[MORPHMET] Re: 2019 CALL FOR NOMINATIONS: The Rohlf Medal for Excellence in Morphometrics

[morphmet_moderator]

*
   
  Rohlf Medal Nomination Deadline  
   
*
This is a reminder that nominations for the 2019 Rohlf Medal are due by 
July 15. 

Recipients must agree to accept the award in person on October 24th, 2019 
at Stony Brook University.

The nominations of those who are not awarded the medal this year will be 
automatically rolled over for consideration in 2021. Any such application 
may be updated as appropriate.

For more information, visit https://life.bio.sunysb.edu/ee/rohlf_medal/

-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.org
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[MORPHMET] morphmet - list problems

[morphmet_moderator]

There seem to be some problems with the mailing list that have come to my 
attention over the past several days, e.g., it thinks every post is spam, 
but doesn't give me the chance to moderate such posts. Even I, the 
moderator, am only able to post via the website intermittently. 

There is a notice that the server-side software will be changed this month, 
so I suspect this is part of the problem, but I don't know. I am in contact 
with support to try to see what is going on. For now, I have no idea if 
your individual posts to the list (including this one - fourth attempt) 
will appear.

In the meantime, please be patient. 

-the moderator

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[MORPHMET] Testing - ignore

[morphmet_moderator]

Don't read this! 

Testing server-side problems. -ds 

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[MORPHMET] Re: PREPRINT: between-group principal components analysis (bgPCA)

[morphmet_moderator]

This and related threads have now been locked.

Non-morphometric issues should be taken up elsewhere.

Non-morphometric posts/replies are subject to deletion from the web site.

Violators are subject to being put back on the "moderation" list.

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[MORPHMET] Test post - ignore

[morphmet_moderator]

Have locked myself out of posting to the list. Trying to test. Ignore this 
message. -ds

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[MORPHMET] Re: New Article: Reflections on a Biometrics of Organismal Form

[morphmet_moderator]

Third time's a charm?
The previous, shorter link directs you through FSU libraries with a 
requisite login.
Trying again. I think this will take you directly to the article...

https://link.springer.com/article/10.1007/s13752-019-00320-y

-ds [the MORPHMET moderator]
On Tuesday, April 30, 2019 at 11:01:15 AM UTC-4, MORPHMET wrote:
>
> [Posted on behalf of Dr. Bookstein] 
>
> Dear MorphMetters, 
>
> I'm happy to announce that my paper "Reflections on a Biometrics of 
> Organismal Form" has just been posted for open access by the Springer 
> journal Biological Theory. You can get a free copy by pointing your browser 
> at 
>
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__link.springer.com_journal_13752&d=DwIBAg&c=HPMtquzZjKY31rtkyGRFnQ&r=T8Sxf-U51iRHIXQayyjGAA&m=xOGtb5kpXyYsx7O1ZPeSGHSsh8sLGcIwYOsLoNWTC3I&s=wQclw8xhArX7488PAUkyik6iPqlhj-vA5-el7VYzF-E&e=
>  
>
> and clicking on what is, for now, the top entry in the Latest Articles 
> table on the home page. 
>
> This article is a sequel to my 2015 article in Benedikt Hallgrimsson's 
> journal Evolutionary Biology that introduced the BE-PwV plot as the best 
> tool for studying integration in GMM data sets. I trace the basic idea here 
> back nearly a hundred years, not to D'Arcy Thompson but to a 
> hitherto-untranslated critique of his ideas by the Vivarium group under 
> Hans Przibram in Vienna arguing that the only valid way that a biologist 
> should study organismal form is by direct experimental observation of 
> transformation grids: "Thompson's holistic deformations can be made 
> comprehensible if we can visualize a space lattice upon the living form, so 
> as to assess how each little piece changes its shape under conditions that 
> vary by species. Here lies open a rich, nearly undeveloped field that 
> invites a mathematization, one whose erection we hope will begin very 
> soon." But the timing seems to have slipped a bit, namely, by 97 years. The 
> new paper argues that BE-PwV is exactly the "mathematization" they were 
> envisioning, which could not be made empirical until the development of 
> geometric morphometrics, and further that it is the only morphometric 
> method consistent with the most fundamental fact in all of biology, "the 
> repetitive production of organized heterogeneity" (Hotchkiss 1958) or, as 
> Walter Elsasser put it in 1987, "the transfer of information over finite 
> intervals of time without an intermediate message." For instance, the new 
> article demonstrates how to recognize a growth-gradient explicitly even in 
> the presence of unstructured residual variability. I close with a plea that 
> others help me build the bridge that we need so urgently between the 
> arithmetic of today's burgeoning image-based data resources and the 
> rhetoric of biological explanations of organismal form both over evolution 
> and over development. 
>
> As always I welcome all comments on these ideas, enthusiastic or 
> otherwise. 
>
>Fred Bookstein 
>

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[MORPHMET] Re: 2019 CALL FOR NOMINATIONS: The Rohlf Medal for Excellence in Morphometrics

[morphmet_moderator]

I especially call your attention to the requirement, "
*The winning candidate must agree to attend the award ceremony in *
*person in order to accept the Rohlf Medal and then deliver the award 
lecture."* 

I would recommend confirming with the potential recipient their willingness 
and ability to attend the award ceremony before following through with the 
effort of nomination.

You are also welcome to distribute this announcement to other groups or 
individuals with relevant interests.

-the moderator (dslice)

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Slicer question

[morphmet_moderator]

- Forwarded message from "Jones, Donna"  -

 Date: Sat, 26 Jul 2014 12:01:24 -0400
  From: "Jones, Donna"
  Reply-To: "Jones, Donna"
  Subject: Slicer question
  To: "morphmet@morphometrics.org"

 Dear Morphmet,

Does anyone have experience working with 3D Slicer and dicom slices from 
microCT? If yes, I’d be interested in asking you some direct questions about 
functionality.

Cheers,

Donna

*
Donna C. Jones, Ph.D.
Research Assistant Professor
Division of Plastic Surgery

Division of Biostatistics and Epidemiology
Cincinnati Children's Hospital Medical Center
 Burnett Ave. ML 2020
Cincinnati, OH 45229
phone: 513-803-0383

donna.jon...@cchmc.org

- End forwarded message -

RE: export scaled aligned specimens fails

[morphmet_moderator]

- Forwarded message from "F. James Rohlf"  -

 Date: Tue, 22 Jul 2014 22:55:41 -0400
  From: "F. James Rohlf" 
  Reply-To: ro...@life.bio.sunysb.edu
  Subject: RE: export scaled aligned specimens fails
  To: morphmet@morphometrics.org

Seems odd. I just tried it again with the current version and it seemed to work 
ok on a couple of my test datasets. Please send me the input files that 
demonstrate the problem as well as the incorrect output file that is produced. 

--

F. James Rohlf, Distinguished Professor Emeritus, Stony Brook University

The much revised 4th editions of Biometry and Statistical Tables are now 
available:

http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-rohlf

P Please consider the environment before printing this email 

From: morphmet_modera...@morphometrics.org 
[mailto:morphmet_modera...@morphometrics.org] 
Sent: Tuesday, July 22, 2014 10:29 PM
To: morphmet@morphometrics.org
Subject: export scaled aligned specimens fails

- Forwarded message from Markus Bastir  -

Date: Fri, 18 Jul 2014 04:52:24 -0400
From: Markus Bastir 
Reply-To: mbas...@mncn.csic.es
Subject: export scaled aligned specimens fails
To: morphmet@morphometrics.org

Dear all, 

I just discovered a new function of TPSRELW that offers to export the scaled 
aligned specimens (after semilandmarks sliding) for analysis in other packages. 

However, the software seems to export an erroneous TPS file. In my case it 
doubles the number of landmarks and adds features that only allow using this 
data after conversion to NTS format. The TPS file cannot be further used in the 
TPS-series. 

Does anybody share this experience?

Dr. Markus Bastir 

Department of Paleobiology

Museo Nacional de Ciencias Naturales CSIC

Tel. +34 91 566 8976

Web

- End forwarded message -

- End forwarded message -

Re: export scaled aligned specimens fails

[morphmet_moderator]

- Forwarded message from andrea cardini  -

 Date: Wed, 23 Jul 2014 02:53:51 -0400
  From: andrea cardini 
  Reply-To: andrea cardini 
  Subject: Re: export scaled aligned specimens fails
  To: morphmet@morphometrics.org

Hi Markus,
Jim kindly (as always) added that option about 
one year ago (if not earlier) after I bother him 
about it. By the way, thanks a lot, Jim!

I've used it a number of time but not very 
recently. I also compared it with doing the same 
thing manually in R or xls. I found virtually no 
differences but I seem to remember there was a 
caveat in the help file about this option (please, give a look at it). 

I suspect one cannot export the data as tps file, 
simply because, after superimposing and 
rescaling, the relationship of the points to the original pictures are lost. 

Cheers

Andrea

At 04:28 23/07/2014, you wrote:

>- Forwarded message from Markus Bastir  -
>
>Date: Fri, 18 Jul 2014 04:52:24 -0400
>From: Markus Bastir 
>Reply-To: mbas...@mncn.csic.es
>Subject: export scaled aligned specimens fails
>To: morphmet@morphometrics.org
>
>Dear all,
>
>
>I just discovered a new function of TPSRELW that 
>offers to export the scaled aligned specimens 
>(after semilandmarks sliding) for analysis in other packages. 
>
>
>
>However, the software seems to export an 
>erroneous TPS file. In my case it doubles the 
>number of landmarks and adds features that only 
>allow using this data after conversion to NTS 
>format. The TPS file cannot be further used in the TPS-series. 
>
>
>
>Does anybody share this experience?
>
>
>
>
>Dr. Markus Bastir
>
>
>Department of Paleobiology
>
>
>Museo Nacional de Ciencias Naturales CSIC
>
>
>Tel. +34 91 566 8976
>
>
>Web
>
>
>
>
>
>
>- End forwarded message -
>
>

Dr. Andrea Cardini
Researcher in Animal Biology, Dipartimento di 
Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, l.go S. Eufemia 19, 41121 Modena, Italy

Adjunct Associate Professor, Centre for Forensic 
Science , The University of Western Australia, 35 
Stirling Highway, Crawley WA 6009, Australia

E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: http://sites.google.com/site/hymsfme/drandreacardini
Summary of research interests at: 
http://www.dscg.unimore.it/site/home/ricerca/aree-di-ricerca/evolution-taxonomy-and-forensics.html

FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/issue/view/405
or full volume at: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf

Editorial board for:
Zoomorphology: 
http://www.springer.com/life+sciences/animal+sciences/journal/435
Journal of Zoological Systematics and 
Evolutionary Research: http://www.wiley.com/bw/journal.asp?ref=0947-5745&site=1
Hystrix, the Italian Journal of 
Mammalogy: http://www.italian-journal-of-mammalogy.it/ 

- End forwarded message -

geomorph 2.1.1 on CRAN

[morphmet_moderator]

- Forwarded message from "Adams, Dean [EEOBS]"  -

 Date: Mon, 21 Jul 2014 10:37:20 -0400
  From: "Adams, Dean [EEOBS]"
  Reply-To: "Adams, Dean [EEOBS]"
  Subject: geomorph 2.1.1 on CRAN
  To: "morphmet@morphometrics.org"

 Hi all,

A new version of geomorph is now up on the main CRAN repository. This version 
has a few small bug fixes, including some for the RRPP permutation options 
(others are described in the NEWS file of the program).

