[MORPHMET] Warped Grids in MorphoJ

2015-02-12 Thread Michael Holmes
Hi All,
I am running MorphoJ on Mac OSX. I am looking at morhological variation
between two datasets. In each dataset, each specimen has four replicates. I
combined the datasets, made classifier files and ran the Procrustes fit and
generated the covariance matrix.  How then do I make a vector diagram/warp
grid that visualizes shape change between the average shape of the two
datasets? Thanks in advance for your help.

Mike


Michael W. Holmes

Ph.D. Candidate
University of California, Berkeley
Advisors: Dr. Rauri Bowie, Dr. Eileen Lacey

Museum of Vertebrate Zoology
3101 Valley Life Sciences Building
University of California
Berkeley, CA   94720  USA

http://ib.berkeley.edu/labs/lacey/holmes2.html

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Re: [MORPHMET] Warped Grids in MorphoJ

2015-02-12 Thread Emma Sherratt
Dear Mike,

One way you can do this is by using the canonical variates analysis
function. Between two groups you will get the shape change graph associate
with the difference between groups. Or you can go to Preliminaries 
average observations by... and choose the groups classifier, and then right
click and disply graphs.

Emma

~~~

Emma Sherratt, PhD.

Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L120 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5041
email: emma.sherr...@une.edu.au

Caecilians are legless amphibians...

*  __
(\   .-.   .-.   /_)
 \\_//^\\_//^\\_//
  ``   ``   ``*

learn more about them here: www.emmasherratt.com/caecilians




On 13 February 2015 at 07:16, Michael Holmes mhol...@berkeley.edu wrote:

 Hi All,
 I am running MorphoJ on Mac OSX. I am looking at morhological variation
 between two datasets. In each dataset, each specimen has four replicates. I
 combined the datasets, made classifier files and ran the Procrustes fit and
 generated the covariance matrix.  How then do I make a vector diagram/warp
 grid that visualizes shape change between the average shape of the two
 datasets? Thanks in advance for your help.

 Mike


 Michael W. Holmes

 Ph.D. Candidate
 University of California, Berkeley
 Advisors: Dr. Rauri Bowie, Dr. Eileen Lacey

 Museum of Vertebrate Zoology
 3101 Valley Life Sciences Building
 University of California
 Berkeley, CA   94720  USA

 http://ib.berkeley.edu/labs/lacey/holmes2.html

 --
 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

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


Re: [MORPHMET] Warped Grids in MorphoJ

2015-02-12 Thread Emma Sherratt
Oh sorry, I think the latter way just shows the group mean from the overall
mean - so you may need to do some cutting and pasting...
Contact Chris Klingenberg, he might have an easier way up his sleeve.

Emma

~~~

Emma Sherratt, PhD.

Lecturer in Zoology,
Zoology Division, School of Environmental and Rural Science,
Room L120 Bldg C02,
University of New England,
Armidale, NSW, Australia, 2351
Tel: +61 2 6773 5041
email: emma.sherr...@une.edu.au

Caecilians are legless amphibians...

*  __
(\   .-.   .-.   /_)
 \\_//^\\_//^\\_//
  ``   ``   ``*

learn more about them here: www.emmasherratt.com/caecilians




On 13 February 2015 at 09:02, Emma Sherratt emma.sherr...@gmail.com wrote:

 Dear Mike,

 One way you can do this is by using the canonical variates analysis
 function. Between two groups you will get the shape change graph associate
 with the difference between groups. Or you can go to Preliminaries 
 average observations by... and choose the groups classifier, and then right
 click and disply graphs.

 Emma

 ~~~

 Emma Sherratt, PhD.

 Lecturer in Zoology,
 Zoology Division, School of Environmental and Rural Science,
 Room L120 Bldg C02,
 University of New England,
 Armidale, NSW, Australia, 2351
 Tel: +61 2 6773 5041
 email: emma.sherr...@une.edu.au

 Caecilians are legless amphibians...

 *  __
 (\   .-.   .-.   /_)
  \\_//^\\_//^\\_//
   ``   ``   ``*

 learn more about them here: www.emmasherratt.com/caecilians




 On 13 February 2015 at 07:16, Michael Holmes mhol...@berkeley.edu wrote:

 Hi All,
 I am running MorphoJ on Mac OSX. I am looking at morhological variation
 between two datasets. In each dataset, each specimen has four replicates. I
 combined the datasets, made classifier files and ran the Procrustes fit and
 generated the covariance matrix.  How then do I make a vector diagram/warp
 grid that visualizes shape change between the average shape of the two
 datasets? Thanks in advance for your help.

 Mike


 Michael W. Holmes

 Ph.D. Candidate
 University of California, Berkeley
 Advisors: Dr. Rauri Bowie, Dr. Eileen Lacey

 Museum of Vertebrate Zoology
 3101 Valley Life Sciences Building
 University of California
 Berkeley, CA   94720  USA

 http://ib.berkeley.edu/labs/lacey/holmes2.html

 --
 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.




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To unsubscribe from this group and stop receiving emails from it, send an email 
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Re: [MORPHMET] 3D images - manipulation and registration?

2015-02-12 Thread Hildur Magnúsdóttir
Hi Stefan, 

Thank you very much for the tip. The *pcAlign* function worked like a charm!

Regards,
Hildur

On Thursday, February 5, 2015 at 3:45:56 PM UTC, Stefan Schlager wrote:

  Hi Hildur,

 you can try to use the function pcAlign (from my R-package Morpho), to 
 align meshes by their PC-axes. 
 And, if you like my (inofficial) package mesheR (
 https://github.com/zarquon42b/mesheR) is sporting a variety of rigid, 
 similarity, affine and elastic ICP registration procedures for 3D-meshes.

 Best 
 Stefan

 On 04/02/15 14:22, Hildur Magnúsdóttir wrote:
  
 Hi everyone,

 I'm using geometric morphometrics to study variation in the shell 
 morphology of the common whelk. I'm really interested in using 3D images as 
 a basis for this study but I'm having problems with manipulation and 
 registration (e.g. rigid registration) of my images prior to digitizing of 
 landmarks. 

 I'm using a MakerBot® Digitizer™ Desktop 3D Scanner for capturing the 3D 
 images and it generates either .stl or .ply files that I read into the R 
 for digitizing. My problem is that when I read those files into the R they 
 are not all oriented in the same way inside the box in the rgl window, thus 
 it is very hard to align them reliably so that the landmarks are truly 
 comparable between individuals. 

 So my question to you all is if you know of a method to align or register 
 the 3D images before I read them into R? Or of a package in R that can 
 perform this action?

 I would be very grateful for any advice on this,

 Hildur


Hildur Magnúsdóttir
 PhD Student
 University of Iceland, Department of Life and Environmental Sciences
  and Hólar University College, Department of Aquaculture and Fish Biology
  Telephone: +354 823 2485
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