Re: [MORPHMET] Elliptic Fourier analysis using PAST 3.05

2015-02-17 Thread marcelo cardillo
Open the coordinate file in Past, then peform elliptic fourier analyses,
then copy the ouput file with the harmonics (you can select the desired
numer of harmonics if you want). Then open a new past window and paste the
harmonics. With the desired number of harmonics you can perform now the pca
using the variance-covariance option. Shapes can be viewed this efa
visualization otion. Beware  that the first column is the size of the
image, don´t select it if you want to analyze only the shape.

   best
 M

2015-02-16 17:50 GMT-03:00 ely raz ely...@mail.com:

 Hi,

 I am trying to perform an Elliptic Fourier analysis using PAST 3.05 and
 the Trilobite outlines file (outlines.dat in
 folk.uio.no/ohammer/past/book.html). Unfortunately, I cannot generate
 using this example the PCA plot shown in Fig. 4.24 of the Paleontological
 Data Analysis book (Page 111 in google books site for this book). Can
 someone please describe me how to do it? What are the steps?

 Thanks.

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[MORPHMET] Elliptic Fourier analysis using PAST 3.05

2015-02-17 Thread ely raz
Hi,
 
I am trying to perform an Elliptic Fourier analysis using PAST 3.05 and the 
Trilobite outlines file (outlines.dat in folk.uio.no/ohammer/past/book.html). 
Unfortunately, I cannot generate using this example the PCA plot shown in Fig. 
4.24 of the Paleontological Data Analysis book (Page 111 in google books site 
for this book). Can someone please describe me how to do it? What are the steps?
 
Thanks.

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[MORPHMET] Ontogenetic changes in morphology

2015-02-17 Thread Adeline Yong
Hi Everyone,

I am exploring the use of GMM to study the ontogenetic changes of claw
morphology in one species of crabs. The tips of the crab claws changes in
curvature (shape) as they grow and there are distinct differences if I
compare the claws of the juvenile crabs and the adults. However, the
intermediate stages are not so obvious. Crabs of various sizes (age) were
collected from two populations and I would like to determine the size when
the change in tip curvature most likely starts for each population. All the
major claws of each crab were photographed and landmarks were placed at the
homologous points of the claws. Semi-landmarks were used for the claw tips
as there were no homologous points along the curvature.  ln centrold size
of each individual claw was computed and plotted against body size
(carapace width) of the crabs.  I am not sure if I am approaching this the
correct way. Any help would be appreciated.

Thanks in advance.

Adeline

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Re: [MORPHMET] Go-to Program of Elliptical Fourier Analysis

2015-02-17 Thread Vincent Bonhomme
Hi Karl,

Try import_jpg in Momocs on segmented images ie black shape on a white
background.
Be sure to get the last version (https://github.com/vbonhomme/Momocs/ ) ,
the one on CRAN and published in JSS is completeley obsolete now
New vignettes are being rewritten, so feel free to contact me for the
hotline.

All the best,
Vincent

2015-02-15 21:52 GMT+01:00 Karl Fetter karl.fet...@gmail.com:

 Hi Everyone,

 I'd like to find out what the 'go-to' program is for collecting elliptical
 fourier descriptors? Is there a favorite? I like to analyze data in R, are
 there programs that are easier to integrate into R than others?

 I see that the R package Momocs has a lot of tools for analyzing EFA data,
 but can one also collect data with Momocs?

 I'm pretty familiar with Landmark GMM workflows, is the EFA workflow
 similar in concept? I.e., image a leaf, collect the data (with some
 program), do some kind of superimposition, work with the data.

 Thanks for the tips,

 Karl Fetter
 UVM - Plant Biology

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Re: [MORPHMET] Getting 3D landmarks and areas from 2D images

2015-02-17 Thread Anneke van Heteren
Dear Marc

You could use photogrammetry to create 3D models, but it would require
several photographs from different angles rather than just one from the
top.
I hope that helps.

Best wishes,

Anneke van Heteren



Darwinweg 2 - 2333 CR LeidenMeckenheimer
Allee 176 - 53115 Bonn

E anneke.vanhete...@naturalis.nlE
anneke.vanhete...@uni-bonn.de anneke.vanhete...@naturalis.nl



anneke.vanhete...@naturalis.nl


2015-02-16 20:00 GMT+01:00 marcsrour marcsr...@gmail.com:

 Dear all,

 I have what might be either a very basic question or an impossible task. I
 am working on quantifying the area covered by epibionts on highly-curved
 oyster shells (500+ specimens). These have been photographed from the top,
 but the amount of curvature on some of them means that using 2D
 measurements is too unreliable.

 Is it possible to use these same images to get 3D areas? If not, is there
 any way to achieve a result photographically, without the need for surface
 scanning?