Dean

Dr. Dean C. Adams

Professor

Department of Ecology, Evolution, and Organismal Biology

   Department of Statistics

Iowa State University

www.public.iastate.edu/~dcadams/

phone: 515-294-3834

- End forwarded message -

On-line morphometrics course from Manchester

[morphmet_moderator]

- Forwarded message from Chris Klingenberg  -

 Date: Sun, 20 Jul 2014 14:03:19 -0400
  From: Chris Klingenberg 
  Reply-To: c...@manchester.ac.uk
  Subject: On-line morphometrics course from Manchester
  To: morphmet@morphometrics.org

Dear morphometricians

I am pleased to announce this year's morphometrics course from the 
University of Manchester. This year's course will run in the six weeks 
from 3 November to 12 December 2014. 

The course information can be found on the following we site:
http://www.flywings.org.uk/MorphoCourse

Course content:
*  Data acquisition: the kinds of data and the equipment used to collect 
them. 
*  Definitions of size and shape
*  Geometric methods to characterise shape from a configuration of 
landmark points (Procrustes superimposition)
*  Statistics of variation, scatter plots, basic multivariate statistics
*  Principal component analysis
*  Measurement error and outliers
*  Shape transformations and 'warping' -- the thin plate spline
*  Analysis of outline shapes
*  Distinguishing between groups (taxonomy, clinical diagnosis, etc.)
*  Allometry and size correction
*  Influence of external factors on shape (ecomorphology, dose-response 
studies)
*  Symmetric forms and measurement of asymmetry. 
*  Morphometric inferences on developmental processes
*  Morphological integration and modularity
*  Genetics of shape: analyses of resemblance between relatives, QTL 
analyses. 
*  Phylogeny: reconstructing the evolution of shape

Practice examples:
As far as possible, practical exercises are provided to accompany the 
course content. These practice exercises consist of data sets and 
explanations on how to run the respective analyses using the MorphoJ 
software (http://www.flywings.org.uk/MorphoJ_page.htm). 
Participants who already have their own data are encouraged to use those 
and to discuss them as part of the course. I hope there will be a bit of 
a 'workshop' feel to the course unit. 

Group work:
Participants will work in small groups to prepare web presentations of 
possible morphometric studies (wikis prepared by the groups). This 
activity stimulates discussion and provides a broad overview of the 
broad range of questions that can be addressed with morphometric methods. 

The fee for the course is GBP 320.00. 

All prospective participants need to pre-register for the course. The 
deadline for this is the *30 September 2014*. 

For further details and the pre-registration form, see the course web page:
http://www.flywings.org.uk/MorphoCourse

Best wishes,
Chris

-- 
***
Christian Peter Klingenberg
Faculty of Life Sciences
The University of Manchester
Michael Smith Building
Oxford Road
Manchester M13 9PT
United Kingdom

Telephone: +44 161 275 3899
Fax: +44 161 275 5082
E-mail: c...@manchester.ac.uk
Web: http://www.flywings.org.uk
Skype: chris_klingenberg
***

- End forwarded message -

RE: Problems with TPS files

[morphmet_moderator]

- Forwarded message from "F. James Rohlf"  -

 Date: Thu, 17 Jul 2014 21:46:14 -0400
  From: "F. James Rohlf"
  Reply-To: ro...@life.bio.sunysb.edu
  Subject: RE: Problems with TPS files
  To: morphmet@morphometrics.org

When encountering such problems,  first make sure you have the latest version. 
If so, then the quickest solution is to send me an email about the problem and 
have the tps file causing the problem attached so I can try to duplicate and 
then fix the problem. it could be a problem in the file but in that case I need 
to add a better error message.

--

F. James Rohlf, Distinguished Professor Emeritus, Stony Brook University

The much revised 4th editions of Biometry and Statistical Tables are now 
available:

http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-rohlf

P Please consider the environment before printing this email

From: morphmet_modera...@morphometrics.org 
[mailto:morphmet_modera...@morphometrics.org]
Sent: Thursday, July 17, 2014 9:17 PM
To: morphmet@morphometrics.org
Subject: Problems with TPS files

- Forwarded message from Margarida Antunes  -

Date: Mon, 14 Jul 2014 09:07:18 -0400
From: Margarida Antunes
Reply-To: Margarida Antunes
Subject: Problems with TPS files
To: morphmet@morphometrics.org

Hi!

I'm having some problems with 4 of my 60 TPS files ... did exactly the same 
thing in all of them, and yet these 4 work in TPSutil (I can make the 
link-file), run on TPSrelw (I can save the centroid-size and the relative warps 
matrix), but in TPSregr, when I try to import the tps file, a window appears 
that says "invalid pointer operation"

Does anyone know why? It has happened to anyone else? Please reply to 
mrgrdantu...@gmail.com

Thank you,

 

Margarida Antunes

- End forwarded message -

- End forwarded message -

export scaled aligned specimens fails

[morphmet_moderator]

- Forwarded message from Markus Bastir  -

 Date: Fri, 18 Jul 2014 04:52:24 -0400
  From: Markus Bastir 
  Reply-To: mbas...@mncn.csic.es
  Subject: export scaled aligned specimens fails
  To: morphmet@morphometrics.org

Dear all, 

I just discovered a new function of TPSRELW that offers to export the scaled 
aligned specimens (after semilandmarks sliding) for analysis in other packages. 

However, the software seems to export an erroneous TPS file. In my case it 
doubles the number of landmarks and adds features that only allow using this 
data after conversion to NTS format. The TPS file cannot be further used in the 
TPS-series. 

Does anybody share this experience?

Dr. Markus Bastir 

Department of Paleobiology

Museo Nacional de Ciencias Naturales CSIC

Tel. +34 91 566 8976

Web

- End forwarded message -

Measuring Landmarks from Point Clouds

[morphmet_moderator]

- Forwarded message from William Sellers  -

 Date: Tue, 15 Jul 2014 18:32:12 -0400
  From: William Sellers 
  Reply-To: William Sellers 
  Subject: Measuring Landmarks from Point Clouds
  To: morphmet@morphometrics.org

Just a little shameless self-promotion... I recently needed to digitise some 
landmarks from a large series of point clouds and couldn't find any software 
that made this process particularly easy so I wrote some. If you have similar 
requirements then you might find the software useful. It is called 
CloudDigitiser, it is open source and runs on Mac, Windows and Linux. You can 
download it from my website at:

http://www.animalsimulation.org

The program uses the letter and number keys to assign points so you can 
digitise up to 36 points per cloud very quickly indeed. It works on whole 
folders full of point clouds and lets you step back and forth between the 3D 
files with the cursor keys. It has various tools that let you align the point 
clouds with arbitrary axes and will allow you to calibrate the clouds if they 
are uncalibrated (e.g. from photogrammetry). However it cannot handle huge 
point clouds very efficiently although it works fine in the 1 million to 10 
million points range. It will probably work on bigger data sets but it will get 
slower. It reads the commonest PLY formats only but they are widely available 
and easy to convert to. The measurement data is stored in a human readable XML 
format (which can easily be read by R and Matlab). The landmarks measured are 
the mean of the points contained in a user specified sphere. 

Let me know if you find it useful and if there are any features that you would 
like. Some might be very easy to add,. 

Cheers
Bill
--
Bill Sellers, T: 0161 275 1719, M: 0785 7655786, 
william.sell...@manchester.ac.uk
University of Manchester, D1239 Michael Smith Building, Manchester, M13 9PT. 

- End forwarded message -

Problems with TPS files

[morphmet_moderator]

- Forwarded message from Margarida Antunes  -

 Date: Mon, 14 Jul 2014 09:07:18 -0400
  From: Margarida Antunes
  Reply-To: Margarida Antunes
  Subject: Problems with TPS files
  To: morphmet@morphometrics.org

Hi!

I'm having some problems with 4 of my 60 TPS files ... did exactly the same 
thing in all of them, and yet these 4 work in TPSutil (I can make the 
link-file), run on TPSrelw (I can save the centroid-size and the relative warps 
matrix), but in TPSregr, when I try to import the tps file, a window appears 
that says "invalid pointer operation"

Does anyone know why? It has happened to anyone else? Please reply to 
mrgrdantu...@gmail.com

Thank you,
 
Margarida Antunes

- End forwarded message -

Morphometrics survey

[morphmet_moderator]

- Forwarded message from David Katz  -

 Date: Sun, 13 Jul 2014 16:50:47 -0700
  From: David Katz
  Reply-To: David Katz
  Subject: Morphometrics survey
  To: morphmet

We've received funding from Building a Community of Natural History 
Collections, an NSF-funded RCN, to assess whether 3D photogrammetry is a 
suitable tool for natural history institutions to use a means to create digital 
archives of curated skeletal material. To focus this analysis, we would like 
input from the morphometrics community regarding which skeletal elements (and 
skeletal element sizes) are most frequently targeted for research.  

So, with your permission, I would like to post the following three-question 
survey on the morphmet listserve: https://www.surveymonkey.com/s/K55ZGLM

Thank you all for your time.

Sincerely,
David Katz

--
David Katz
Doctoral Candidate
Department of Anthropology--Evolutionary Wing
University of California, Davis
Young Hall 204

- End forwarded message -

Re: 3D surface and landmark visualization software - similarto EVAN

[morphmet_moderator]

- Forwarded message from andrea cardini  -

 Date: Thu, 10 Jul 2014 03:53:44 -0400
  From: andrea cardini 
  Reply-To: andrea cardini 
  Subject: Re: 3D surface and landmark visualization software - similarto 
EVAN
  To: morphmet@morphometrics.org

Did you try already landmark.exe? There should be a link in the SUNY webpage. 

To avoid rebooting when I need a Windows software 
on a Linux machine I've installed XP in VBox or VMware. 

Cheers

Andrea

At 06:16 10/07/2014, you wrote:

>- Forwarded message from Bill Beluch 
> -
>
>Date: Wed, 9 Jul 2014 04:57:48 -0400
>From: Bill Beluch 
>Reply-To: Bill Beluch 
>Subject: 3D surface and landmark visualization software - similar to EVAN
>To: morphmet@morphometrics.org
>
>Hello everyone,
>
>Unfortunately on my release of Ubuntu the EVAN 
>toolbox is not supported and I can not 
>successfully install it due to a missing 
>dependency.  Does anyone know of a program that 
>simply enables the user to visualize landmarks 
>on a 3D surface that is moveable and rotatable? 
>I use EVAN for this but have to reboot to a 
>Windows machine which is rather a pain to do.Â
>
>Best,
>Bill Beluch
>
>william.bel...@tuebingen.mpg.de
>
>
>
>- End forwarded message -
>
>

Dr. Andrea Cardini
Researcher in Animal Biology, Dipartimento di 
Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, l.go S. Eufemia 19, 41121 Modena, Italy

Adjunct Associate Professor, Centre for Forensic 
Science , The University of Western Australia, 35 
Stirling Highway, Crawley WA 6009, Australia

E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: http://sites.google.com/site/hymsfme/drandreacardini
Summary of research interests at: 
http://www.dscg.unimore.it/site/home/ricerca/aree-di-ricerca/evolution-taxonomy-and-forensics.html

FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/issue/view/405
or full volume at: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf

Editorial board for:
Zoomorphology: 
http://www.springer.com/life+sciences/animal+sciences/journal/435
Journal of Zoological Systematics and 
Evolutionary Research: http://www.wiley.com/bw/journal.asp?ref=0947-5745&site=1
Hystrix, the Italian Journal of 
Mammalogy: http://www.italian-journal-of-mammalogy.it/ 

- End forwarded message -

Fwd: Re: 3D surface and landmark visualization software - similar to EVAN

[morphmet_moderator]

- Forwarded message from Stefan Schlager  -

 Date: Thu, 10 Jul 2014 03:08:38 -0400
  From: Stefan Schlager
  Reply-To: Stefan Schlager
  Subject: Re: 3D surface and landmark visualization software - similar to 
EVAN
  To: morphmet@morphometrics.org

Hi Bill,

You can do this easily in R using the package rgl (wire3d, shade3d for meshes) 
and (points3d, spheres3d) for landmark matrices.

