: Software for generating centreline

2014-11-10 Thread Paolo Piras
Maybe FIJI?
http://fiji.sc/Fiji




Il giorno lunedì 10 novembre 2014 20:45:56 UTC+1, Blake Dickson ha scritto:

 Hi everyone, 

 I am looking for software that can find and generate the centreline of a 
 relatively curvy lumen in 3D. 

 I am using Mimics to create an endocast and exporting in STL. I have tried 
 Amira/Avizo but wasn't satisfied with the result (the centreline wasnt in 
 the centre). I know mimics has a centreline function type thing in one of 
 its modules, but I would much prefer to find something slightly more free. 

 Cheers, 
 Blake Dickson 
 PhD Candidate, 
 Harvard Museum of Comparative Zoology

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[MORPHMET] old/new publication

2014-09-22 Thread Paolo Piras
I just write to signal that this paper just came out.

Paolo PIRAS, Angela D. BUSCALIONI, Luciano TERESI, Pasquale RAIA, Gabriele 
SANSALONE, Tassos KOTSAKIS and Jorge CUBO. 
Morphological integration and functional modularity in the crocodilian skull​.
2014. INTEGRATIVE ZOOLOGY Volume 9, Issue 4, August 2014, Pages: 498–516.

I already alerted about this in the past but it remained unpublished for an 
embarrassing time delay.

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