 Any help or ideas would be deeply appreciated,and apologies for the novice
 question!

 Marc

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Re: [MORPHMET] Go-to Program of Elliptical Fourier Analysis

2015-02-17 Thread Ricardo Kriebel
Hi Karl,

I would highly recommend Momocs. You can read in the images into R with the
import_jpeg function. The author has a lot of documentation on his website
and on github.

Ricardo


On Mon, Feb 16, 2015 at 2:04 PM, Garvin, Heather hgar...@mercyhurst.edu
wrote:

  Hi Karl,



 I’ve used the Shape software package to complete EFA before, and it worked
 very well. You can find the files to download on the SB Morphometrics
 website (http://life.bio.sunysb.edu/morph/soft-outlines.html)



 Along with the download is a manual and tutorial – it’s very easy to
 follow and simple to use. If you have 2D images you’re using it’s
 particularly useful, as you can just upload the picture files and the
 software will allow you to binarize it and will analyze the outlines right
 from the image.



 Hope that helps,

 --Heather



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 *Assistant Professor of Anthropology*

 *Dept of Applied Forensic Sciences*

 *Dept of Anthropology/Archaeology*

 *Mercyhurst University*

 *Zurn 69*

 *(814)824-3953 %28814%29824-3953*



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 *From:* Karl Fetter [mailto:karl.fet...@gmail.com]
 *Sent:* Sunday, February 15, 2015 3:53 PM
 *To:* morphmet@morphometrics.org
 *Subject:* [MORPHMET] Go-to Program of Elliptical Fourier Analysis



 Hi Everyone,



 I'd like to find out what the 'go-to' program is for collecting elliptical
 fourier descriptors? Is there a favorite? I like to analyze data in R, are
 there programs that are easier to integrate into R than others?



 I see that the R package Momocs has a lot of tools for analyzing EFA data,
 but can one also collect data with Momocs?



 I'm pretty familiar with Landmark GMM workflows, is the EFA workflow
 similar in concept? I.e., image a leaf, collect the data (with some
 program), do some kind of superimposition, work with the data.



 Thanks for the tips,



 Karl Fetter

 UVM - Plant Biology

 --
 MORPHMET may be accessed via its webpage at http://www.morphometrics.org

 To unsubscribe from this group and stop receiving emails from it, send an
 email to morphmet+unsubscr...@morphometrics.org.

 --
 MORPHMET may be accessed via its webpage at http://www.morphometrics.org

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-- 
Ricardo Kriebel, Ph.D.
Research Associate
University of Wisconsin-Madison
Department of Botany
430 Lincoln Drive
Madison, WI 53706

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Re: [MORPHMET] Ontogenetic changes in morphology

2015-02-17 Thread Carmelo Fruciano

Hi Adeline,
I'm not sure if this helps with your problems, but what you are  
describing reminds me of two things:


- MANCOVA using shape variables as dependent, species as categorical  
predictor and size (either of the claw or of the body) as covariate  
and testing not only for the main effects but also for the interaction  
between species and size


- So called relative warps in size-shape space (Mitteroecker et al  
2004 - J Hum Evol), which I personally used on some fish (Fruciano et  
al 2012 - Env Biol Fish), and can be used in your case as an  
exploratory tool to see if and where there is an abrupt change in  
the trajectory of each species


I am not sure how plotting claw size on body size would help you with  
shape, although maybe that's useful to find how much different  
descriptors of size are consistent with each other.


I hope this helps.
Best,
Carmelo



Adeline Yong adeline.yon...@gmail.com ha scritto:


Hi Everyone,

I am exploring the use of GMM to study the ontogenetic changes of claw
morphology in one species of crabs. The tips of the crab claws changes in
curvature (shape) as they grow and there are distinct differences if I
compare the claws of the juvenile crabs and the adults. However, the
intermediate stages are not so obvious. Crabs of various sizes (age) were
collected from two populations and I would like to determine the size when
the change in tip curvature most likely starts for each population. All the
major claws of each crab were photographed and landmarks were placed at the
homologous points of the claws. Semi-landmarks were used for the claw tips
as there were no homologous points along the curvature.  ln centrold size
of each individual claw was computed and plotted against body size
(carapace width) of the crabs.  I am not sure if I am approaching this the
correct way. Any help would be appreciated.

Thanks in advance.

Adeline

--
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send an email to morphmet+unsubscr...@morphometrics.org.






--
Carmelo Fruciano
Marie Curie Fellow - University of Konstanz - Konstanz, Germany
Honorary Fellow - University of Catania - Catania, Italy
e-mail c.fruci...@unict.it
http://www.fruciano.it/research/

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