Meshes (obj, ply, stl) can be imported using for example the function vcgImport 
from my package Rvcg.

Here is an example (from my other package Morpho)

require(Morpho);require(rgl)
data(nose)
wire3d(shortnose.mesh,col="white")
spheres3d(shortnose.lm,col=3)

Or if you have a mix of semi-landmarks and classic landmarks you can use a 
wrapper:
require(Morpho)
 data(nose)
 atlas 

signature.asc
Description: PGP signature

3D surface and landmark visualization software - similar to EVAN

[morphmet_moderator]

- Forwarded message from Bill Beluch  -

 Date: Wed, 9 Jul 2014 04:57:48 -0400
  From: Bill Beluch
  Reply-To: Bill Beluch
  Subject: 3D surface and landmark visualization software - similar to EVAN
  To: morphmet@morphometrics.org

Hello everyone,

Unfortunately on my release of Ubuntu the EVAN toolbox is not supported and I 
can not successfully install it due to a missing dependency.  Does anyone know 
of a program that simply enables the user to visualize landmarks on a 3D 
surface that is moveable and rotatable? I use EVAN for this but have to reboot 
to a Windows machine which is rather a pain to do. 

Best,
Bill Beluch

william.bel...@tuebingen.mpg.de

- End forwarded message -

new publication on retrodeformation of fossils utilizing 3D GM

[morphmet_moderator]

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Sat, 05 Jul 2014 21:01:50 -0700
  From: morphmet_modera...@morphometrics.org
  Reply-To: morphmet_modera...@morphometrics.org
  Subject: new publication on retrodeformation of fossils utilizing 3D GM
  To: morphmet@morphometrics.org

- Forwarded message from Eric Delson  -

 Date: Fri, 4 Jul 2014 16:18:26 -0400
  From: Eric Delson
  Reply-To: Eric Delson
  Subject: new publication on retrodeformation of fossils utilizing 3D GM
  To: Morphmet Discussion Group

Dear Colleagues, some of you might be interested in this publication about a 
new method of retrodeformation of fossils utilizing 3D GM. If you would like to 
make use of the surface scans we have developed to test our approach, please 
let me know, and I will arrange to share them with you. We would love to see 
alternative methods applied to this dataset. Best regards, Eric

  * City University of New York, NYCEP and American Museum of Natural History

 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0100833

 It will also be available soon on the NYCEP Morphometrics Group site:  
http://pages.nycep.org/nmg
  *

- End forwarded message -

- End forwarded message -

Re: divide dataset

[morphmet_moderator]

- Forwarded message from "Collyer, Michael"  -

 Date: Fri, 4 Jul 2014 09:08:00 -0400
  From: "Collyer, Michael"
  Reply-To: "Collyer, Michael"
  Subject: Re: divide dataset
  To: ""

 Damien,

 If you plan on using geomorph, you can take advantage of the R environment to 
subset your landmarks.  Assuming you have used arrayspecs() to create a 
landmark array (call this e.g., my.landmarks) with p x k x n dimensions for the 
p landmarks in k landmark dimensions for n specimens, you can simply do 
something like,

 subset.a 

New publication - genetic introgression and morphospace occupationin brown trout

[morphmet_moderator]

- Forwarded message from Carmelo Fruciano  -

 Date: Fri, 4 Jul 2014 08:51:15 -0400
  From: Carmelo Fruciano 
  Reply-To: Carmelo Fruciano 
  Subject: New publication - genetic introgression and morphospace 
occupationin brown trout
  To: morphmet@morphometrics.org

Fruciano, C., Pappalardo, A.M., Tigano, C., Ferrito, V. 2014.  
Phylogeographic relationships of Sicilian brown trout and the effects  
of genetic introgression on morphospace occupation. Biological Journal  
of the Linnean Society 112:387-398. 
http://onlinelibrary.wiley.com/doi/10./bij.12279/

Best,
Carmelo

-- 
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/

- End forwarded message -

RE: divide dataset

[morphmet_moderator]

- Forwarded message from "F. James Rohlf"  -

 Date: Fri, 4 Jul 2014 08:39:20 -0400
  From: "F. James Rohlf"
  Reply-To: ro...@life.bio.sunysb.edu
  Subject: RE: divide dataset
  To: morphmet@morphometrics.org

The tpsUtil program can be used to split a tps into two or more tps files but 
the specimens to be placed in different groups must be contiguous in the 
original tps file. The software can also be used to reorder the specimens. Both 
of these are “manual” operation not ones based on information within the tps 
file.

--

F. James Rohlf, Distinguished Professor Emeritus, Stony Brook University

The much revised 4th editions of Biometry and Statistical Tables are now 
available:

http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-rohlf

P Please consider the environment before printing this email

From: morphmet_modera...@morphometrics.org 
[mailto:morphmet_modera...@morphometrics.org]
Sent: Friday, July 04, 2014 1:38 AM
To: morphmet@morphometrics.org
Subject: divide dataset

- Forwarded message from Damien Esquerre Gheur  -

Date: Thu, 3 Jul 2014 02:32:45 -0400
From: Damien Esquerre Gheur
Reply-To: Damien Esquerre Gheur
Subject: divide dataset
To: "morphmet@morphometrics.org"

Hello,

I have a huge tps file with hundreds of digitised photographs, but these are 
now going to be used in different analyses so I need to perform analyses with 
different softwares on different subsets of these data. Is there a way to 
divide this dataset using different classfiers and make different tps files?

I know MorphoJ can do something like this but I don't think it can export this 
dataset so it can be used in Geomorph for example.

Thank you very much!

Damien Esquerre

The Australian National University

- End forwarded message -

- End forwarded message -

Re: divide dataset

[morphmet_moderator]

- Forwarded message from andrea cardini  -

 Date: Fri, 4 Jul 2014 03:04:11 -0400
  From: andrea cardini 
  Reply-To: andrea cardini 
  Subject: Re: divide dataset
  To: morphmet@morphometrics.org

Damien, there's many ways of doing this. 

TPSUtil has options for subdividing files (if I 
remember well) and selecting specimens. 
Sometimes I use textwedge (free software) to 
split files (any type of ascii file). You'll 
need, probably, a bit of work to make it the way you want. 
Certainly you can import TPS in MorphoJ, split it 
according to classifiers and then import the 
output in R (maybe, again, with a few manual before doing it). 
In R there are various ways of subsetting data, 
but this is something you'll get a better advice 
from the 'R people' in the list. This last 
option, I have little doubt, is the most efficient, if you know how to do it. 

Good luck

Andrea

At 07:38 04/07/2014, you wrote:

>- Forwarded message from Damien Esquerre 
>Gheur  -
>
>Date: Thu, 3 Jul 2014 02:32:45 -0400
>From: Damien Esquerre Gheur 
>Reply-To: Damien Esquerre Gheur 
>Subject: divide dataset
>To: "morphmet@morphometrics.org" 
>
>Hello,
>
>I have a huge tps file with hundreds of 
>digitised photographs, but these are now going 
>to be used in different analyses so I need to 
>perform analyses with different softwares on 
>different subsets of these data. Is there a way 
>to divide this dataset using different classfiers and make different tps files?
>
>I know MorphoJ can do something like this but I 
>don't think it can export this dataset so it can 
>be used in Geomorph for example. 
>
>Thank you very much!
>
>Damien Esquerre
>
>The Australian National University
>
>
>
>- End forwarded message -
>
>

Dr. Andrea Cardini
Researcher in Animal Biology, Dipartimento di 
Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, l.go S. Eufemia 19, 41121 Modena, Italy

Adjunct Associate Professor, Centre for Forensic 
Science , The University of Western Australia, 35 
Stirling Highway, Crawley WA 6009, Australia

E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: http://sites.google.com/site/hymsfme/drandreacardini
Summary of research interests at: 
http://www.dscg.unimore.it/site/home/ricerca/aree-di-ricerca/evolution-taxonomy-and-forensics.html

FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/issue/view/405
or full volume at: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf

Editorial board for:
Zoomorphology: 
http://www.springer.com/life+sciences/animal+sciences/journal/435
Journal of Zoological Systematics and 
Evolutionary Research: http://www.wiley.com/bw/journal.asp?ref=0947-5745&site=1
Hystrix, the Italian Journal of 
Mammalogy: http://www.italian-journal-of-mammalogy.it/ 

- End forwarded message -

Re: Data sharing query - 3D modern human skulls

[morphmet_moderator]

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Thu, 03 Jul 2014 22:46:41 -0700
  From: morphmet_modera...@morphometrics.org
  Reply-To: morphmet_modera...@morphometrics.org
  Subject: Re: Data sharing query - 3D modern human skulls
  To: morphmet@morphometrics.org

- Forwarded message from Jo Gooding  -

 Date: Thu, 3 Jul 2014 16:12:51 -0400
  From: Jo Gooding
  Reply-To: jg1753.2...@my.bristol.ac.uk
  Subject: Re: Data sharing query - 3D modern human skulls
  To: morphmet@morphometrics.org

Hi Don, 
Thanks for getting in touch and I'm more than willing to share! I'm in the very 
early stages of my study so not too much to say at the moment, but the idea is 
to investigate cranio-facial variation within a local population of modern 
humans to try and aid understanding/interpretation of intra vs inter specific 
variation in fossil contexts. I'm planning to digitise at least 250 crania from 
a local Bristol population who died in the 1700's. As my time will be a bit 
limited, the Principle Variance analysis on an existing dataset will hopefully 
identify landmarks that are particularly good predictors of others/don't offer 
significant additional information and if so I can make an educated choice for 
a really informative subset.  A couple of people have got in touch with 
suitable data which is great, so also more than happy to let you know how it 
turns out. 

I'd be really interested to know more about your research if you could send me 
a link? Thanks again for getting in touch. 

Jo

On Thu, Jul 3, 2014 at 5:02 AM,   wrote:

- Forwarded message from "Lewis, Dr. Donald"  -

 Date: Wed, 2 Jul 2014 01:07:33 -0400
  From: "Lewis, Dr. Donald"
Reply-To: "Lewis, Dr. Donald"
  Subject: Re: Data sharing query - 3D modern human skulls
  To: morphmet@morphometrics.org

Jo,
As I use the MicroScribe on studying human and proto-human skulls, I would like 
to hear more about your study, assuming you are willing to share.
Please contact me off MorphMet at 
dle...@ksbhospital.com

Good luck. 
Don Lewis

Donald R. lewis MD FACS
NIU, DeKalb, Illinois and
Univ. of IL, Chicago,
Sch. of Med. (Rockford)

Sent from my iPhone

On Jul 1, 2014, at 8:17 PM, "morphmet_modera...@morphometrics.org"  wrote:

- Forwarded message from Jo Gooding  -

 Date: Tue, 1 Jul 2014 11:12:26 +0100
  From: Jo Gooding
  Reply-To: jg1753.2...@my.bristol.ac.uk
  Subject: Data sharing query - 3D modern human skulls
  To: morphmet_modera...@morphometrics.org

 Hi all, 

 I'm a MSc Palaeobiology student at the University of Bristol and I'm about to 
start a 3-D Geometric Morphometric study on a sample of modern human skulls, 
using a microscribe. 

I'm working with a statistician to explore how to minimise information loss if 
using a carefully-selected subset of landmarks. To this end we'd like to carry 
out a procedure called Principle Variables on an existing dataset of 3-D 
co-ordinates. I wondered if anyone's aware of any freely available datasets we 
could run an analysis on or if anyone would be able/willing to share raw data 
with me. The outcome might be quite useful in general. 

Thanks and best wishes

Jo

- End forwarded message -

Please
consider
the environment before printing this email.

Confidentiality Notice
This electronic mail transmission and any accompanying documents contain
information belonging to the sender, which may be confidential and legally
privileged. This information is intended only for the use of the individual or
entity to whom this electronic mail transmission was sent as indicated above. If
you are not the intended recipient, any disclosure, copying, distribution, or
action taken in reliance on the contents of the information contained in this
transmission is strictly prohibited. If you are not the addressee identified
above, you have received this transmission in error. We ask that you please call
us collect at 815.288.5531 to report the receipt, and that you immediately
delete the transmission.
Thank you.

- End forwarded message -

- End forwarded message -

- End forwarded message -

Re: Data sharing query - 3D modern human skulls

[morphmet_moderator]

- Forwarded message from Ann Ross  -

 Date: Thu, 3 Jul 2014 07:45:27 -0400
  From: Ann Ross
  Reply-To: Ann Ross
  Subject: Re: Data sharing query - 3D modern human skulls
  To: morphmet@morphometrics.org

Dear All,
I have shared links to two databases we have just made public.
 
One is a contemporary/modern coordinate landmark database with approximately 
800 individuals from different regions of the world and the other is a 
traditional craniometric database with "Hispanic" populations with 
prehistoric/contemporary New World samples and Spanish samples.
 
You can access both databases through the new 3D-ID website (it will be 
available through www.3d-id.org once we have completed the re-mapping of the 
site).
 
https://sites.google.com/a/ncsu.edu/forensic-3d-and-traditional-craniometric-database/

 
 
Best,
Ann

On Thu, Jul 3, 2014 at 12:02 AM,   wrote:

- Forwarded message from "Lewis, Dr. Donald"  -

 Date: Wed, 2 Jul 2014 01:07:33 -0400
  From: "Lewis, Dr. Donald"
Reply-To: "Lewis, Dr. Donald"
  Subject: Re: Data sharing query - 3D modern human skulls
  To: morphmet@morphometrics.org

Jo,
As I use the MicroScribe on studying human and proto-human skulls, I would like 
to hear more about your study, assuming you are willing to share.
Please contact me off MorphMet at 
dle...@ksbhospital.com

Good luck. 
Don Lewis

Donald R. lewis MD FACS
NIU, DeKalb, Illinois and
Univ. of IL, Chicago,
Sch. of Med. (Rockford)

Sent from my iPhone

On Jul 1, 2014, at 8:17 PM, "morphmet_modera...@morphometrics.org"  wrote:

- Forwarded message from Jo Gooding  -

 Date: Tue, 1 Jul 2014 11:12:26 +0100
  From: Jo Gooding
  Reply-To: jg1753.2...@my.bristol.ac.uk
  Subject: Data sharing query - 3D modern human skulls
  To: morphmet_modera...@morphometrics.org

Hi all, 

 I'm a MSc Palaeobiology student at the University of Bristol and I'm about to 
start a 3-D Geometric Morphometric study on a sample of modern human skulls, 
using a microscribe. 

I'm working with a statistician to explore how to minimise information loss if 
using a carefully-selected subset of landmarks. To this end we'd like to carry 
out a procedure called Principle Variables on an existing dataset of 3-D 
co-ordinates. I wondered if anyone's aware of any freely available datasets we 
could run an analysis on or if anyone would be able/willing to share raw data 
with me. The outcome might be quite useful in general. 

Thanks and best wishes

Jo

- End forwarded message -

Please consider
the environment before printing this email.

Confidentiality Notice
This electronic mail transmission and any accompanying documents contain
information belonging to the sender, which may be confidential and legally
privileged. This information is intended only for the use of the individual or
entity to whom this electronic mail transmission was sent as indicated above. If
you are not the intended recipient, any disclosure, copying, distribution, or
action taken in reliance on the contents of the information contained in this
transmission is strictly prohibited. If you are not the addressee identified
above, you have received this transmission in error. We ask that you please call
us collect at 815.288.5531 to report the receipt, and that you immediately
delete the transmission.
Thank you.

- End forwarded message -

--
Ann H. Ross, Ph.D.,D-ABFA
Professor of Anthropology
University Faculty Scholar
Co-Director Forensic Sciences Institute
NC State University
Department of Sociology
and Anthropology
Campus Box 8107
Raleigh, NC 27695-8107

Tel. 919-515-9021
Fax 919-513-0866
http://anthropology.chass.ncsu.edu/forensics/

 
fsi.ncsu.edu

Research Collaborator,
NMNH, Smithsonian Institution

Trustee, Montessori School of Raleigh
https://msr.org/msr-orgiam/

- End forwarded message -

Re: Converting jpeg to tps

[morphmet_moderator]

- Forwarded message from "M. Viviana Toro Ibacache"  -

 Date: Thu, 3 Jul 2014 09:16:08 -0400
  From: "M. Viviana Toro Ibacache"
  Reply-To: "M. Viviana Toro Ibacache"
  Subject: Re: Converting jpeg to tps
  To: morphmet@morphometrics.org

Dear Winnie,

I am not sure I understand correctly. Do you want to use pictures, place 
landmarks, and then use these to perform analyses in MorphoJ? If so:

- Landmarks are to be placed in software other than MorphoJ. MorphoJ is for 
analysis, not for aquiring landmark data.
 - You can open your pictures as JPG in TPSDig. Then, you place landmarks. The 
output file containing the landmark data is a TPS file.
- You can append the landmark data of several individuals into one single TPS 
file, using TPSUtil.
 - Then, you can use this TPS file (with several individuals) to perform 
analyses in MorphoJ.

I hope this clarifies it a bit.

Best wishes,

Viviana

2014-07-03 6:05 GMT+02:00  :

- Forwarded message from "Okeyo, Winnie Akoth"  -

 Date: Wed, 2 Jul 2014 05:21:04 -0400
  From: "Okeyo, Winnie Akoth"
Reply-To: "Okeyo, Winnie Akoth"
  Subject: Converting jpeg to tps
  To: "morphmet@morphometrics.org"

Hello guys,

I am a research assistant and this is my first time dealing with morphometrics.

I know I need to change my wing pictures from Jpeg to tps for me to input them 
into MorphoJ for further analysis. I already have tpsUtil and tpsDig2 on my 
laptop but I just can’t figure out how to make the conversion do that I put in 
the landmarks?  

Regards,

Winnie Okeyo.

- End forwarded message -

--
Viviana Toro-Ibacache DDS MSc PhD
Universidad de Chile - Hull York Medical School

- End forwarded message -

RE: Converting jpeg to tps

[morphmet_moderator]

- Forwarded message from Markus Bastir  -

 Date: Thu, 3 Jul 2014 06:08:55 -0400
  From: Markus Bastir
  Reply-To: mbas...@mncn.csic.es
  Subject: RE: Converting jpeg to tps
  To: morphmet@morphometrics.org

Hi Winnie

Thats easy. Just put all your jpgs, properly named, into one folder. Then use 
tpsUTIL to “build tps file from images”, go through the path to the jpg folder 
and select on image, and save the file as “data.tps” or whateveryouwnat.tps 
Then use tpsDIG to open the just created tps file and start digitizing.

Best

markus

De: morphmet_modera...@morphometrics.org 
[mailto:morphmet_modera...@morphometrics.org]
Enviado el: jueves, 03 de julio de 2014 6:06
Para: morphmet@morphometrics.org
Asunto: Converting jpeg to tps

- Forwarded message from "Okeyo, Winnie Akoth"  -

Date: Wed, 2 Jul 2014 05:21:04 -0400
From: "Okeyo, Winnie Akoth"
Reply-To: "Okeyo, Winnie Akoth"
Subject: Converting jpeg to tps
To: "morphmet@morphometrics.org"

Hello guys,

I am a research assistant and this is my first time dealing with morphometrics.

I know I need to change my wing pictures from Jpeg to tps for me to input them 
into MorphoJ for further analysis. I already have tpsUtil and tpsDig2 on my 
laptop but I just can’t figure out how to make the conversion do that I put in 
the landmarks?  

Regards,

Winnie Okeyo.

- End forwarded message -

- End forwarded message -

Re: Converting jpeg to tps

[morphmet_moderator]

- Forwarded message from andrea cardini  -

 Date: Thu, 3 Jul 2014 04:54:07 -0400
  From: andrea cardini 
  Reply-To: andrea cardini 
  Subject: Re: Converting jpeg to tps
  To: morphmet@morphometrics.org

Winnie, TPS is not an image file format. It's 
ascii file with information that allows TPSDig to 
'find' the pictures and load them to digitize the 
landmarks. In the same file you will then save the landmark coordinates. 

All the programs of the TPS Series have extensive 
help files. You may want to start from there 
(first TPSDig and TPSUtil help files). You'll see 
how easy it is to build the tps TPS file in Util 
and later use it in Dig. In TPSDig, don't forget the scale factor!

Cheers

Andrea

At 06:05 03/07/2014, you wrote:

>- Forwarded message from "Okeyo, Winnie Akoth"  -
>
>Date: Wed, 2 Jul 2014 05:21:04 -0400
>From: "Okeyo, Winnie Akoth" 
>Reply-To: "Okeyo, Winnie Akoth" 
>Subject: Converting jpeg to tps
>To: "morphmet@morphometrics.org" 
>
>Hello guys,
>
>
>
>I am a research assistant and this is my first 
>time dealing with morphometrics. 
>
>
>
>I know I need to change my wing pictures from 
>Jpeg to tps for me to input them into MorphoJ 
>for further analysis. I already have tpsUtil and 
>tpsDig2 on my laptop but I just can’t figure 
>out how to make the conversion do that I put in the landmarks? Â
>
>
>
>Regards,
>
>
>Winnie Okeyo. 
>
>
>
>
>
>- End forwarded message -
>
>

Dr. Andrea Cardini
Researcher in Animal Biology, Dipartimento di 
Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, l.go S. Eufemia 19, 41121 Modena, Italy

Adjunct Associate Professor, Centre for Forensic 
Science , The University of Western Australia, 35 
Stirling Highway, Crawley WA 6009, Australia

E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: http://sites.google.com/site/hymsfme/drandreacardini
Summary of research interests at: 
http://www.dscg.unimore.it/site/home/ricerca/aree-di-ricerca/evolution-taxonomy-and-forensics.html

FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/issue/view/405
or full volume at: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf

Editorial board for:
Zoomorphology: 
http://www.springer.com/life+sciences/animal+sciences/journal/435
Journal of Zoological Systematics and 
Evolutionary Research: http://www.wiley.com/bw/journal.asp?ref=0947-5745&site=1
Hystrix, the Italian Journal of 
Mammalogy: http://www.italian-journal-of-mammalogy.it/ 

- End forwarded message -

divide dataset

[morphmet_moderator]

- Forwarded message from Damien Esquerre Gheur  -

 Date: Thu, 3 Jul 2014 02:32:45 -0400
  From: Damien Esquerre Gheur
  Reply-To: Damien Esquerre Gheur
  Subject: divide dataset
  To: "morphmet@morphometrics.org"

 Hello,

 I have a huge tps file with hundreds of digitised photographs, but these are 
now going to be used in different analyses so I need to perform analyses with 
different softwares on different subsets of these data. Is there a way to 
divide this dataset using different classfiers and make different tps files?

 I know MorphoJ can do something like this but I don't think it can export this 
dataset so it can be used in Geomorph for example.

 Thank you very much!

 Damien Esquerre

 The Australian National University

- End forwarded message -

Converting jpeg to tps

[morphmet_moderator]

- Forwarded message from "Okeyo, Winnie Akoth"  -

 Date: Wed, 2 Jul 2014 05:21:04 -0400
  From: "Okeyo, Winnie Akoth"
  Reply-To: "Okeyo, Winnie Akoth"
  Subject: Converting jpeg to tps
  To: "morphmet@morphometrics.org"

Hello guys,

I am a research assistant and this is my first time dealing with morphometrics.

I know I need to change my wing pictures from Jpeg to tps for me to input them 
into MorphoJ for further analysis. I already have tpsUtil and tpsDig2 on my 
laptop but I just can’t figure out how to make the conversion do that I put in 
the landmarks?  

Regards,

Winnie Okeyo.

- End forwarded message -

Re: Data sharing query - 3D modern human skulls

[morphmet_moderator]

- Forwarded message from "Lewis, Dr. Donald"  -

 Date: Wed, 2 Jul 2014 01:07:33 -0400
  From: "Lewis, Dr. Donald"
  Reply-To: "Lewis, Dr. Donald"
  Subject: Re: Data sharing query - 3D modern human skulls
  To: morphmet@morphometrics.org

Jo,
As I use the MicroScribe on studying human and proto-human skulls, I would like 
to hear more about your study, assuming you are willing to share.
Please contact me off MorphMet at 
dle...@ksbhospital.com

Good luck. 
Don Lewis

Donald R. lewis MD FACS
NIU, DeKalb, Illinois and
Univ. of IL, Chicago,
Sch. of Med. (Rockford)

Sent from my iPhone

On Jul 1, 2014, at 8:17 PM, "morphmet_modera...@morphometrics.org"  wrote:

- Forwarded message from Jo Gooding  -

 Date: Tue, 1 Jul 2014 11:12:26 +0100
  From: Jo Gooding
  Reply-To: jg1753.2...@my.bristol.ac.uk
  Subject: Data sharing query - 3D modern human skulls
  To: morphmet_modera...@morphometrics.org

Hi all, 

 I'm a MSc Palaeobiology student at the University of Bristol and I'm about to 
start a 3-D Geometric Morphometric study on a sample of modern human skulls, 
using a microscribe. 

I'm working with a statistician to explore how to minimise information loss if 
using a carefully-selected subset of landmarks. To this end we'd like to carry 
out a procedure called Principle Variables on an existing dataset of 3-D 
co-ordinates. I wondered if anyone's aware of any freely available datasets we 
could run an analysis on or if anyone would be able/willing to share raw data 
with me. The outcome might be quite useful in general. 

Thanks and best wishes

Jo

- End forwarded message -

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- End forwarded message -

RE: Image rotation data loss

[morphmet_moderator]

- Forwarded message from "F. James Rohlf"  -

 Date: Mon, 30 Jun 2014 13:15:24 -0400
  From: "F. James Rohlf"
  Reply-To: ro...@life.bio.sunysb.edu
  Subject: RE: Image rotation data loss
  To: morphmet@morphometrics.org

My tps software explicitly takes images as they are and does not reflect them 
(except by a direct transformation in tpsDig2). Some equations for Procrustes 
fitting are given on page 42 of Rohlf and Slice (1990, Systematic Zoology). 
While straight-forward matrix algebra for a Procrustes fit would automatically 
reflect if it would achieve a better fit, we used Gower’s (1971, Biometrika) 
formulation that prevents reflections.  In recent versions of the software I 
use a method based on complex regression because it is somewhat faster and 
still prevents reflections.

The reason for not permitting reflections is that it is possible for some 
simple shapes to vary in ways that look like reflections although the organism 
has not actually been reflected. However, general purpose software has to guard 
against cases in which some of the images are reflected relative to the others. 
I guess I could/should have added it as an option in the software - but that 
has not happened yet. An illustration of some of the statistical problems in 
blindly ignoring reflections are described on page 680 of Rohlf (2003, J. of 
Human Evolution). In certain cases it can introduce a systematic bias. This is 
one of the problems with EDMA and other morphometric methods that ignore 
reflections.

A simple example that I often use in class is shown on page 127 of the “white 
book”. One could create similar examples for 3D landmarks. This point is 
normally not important in practice because more landmarks are usually used and 
their arrangement usually does not allow their actual shape variation to be 
confused with their reflections.

Hope this helps.

--

F. James Rohlf, Distinguished Professor Emeritus, Stony Brook University

The much revised 4th editions of Biometry and Statistical Tables are now 
available:

http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-rohlf

P Please consider the environment before printing this email

From: morphmet_modera...@morphometrics.org 
[mailto:morphmet_modera...@morphometrics.org]
Sent: Monday, June 30, 2014 1:03 AM
To: morphmet@morphometrics.org
Subject: Re: Image rotation data loss

- Forwarded message from Joseph Kunkel  -

Date: Sun, 29 Jun 2014 19:47:55 -0400
From: Joseph Kunkel
Reply-To: Joseph Kunkel
Subject: Re: Image rotation data loss
To: morphmet@morphometrics.org

I know that in Rohlf's tpsSuite of software that the geometric equations allow 
for accepting left and right wing data without reflecting them.  I do the 
algebra myself in R and there I also find that the matrix algebra will 
automatically fit a left or right wing onto the model.  Mirror wings are a 
simple rotation onto the model.  Being mostly 2-D with wings,  I would have to 
think it over whether the 3-D landmarks would be treated similarly.  Jim needs 
to chime in here about the 3-D symmetry and how automatic the matrix algebra 
and rotation matrices deal with symmetry.

Joe

On Jun 29, 2014, at 4:44 AM, morphmet  wrote:

 Original Message 
Subject: Re: Fwd: Re: Image rotation data loss
Date: Sun, 29 Jun 2014 04:43:20 -0400
From: Dennis E. Slice
To: morphmet@morphometrics.org

Also, your message suggests all images were in the same orientation. If some 
were reflected and others not, I don't think tps allows reflection by default. 
-ds

On 6/29/14, 3:53 AM, morphmet wrote:

 Original Message 
Subject: Re: Image rotation data loss
Date: Sun, 29 Jun 2014 03:38:32 -0400
From: Dennis E. Slice
To: morphmet@morphometrics.org

First guess would be your landmarks are out of order on one or more
specimens. You can check this by creating a set of links in tpsUtil and
plotting the data showing the links. And/or, in tps, plot the data
showing points and vectors. -ds

On 6/29/14, 12:27 AM, morphmet_modera...@morphometrics.org wrote:

Hello all,

I'm trying to digitize photos in tpsDig for a geometric morphometrics
study on Notropis fishes. In order to test for digitization error I've
copied the first fish photo I took 10 times and digitized each one onto
the same TPS file (made in tpsUtil). I then performed a relative warps
analysis in tpsRelw and performed a Procruste's superimposition in R
(package geomorph) to glance and see if any landmarks varied
significantly. My results show very drastic variation in landmark
placement, with dots all over the place in the GPA plot. I know my
landmark placement isn't that bad, so I think it might have something to
do with data loss. When I photographed the specimen the fish was
flipped, so I had to rotate and flip it to turn it rightside up before
digitization. Is it possible that rotating t

Data sharing query - 3D modern human skulls

[morphmet_moderator]

- Forwarded message from Jo Gooding  -

 Date: Tue, 1 Jul 2014 11:12:26 +0100
  From: Jo Gooding
  Reply-To: jg1753.2...@my.bristol.ac.uk
  Subject: Data sharing query - 3D modern human skulls
  To: morphmet_modera...@morphometrics.org

Hi all, 

 I'm a MSc Palaeobiology student at the University of Bristol and I'm about to 
start a 3-D Geometric Morphometric study on a sample of modern human skulls, 
using a microscribe. 

I'm working with a statistician to explore how to minimise information loss if 
using a carefully-selected subset of landmarks. To this end we'd like to carry 
out a procedure called Principle Variables on an existing dataset of 3-D 
co-ordinates. I wondered if anyone's aware of any freely available datasets we 
could run an analysis on or if anyone would be able/willing to share raw data 
with me. The outcome might be quite useful in general. 

Thanks and best wishes

Jo

- End forwarded message -

Re: Image rotation data loss

[morphmet_moderator]

- Forwarded message from Joseph Kunkel  -

 Date: Sun, 29 Jun 2014 19:47:55 -0400
  From: Joseph Kunkel
  Reply-To: Joseph Kunkel
  Subject: Re: Image rotation data loss
  To: morphmet@morphometrics.org

I know that in Rohlf's tpsSuite of software that the geometric equations allow 
for accepting left and right wing data without reflecting them.  I do the 
algebra myself in R and there I also find that the matrix algebra will 
automatically fit a left or right wing onto the model.  Mirror wings are a 
simple rotation onto the model.  Being mostly 2-D with wings,  I would have to 
think it over whether the 3-D landmarks would be treated similarly.  Jim needs 
to chime in here about the 3-D symmetry and how automatic the matrix algebra 
and rotation matrices deal with symmetry.Joe

On Jun 29, 2014, at 4:44 AM, morphmet  wrote:

 Original Message 
Subject: Re: Fwd: Re: Image rotation data loss
Date: Sun, 29 Jun 2014 04:43:20 -0400
From: Dennis E. Slice
To: morphmet@morphometrics.org

Also, your message suggests all images were in the same orientation. If some 
were reflected and others not, I don't think tps allows reflection by default. 
-ds

On 6/29/14, 3:53 AM, morphmet wrote:

 Original Message 
Subject: Re: Image rotation data loss
Date: Sun, 29 Jun 2014 03:38:32 -0400
From: Dennis E. Slice
To: morphmet@morphometrics.org

First guess would be your landmarks are out of order on one or more
specimens. You can check this by creating a set of links in tpsUtil and
plotting the data showing the links. And/or, in tps, plot the data
showing points and vectors. -ds

On 6/29/14, 12:27 AM, morphmet_modera...@morphometrics.org wrote:

  Hello all,

I'm trying to digitize photos in tpsDig for a geometric morphometrics
study on Notropis fishes. In order to test for digitization error I've
copied the first fish photo I took 10 times and digitized each one onto
the same TPS file (made in tpsUtil). I then performed a relative warps
analysis in tpsRelw and performed a Procruste's superimposition in R
(package geomorph) to glance and see if any landmarks varied
significantly. My results show very drastic variation in landmark
placement, with dots all over the place in the GPA plot. I know my
landmark placement isn't that bad, so I think it might have something to
do with data loss. When I photographed the specimen the fish was
flipped, so I had to rotate and flip it to turn it rightside up before
digitization. Is it possible that rotating the photo resulted in data
loss and therefore digitization error? The TPS file had the landmark
coordinates for each specimen pretty close together (about normal
landmark placement error), but the GPA and relative warps plots showed
drastic variance. I've attached the GPA plot to show what I mean. The
landmarks are supposed to go around the entire fish. Also let me know if
you have any other ideas for why there might be crazy variance.

Best,

Connor
connorfre...@utexas.edu

- End forwarded message -

- End forwarded message -

- End forwarded message -

 -·.  .· ·.  .>·.  .· ·.  .>·.  .· ·.  .> .··.· >=-   =º}><
Joseph G. Kunkel, Research Professor
112A Marine Science Center
University of New England
Biddeford ME 04005
http://www.bio.umass.edu/biology/kunkel/

- End forwarded message -

New GM Arthropod Bibliography

[morphmet_moderator]

- Forwarded message from Ivan Huber  -

 Date: Sun, 29 Jun 2014 15:46:48 +
  From: Ivan Huber
  Reply-To: Ivan Huber
  Subject: New GM Arthropod Bibliography
  To: "morphmet_modera...@morphometrics.org"

 When sending me emails, please include the word MorphoLib on the Subject line 
so that your message will not be sorted into a spam folder. Thanks.  Ivan

- End forwarded message -

Arthropod bibliography list on MorphoLib

[morphmet_moderator]

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Fri, 27 Jun 2014 21:37:22 -0700
  From: morphmet_modera...@morphometrics.org
  Reply-To: morphmet_modera...@morphometrics.org
  Subject: Arthropod bibliography list on MorphoLib
  To: morphmet@morphometrics.org

- Forwarded message from Mauro Cavalcanti  -

 Date: Thu, 26 Jun 2014 21:59:27 -0400
  From: Mauro Cavalcanti
Reply-To: Mauro Cavalcanti
  Subject: Arthropod bibliography list on MorphoLib
  To: morphmet@morphometrics.org

Dear Morphometricians:

I am pleased to announce another bibliography to be added to MorphoLib.  It is 
to be on the Arthropoda and will be curated by Ivan Huber, a retired 
entomologist, now living in Los Angeles.  He studied with Robert Sokal  and his 
dissertation was a numerical taxonomic (phenetic) study of cockroaches.  In 
particular, he was interested in classifications produced from data on nymphs 
as well as adults.  His email is  i...@randomtech.com.  He may also be 
contacted by phone or Skype. Please send him information on your own 
contributions in addition to any others known to you. Relevant pre-GM 
publications may also be suitable for inclusion.  He plans to group the papers 
under major groupings:  Insecta, Crustacea, etc., subject to users’ comments 
and suggestions.  As is true of my other bibliographies, he will take your 
references and submit them to JabRef to convert them to BibTeX and then both 
will be made available online.  

He also asked me to say that, since he is retired and lacks adequate library 
support, he would appreciate copies of any publications that are not freely 
available which you might care to send him.

Visit http://morpholib.eu.pn/ for accessing this and other (fishes, mollusks) 
bibliography lists.

Hope this helps!

With best regards,

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

- End forwarded message -

- End forwarded message -

Re: landmark configuration reflection

[morphmet_moderator]

- Forwarded message from Miguel Eduardo Delgado Burbano  -

 Date: Wed, 25 Jun 2014 11:38:07 -0400
  From: Miguel Eduardo Delgado Burbano
  Reply-To: Miguel Eduardo Delgado Burbano
  Subject: Re: landmark configuration reflection
  To: morphmet@morphometrics.org

Hi Andrea

Again thanks for your guidelines. Yes actually Denis Slice sent me days ago a 
new version of Morpheus where it is possible to reflect a landmark 
configuration, I tested such interface in Morpheus and works quite fine!!. 
However, the procedure in PAST is new for me so I will explore. 

best

Miguel  

On Wed, Jun 25, 2014 at 3:07 AM,   wrote:

- Forwarded message from morphmet_modera...@morphometrics.org -

     Date: Thu, 19 Jun 2014 21:10:19 -0700
      From: morphmet_modera...@morphometrics.org
      Reply-To: morphmet_modera...@morphometrics.org
      Subject: Re: landmark configuration reflection
      To: morphmet@morphometrics.org

- Forwarded message from andrea cardini  -

Date: Tue, 17 Jun 2014 02:38:19 -0400
From: andrea cardini
Reply-To: andrea cardini
Subject: Re: landmark configuration reflection

To: morphmet@morphometrics.org, morphmet@morphometrics.org

Not sure if I had replied yet. If so, my apologies for re-replying.

We wrote a mini-tutorial about how to do this
'exploiting' some of the options of the old Morpheus et al.:
Cardini A., Diniz Filho J. A. F., Polly P. D.,
Elton S., 2010 -
Biogeographic
analysis using geometric morphometrics: clines in
skull size and shape in a widespread African
arboreal monkey. A. M. T. Elewa (Ed.),
Morphometrics for Nonmorphometricians, Lecture
Notes in Earth Sciences 124, Springer-Verlag
Publishers, Heidelberg, Germany. DOI 10.1007/978-3-540-95853-6_8.

For 2D data it's even easier using a baseline
superimposition (and then rescaling back the
specimens) as an intermediate step. I don't think
I wrote somewhere how to do it step by step by,
again, it can be done in both PAST and Morpheus with a tiny bit of effort.

Contrary to something (inaccurate) I may have
written in older papers, I would do all analyses
using the 'symmetrized' left side (or right side,
whatever ...) after removing small asymmetries on
the midplane (assuming one is not working on
dolphins or the like and asymmetries are really
small). One gets a better superimposition where
midplane landmarks cannot be off the midplane (as
it happens using just one side). Data contains
redundant info but that can be dealt with either
using PCs with non-zero eigenvalues or using resampling methods for testing.

Cheers

Andrea

At 21:50 13/06/2014, morphmet_modera...@morphometrics.org wrote:

>- Forwarded message from Carmelo Fruciano  -
>
>      Date: Tue, 10 Jun 2014 04:01:02 -0400
>       From: Carmelo Fruciano
>       Reply-To: Carmelo Fruciano
>       Subject: Re: landmark configuration reflection
>       To: morphmet@morphometrics.org
>
>morphmet_modera...@morphometrics.org ha scritto:
>
> >
> > - Forwarded message from Miguel Eduardo Delgado Burbano  -
> >
> >      Date: Thu, 5 Jun 2014 17:59:15 -0300
> >       From: Miguel Eduardo Delgado Burbano
> >       Reply-To: Miguel Eduardo Delgado Burbano
> >       Subject: landmark configuration reflection
> >       To: morphmet_modera...@morphometrics.org
> >
> > Hi all
> >
> > I am performing a 2D geometric morphometric study using human
> > skulls. In a previous research I digitized several landmarks and
> > semilandmarks in the right half of the face, but now I am trying to
> > perform an analysis using the complete face (i.e both halfs), so in
> > order to not digitized again perhaps I can reflect the right
> > landmark configuration on the left side. Since the reflection is
> > performed during the procrustes (GPA) perhaps a particular software

> > allows to reflect the landmark configuration  TPS, MorphoJ, GeoMorph
> > etc??Â
> >
> > Â  Â any suggestions?
>
>Hi Miguel,
>Normally these days when I have to do these reflections I use Matlab.
>For an older paper (Fruciano et al. 2011 - It J Zool) I think I used
>LMedit from the IMP package (it's been a while now).
>However, if your data is only on half of the face, I would perform the
>analysis only on half the face and then use reflection across a
>symmetry axis only to display the results...
>Best,
>Carmelo
>
>--
>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/
>
>- End forwarded message -

Dr. Andrea Cardini
Researcher in Animal Biology, Dipartimento di
Scienze Chimiche e Geologiche, Università di
Modena e Reggio Emilia, l.go S. Eufemia 19, 41121 Modena, Italy

Adjunct Associate Professor, Centre for Forensic
Science , The University of Western Australia, 35
Stirling Highway, Crawley WA 6009, Australia

E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: http://sites.google.com/site/hy

Yellow Book one year after

[morphmet_moderator]

- Forwarded message from andrea cardini  -

 Date: Mon, 23 Jun 2014 06:50:36 -0400
  From: andrea cardini 
  Reply-To: andrea cardini 
  Subject: Yellow Book one year after
  To: morphmet@morphometrics.org

Dear All,
I'd like to thank once more all those who 
contributed to the Yellow Book and especially 
Anna Loy (the other editor of the book), Damiano 
Preatoni (Hystrix technical editor) and all the authors. 
A few days ago I quickly checked in Google 
Scholar and it seems that, one year after its 
publication, the book has already got almost 100 citations. 

Again, thanks to all contributors and many thanks also to all readers!

For those who haven't yet got the book and are 
interested, it can be still downloaded for free using one of the links below:
WHOLE BOOK
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf
SINGLE ARTICLES
http://www.italian-journal-of-mammalogy.it/issue/view/405

Cheers

Andrea

Dr. Andrea Cardini
Researcher in Animal Biology, Dipartimento di 
Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, l.go S. Eufemia 19, 41121 Modena, Italy

Adjunct Associate Professor, Centre for Forensic 
Science , The University of Western Australia, 35 
Stirling Highway, Crawley WA 6009, Australia

E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: http://sites.google.com/site/hymsfme/drandreacardini
Summary of research interests at: 
http://www.dscg.unimore.it/site/home/ricerca/aree-di-ricerca/evolution-taxonomy-and-forensics.html

FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/issue/view/405
or full volume at: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf

Editorial board for:
Zoomorphology: 
http://www.springer.com/life+sciences/animal+sciences/journal/435
Journal of Zoological Systematics and 
Evolutionary Research: http://www.wiley.com/bw/journal.asp?ref=0947-5745&site=1
Hystrix, the Italian Journal of 
Mammalogy: http://www.italian-journal-of-mammalogy.it/ 

- End forwarded message -

Re: landmark configuration reflection

[morphmet_moderator]

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Tue, 24 Jun 2014 23:13:58 -0700
  From: morphmet_modera...@morphometrics.org
  Reply-To: morphmet_modera...@morphometrics.org
  Subject: Re: landmark configuration reflection
  To: morphmet@morphometrics.org

- Forwarded message from Carmelo Fruciano  -

Date: Thu, 19 Jun 2014 17:39:49 -0400
From: Carmelo Fruciano 
Reply-To: Carmelo Fruciano 
Subject: Re: landmark configuration reflection
To: morphmet@morphometrics.org

> - Forwarded message from Miguel Eduardo Delgado Burbano  -
>
>  Date: Fri, 13 Jun 2014 23:46:37 -0400
>   From: Miguel Eduardo Delgado Burbano
>   Reply-To: Miguel Eduardo Delgado Burbano
>   Subject: Re: landmark configuration reflection
>   To: morphmet@morphometrics.org
>
> Hi  Carmelo
>
> Thank you for your response. Yes I know that Matlab is a very useful  
> software, perhaps you can share with me your code or procedures in  
> Matlab??

Dear Miguel,
sure, it simply applies some formula for reflection of points relative  
to an axis (of course you need to have two points defining your axis).  
And, again, this would be appropriate only to visualize the results  
NOT to produce a dataset to analyze with commonly used landmark-based  
methods. 

> Purposely do you know if it is possible to obtain the z coordinate  
> if I only have the x and y coordinates??. I mean it is possible  
> perform a reconstruction of the z coordinate of a landmark using  
> the information on the x and y coordinates ??

Not sure what do you mean by "z" coordinate, do you mean the third  
dimension? If your digitized configurations of landmarks all lay on a  
plane and/or they are digitized from the same projection (i.e. a  
single picture, for example), obviously you cannot obtain any "z"  
coordinate from them... 

Best,
Carmelo

> On Fri, Jun 13, 2014 at 4:50 PM,   wrote:
>
> - Forwarded message from Carmelo Fruciano  -
>
>      Date: Tue, 10 Jun 2014 04:01:02 -0400
>       From: Carmelo Fruciano
>       Reply-To: Carmelo Fruciano
>       Subject: Re: landmark configuration reflection
>       To: morphmet@morphometrics.org
>
> morphmet_modera...@morphometrics.org ha scritto:
>
>>
>> - Forwarded message from Miguel Eduardo Delgado Burbano  -
>>
>>      Date: Thu, 5 Jun 2014 17:59:15 -0300
>>       From: Miguel Eduardo Delgado Burbano
>
>>       Reply-To: Miguel Eduardo Delgado Burbano
>
>>       Subject: landmark configuration reflection
>>       To: morphmet_modera...@morphometrics.org
>>
>> Hi all
>>
>> I am performing a 2D geometric morphometric study using human
>> skulls. In a previous research I digitized several landmarks and
>> semilandmarks in the right half of the face, but now I am trying to
>> perform an analysis using the complete face (i.e both halfs), so in
>> order to not digitized again perhaps I can reflect the right
>> landmark configuration on the left side. Since the reflection is
>> performed during the procrustes (GPA) perhaps a particular software
>> allows to reflect the landmark configuration  TPS, MorphoJ, GeoMorph
>> etc?? 
>>
>>    any suggestions?
>
> Hi Miguel,
> Normally these days when I have to do these reflections I use Matlab. 
> For an older paper (Fruciano et al. 2011 - It J Zool) I think I used
> LMedit from the IMP package (it's been a while now). 
> However, if your data is only on half of the face, I would perform the
> analysis only on half the face and then use reflection across a
> symmetry axis only to display the results... 
> Best,
> Carmelo
>
> --
> 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/
>
> - End forwarded message -
>
> - End forwarded message -
>
> - End forwarded message -
>
>

-- 
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/

- End forwarded message -

- End forwarded message -

Re: landmark configuration reflection

[morphmet_moderator]

- Forwarded message from Miguel Eduardo Delgado Burbano  -

 Date: Wed, 18 Jun 2014 17:33:56 -0400
  From: Miguel Eduardo Delgado Burbano
  Reply-To: Miguel Eduardo Delgado Burbano
  Subject: Re: landmark configuration reflection
  To: morphmet@morphometrics.org

Dear Gred

Of course this is not for publication only to simulate data and evaluate 
differences within a alleged perfect left-side right-side  symmetry. However 
actually human faces are basically symmetric and any deviation of symmetry is 
caused by developing  noise (i.e. fluctuating asymmetry). Any way your r-script 
is useful in my case to simulate and compare data.

best

Miguel 

On Wed, Jun 18, 2014 at 1:55 AM,   wrote:

- Forwarded message from GREG CAMPBELL  -

 Date: Tue, 10 Jun 2014 04:50:44 -0400
  From: GREG CAMPBELL
  Reply-To: GREG CAMPBELL

  Subject: Re: landmark configuration reflection

  To: "morphmet@morphometrics.org"

 Dear Miguel: You cannot reflect your points.  Human faces are not symmetric (a 
quick search in Google Scholar or PubMed will show this).  I think I recall 
that there is less sexual selection for symmetry in human males, but strong 
sexual selection for symmetry in human females.  The sexual selection is never 
strong enough to produce exact symmetry in individuals.  

Anybody reviewing your paper for publication would immediately suspect your 
results, if you just mirror your landmarks. Either stick to left sides, or 
digitize both sides and examine the extent and direction of assymetry with 
genetic diversity, or between males/females.

 Greg Campbel
The Naive Chemist

-
 From: "morphmet_modera...@morphometrics.org"
To: morphmet@morphometrics.org
Sent: Tuesday, 10 June 2014, 8:43
Subject: landmark configuration reflection

- Forwarded message from Miguel Eduardo Delgado Burbano  -

 Date: Thu, 5 Jun 2014 17:59:15 -0300

  From: Miguel Eduardo Delgado Burbano
  Reply-To: Miguel Eduardo Delgado Burbano
  Subject: landmark configuration reflection
  To: morphmet_modera...@morphometrics.org

Hi all

I am performing a 2D geometric morphometric study using human skulls. In a 
previous research I digitized several landmarks and semilandmarks in the right 
half of the face, but now I am trying to perform an analysis using the complete 
face (i.e both halfs), so in order to not digitized again perhaps I can reflect 
the right landmark configuration on the left side. Since the reflection is 
performed during the procrustes (GPA) perhaps a particular software allows to 
reflect the landmark configuration  TPS, MorphoJ, GeoMorph etc?? 

   any suggestions?

thank you in advance

best 

Miguel

- End forwarded message -

- End forwarded message -

- End forwarded message -

Re: landmark configuration reflection

[morphmet_moderator]

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Thu, 19 Jun 2014 21:10:19 -0700
  From: morphmet_modera...@morphometrics.org
  Reply-To: morphmet_modera...@morphometrics.org
  Subject: Re: landmark configuration reflection
  To: morphmet@morphometrics.org

- Forwarded message from andrea cardini  -

Date: Tue, 17 Jun 2014 02:38:19 -0400
From: andrea cardini 
Reply-To: andrea cardini 
Subject: Re: landmark configuration reflection
To: morphmet@morphometrics.org, morphmet@morphometrics.org

Not sure if I had replied yet. If so, my apologies for re-replying. 

We wrote a mini-tutorial about how to do this 
'exploiting' some of the options of the old Morpheus et al.:
Cardini A., Diniz Filho J. A. F., Polly P. D., 
Elton S., 2010 - 
Biogeographic
 
analysis using geometric morphometrics: clines in 
skull size and shape in a widespread African 
arboreal monkey. A. M. T. Elewa (Ed.), 
Morphometrics for Nonmorphometricians, Lecture 
Notes in Earth Sciences 124, Springer-Verlag 
Publishers, Heidelberg, Germany. DOI 10.1007/978-3-540-95853-6_8. 

For 2D data it's even easier using a baseline 
superimposition (and then rescaling back the 
specimens) as an intermediate step. I don't think 
I wrote somewhere how to do it step by step by, 
again, it can be done in both PAST and Morpheus with a tiny bit of effort. 

Contrary to something (inaccurate) I may have 
written in older papers, I would do all analyses 
using the 'symmetrized' left side (or right side, 
whatever ...) after removing small asymmetries on 
the midplane (assuming one is not working on 
dolphins or the like and asymmetries are really 
small). One gets a better superimposition where 
midplane landmarks cannot be off the midplane (as 
it happens using just one side). Data contains 
redundant info but that can be dealt with either 
using PCs with non-zero eigenvalues or using resampling methods for testing. 

Cheers

Andrea

At 21:50 13/06/2014, morphmet_modera...@morphometrics.org wrote:

>- Forwarded message from Carmelo Fruciano  -
>
>  Date: Tue, 10 Jun 2014 04:01:02 -0400
>   From: Carmelo Fruciano 
>   Reply-To: Carmelo Fruciano 
>   Subject: Re: landmark configuration reflection
>   To: morphmet@morphometrics.org
>
>morphmet_modera...@morphometrics.org ha scritto:
>
> >
> > - Forwarded message from Miguel Eduardo Delgado Burbano  -
> >
> >  Date: Thu, 5 Jun 2014 17:59:15 -0300
> >   From: Miguel Eduardo Delgado Burbano
> >   Reply-To: Miguel Eduardo Delgado Burbano
> >   Subject: landmark configuration reflection
> >   To: morphmet_modera...@morphometrics.org
> >
> > Hi all
> >
> > I am performing a 2D geometric morphometric study using human
> > skulls. In a previous research I digitized several landmarks and
> > semilandmarks in the right half of the face, but now I am trying to
> > perform an analysis using the complete face (i.e both halfs), so in
> > order to not digitized again perhaps I can reflect the right
> > landmark configuration on the left side. Since the reflection is
> > performed during the procrustes (GPA) perhaps a particular software
> > allows to reflect the landmark configuration  TPS, MorphoJ, GeoMorph
> > etc??Â
> >
> > Â  Â any suggestions?
>
>Hi Miguel,
>Normally these days when I have to do these reflections I use Matlab. 
>For an older paper (Fruciano et al. 2011 - It J Zool) I think I used
>LMedit from the IMP package (it's been a while now). 
>However, if your data is only on half of the face, I would perform the
>analysis only on half the face and then use reflection across a
>symmetry axis only to display the results... 
>Best,
>Carmelo
>
>--
>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/
>
>- End forwarded message -

Dr. Andrea Cardini
Researcher in Animal Biology, Dipartimento di 
Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, l.go S. Eufemia 19, 41121 Modena, Italy

Adjunct Associate Professor, Centre for Forensic 
Science , The University of Western Australia, 35 
Stirling Highway, Crawley WA 6009, Australia

E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: http://sites.google.com/site/hymsfme/drandreacardini
Summary of research interests at: 
http://www.dscg.unimore.it/site/home/ricerca/aree-di-ricerca/evolution-taxonomy-and-forensics.html

FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/issue/view/405
or full volume at: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf

Editorial board for:
Zoomorphology: 
http://www.springer.com/life+sciences/animal+sciences/journal/435
Journal of Zoological Systematics 

Outline file problem

[morphmet_moderator]

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Thu, 19 Jun 2014 21:11:46 -0700
  From: morphmet_modera...@morphometrics.org
  Reply-To: morphmet_modera...@morphometrics.org
  Subject: Outline file problem
  To: morphmet@morphometrics.org

- Forwarded message from "Pere M. Parés-Casanova" 
 -

Date: Wed, 18 Jun 2014 08:47:39 +0200
From: "Pere M. Parés-Casanova" 
Reply-To: "Pere M. Parés-Casanova" 
Subject: Outline file problem
To: morphmet_modera...@morphometrics.org

Dear all. 
When trying to import an outline file (for occlusal views in horse cheek
teeth) with MorhoJ, the following message appears: "Problem: the input is
no interpretable as a number. empty string". I am sure it must be a simple
problem. Any suggestion?
Thanks in advance!

-- 
Pere M. Parés-Casanova PhD
Part-time Lecturer
Dep. of Animal Production
University of Lleida
Av. Rovira Roure 191
25198 Lleida (CATALUNYA, Spain)
Phone:+34973706460
Fax:  +34973702874
_
(" \__
\   )
\ ---¬/
/ |
Confidentiality Note:  This message is intended for use only by the
individual or entity to which it is addressed and may contain information
that is privileged, confidential, and exempt from disclosure under
applicable law. If you have received this communication in error,  please
contact the sender immediately and destroy the material in its entirety,
whether electronic or hard copy. Kindly note that, E-mail transmission
cannot be guaranteed to be secured or error-free as information could be
intercepted, corrupted,lost, destroyed, arrive late or incomplete, or
contain viruses. The sender therefore does not accept liability for any
errors or omissions in the contents of this message, which arise as a
result of e-mail transmission. If verification is required please request
a signed hard-copy/scanned version. Thank you, gràcies. 

- End forwarded message -

- End forwarded message -

PhD in USA?

[morphmet_moderator]

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Wed, 18 Jun 2014 22:31:10 -0700
  From: morphmet_modera...@morphometrics.org
  Reply-To: morphmet_modera...@morphometrics.org
  Subject: PhD in USA?
  To: morphmet@morphometrics.org

- Forwarded message from Lewis  -

 Date: Sun, 15 Jun 2014 23:45:30 -0400
  From: Lewis
  Reply-To: Lewis
  Subject: PhD in USA?
  To: "morphmet@morphometrics.org"

 
Hello,.I am a Chinese student and want to pursue a Phd in geometric 
morphometrics. I already have a Master in this.

Can you tell me a universities in USA that offer this major PhD degree?
 Thank you

- End forwarded message -

- End forwarded message -

Last call course GMM and phylogeny, Barcelona, September 2014

[morphmet_moderator]

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Wed, 18 Jun 2014 22:31:45 -0700
  From: morphmet_modera...@morphometrics.org
  Reply-To: morphmet_modera...@morphometrics.org
  Subject: Last call course GMM and phylogeny, Barcelona, September 2014
  To: morphmet@morphometrics.org

- Forwarded message from "soledad.esteban"  -

Date: Mon, 16 Jun 2014 11:28:47 +0200
From: "soledad.esteban" 
Reply-To: "soledad.esteban" 
Subject: Last call course GMM and phylogeny, Barcelona, September 2014
To: morphmet_modera...@morphometrics.org

Dear colleagues, 

This is the last call for the course "GEOMETRIC MORPHOMETRICS AND PHYLOGENY- 
5th edition". 

INSTRUCTOR: Professor Chris Klingenberg (University of Manchester, UK). 

DATES: SEPTEMBER 8-12, 2014; 38 teaching hours. 

PLACE:  Facilities of the Centre of Restauració i Interpretació Paleontologica, 
Els Hostalets de Pierola,  Barcelona (Spain). 

Organized by: Transmitting Science, the Institut Catalá de Paleontologia Miquel 
 Crusafont and the Council of Hostalets de Pierola. 

More information:  
http://www.transmittingscience.org/courses/gm/gm-and-phylogeny/   or  writing 
to cour...@transmittingscience.org 

This course provides an overview of the interface between geometric 
morphometrics and phylogenetics. It aims to give an overview of the different 
approaches and methods that link the two fields and to enable participants to 
apply them to their own research problems. Lectures that introduce concepts and 
methods are integrated with demonstrations of software that put them into 
practice right away. The main emphasis is on mapping shape data on existing 
phylogenies to reconstruct the evolutionary history of shape diversification, 
as well as comparative methods that take phylogeny into account. To enhance the 
practical approach of the course, participants are encouraged to bring their 
own data to conduct analyses and discuss results. 

Please feel free to distribute this information between your colleagues if you  
consider it appropriate. 

With best regards 

Soledad De Esteban-Trivigno
Investigadora Area de Paleontologia Virtual
Institut Català de Paleontologia M. Crusafont (ICP) 
soledad.este...@icp.cat 
Mòdul ICP - Facultat de Biociències 
Campus de la Universitat Autònoma de Barcelona 
E-08193 Cerdanyola del Vallès 
www.icp.cat

- End forwarded message -

- End forwarded message -

Re: Average contours

[morphmet_moderator]

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Wed, 18 Jun 2014 22:30:25 -0700
  From: morphmet_modera...@morphometrics.org
  Reply-To: morphmet_modera...@morphometrics.org
  Subject: Re: Average contours
  To: morphmet@morphometrics.org

- Forwarded message from gonzalo ernesto fajardo medina  -

 Date: Sun, 15 Jun 2014 08:16:11 -0400
  From: gonzalo ernesto fajardo medina
  Reply-To: gonzalo ernesto fajardo medina
  Subject: Re: Average contours
  To: morphmet@morphometrics.org

with elliptic fourier analysis..using EFA. 

On Fri, Jun 13, 2014 at 12:40 PM,   wrote:

- Forwarded message from morphmet_modera...@morphometrics.org -

     Date: Thu, 12 Jun 2014 06:40:34 -0700
      From: morphmet_modera...@morphometrics.org
      Reply-To: morphmet_modera...@morphometrics.org
      Subject: Average contours
      To: morphmet@morphometrics.org

- Forwarded message from "Pere M. Parés-Casanova"
 -

Date: Sat, 7 Jun 2014 10:16:45 -0400
From: "Pere M. Parés-Casanova"

Reply-To: "Pere M. Parés-Casanova"

Subject: Average contours
To: morphmet@morphometrics.org

Dear morphometricians.
I know it is quite simple, but how to "countour" a figure in order to
illustrate the total form, i.e., not considering only landmarks? Just for
superimposing the "standard" sample with landmarked samples.
Thanks in advance!

Pere-Miquel

- End forwarded message -

- End forwarded message -

--
Gonzalo Fajardo Bio. M.Sc.
Bogotá Colombia
America del Sur

- End forwarded message -

- End forwarded message -

Re: landmark configuration reflection

[morphmet_moderator]

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Tue, 17 Jun 2014 22:01:13 -0700
  From: morphmet_modera...@morphometrics.org
  Reply-To: morphmet_modera...@morphometrics.org
  Subject: Re: landmark configuration reflection
  To: morphmet@morphometrics.org

- Forwarded message from Miguel Eduardo Delgado Burbano  -

 Date: Fri, 13 Jun 2014 23:22:30 -0400
  From: Miguel Eduardo Delgado Burbano
  Reply-To: Miguel Eduardo Delgado Burbano
  Subject: Re: landmark configuration reflection
  To: morphmet@morphometrics.org

Hi Tim

thank you for your response. Yes now I am exploring geomorph, but until now 
nothing. Of course I am very interested in your code, how I can obtain such 
code??

best

Miguel

On Fri, Jun 13, 2014 at 4:49 PM,   wrote:

- Forwarded message from Tim Astrop  -

 Date: Tue, 10 Jun 2014 03:57:26 -0400
  From: Tim Astrop
  Reply-To: Tim Astrop
  Subject: Re: landmark configuration reflection
  To: morphmet@morphometrics.org

Hi Miguel!

I have not found a piece of GUI based software that will do this, however, I do 
have some code for the R package Geomorph that does landmark reflection on the 
x axis if you are interested?

Cheers

Tim

Tim Astrop PhD
Department of Biology & Biochemistry

University of Bath
timastrop.wordpress.com

On 10 June 2014 08:43,   wrote:

- Forwarded message from Miguel Eduardo Delgado Burbano  -

 Date: Thu, 5 Jun 2014 17:59:15 -0300
  From: Miguel Eduardo Delgado Burbano
  Reply-To: Miguel Eduardo Delgado Burbano
  Subject: landmark configuration reflection
  To: morphmet_modera...@morphometrics.org

Hi all

I am performing a 2D geometric morphometric study using human skulls. In a 
previous research I digitized several landmarks and semilandmarks in the right 
half of the face, but now I am trying to perform an analysis using the complete 
face (i.e both halfs), so in order to not digitized again perhaps I can reflect 
the right landmark configuration on the left side. Since the reflection is 
performed during the procrustes (GPA) perhaps a particular software allows to 
reflect the landmark configuration  TPS, MorphoJ, GeoMorph etc?? 

   any suggestions?

thank you in advance

best 

Miguel

- End forwarded message -

- End forwarded message -

- End forwarded message -

- End forwarded message -

Re: landmark configuration reflection

[morphmet_moderator]

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Tue, 17 Jun 2014 22:01:38 -0700
  From: morphmet_modera...@morphometrics.org
  Reply-To: morphmet_modera...@morphometrics.org
  Subject: Re: landmark configuration reflection
  To: morphmet@morphometrics.org

- Forwarded message from Miguel Eduardo Delgado Burbano  -

 Date: Fri, 13 Jun 2014 23:46:37 -0400
  From: Miguel Eduardo Delgado Burbano
  Reply-To: Miguel Eduardo Delgado Burbano
  Subject: Re: landmark configuration reflection
  To: morphmet@morphometrics.org

Hi  Carmelo

Thank you for your response. Yes I know that Matlab is a very useful software, 
perhaps you can share with me your code or procedures in Matlab??. Purposely do 
you know if it is possible to obtain the z coordinate if I only have the x and 
y coordinates??. I mean it is possible perform a reconstruction of the z 
coordinate of a landmark using the information on the x and y coordinates ?? 
thank you

best

Miguel   

On Fri, Jun 13, 2014 at 4:50 PM,   wrote:

- Forwarded message from Carmelo Fruciano  -

     Date: Tue, 10 Jun 2014 04:01:02 -0400
      From: Carmelo Fruciano
      Reply-To: Carmelo Fruciano
      Subject: Re: landmark configuration reflection
      To: morphmet@morphometrics.org

morphmet_modera...@morphometrics.org ha scritto:

>
> - Forwarded message from Miguel Eduardo Delgado Burbano  -
>
>      Date: Thu, 5 Jun 2014 17:59:15 -0300
>       From: Miguel Eduardo Delgado Burbano

>       Reply-To: Miguel Eduardo Delgado Burbano

>       Subject: landmark configuration reflection
>       To: morphmet_modera...@morphometrics.org
>
> Hi all
>
> I am performing a 2D geometric morphometric study using human
> skulls. In a previous research I digitized several landmarks and
> semilandmarks in the right half of the face, but now I am trying to
> perform an analysis using the complete face (i.e both halfs), so in
> order to not digitized again perhaps I can reflect the right
> landmark configuration on the left side. Since the reflection is
> performed during the procrustes (GPA) perhaps a particular software
> allows to reflect the landmark configuration  TPS, MorphoJ, GeoMorph
> etc?? 
>
>    any suggestions?

Hi Miguel,
Normally these days when I have to do these reflections I use Matlab.
For an older paper (Fruciano et al. 2011 - It J Zool) I think I used
LMedit from the IMP package (it's been a while now).
However, if your data is only on half of the face, I would perform the
analysis only on half the face and then use reflection across a
symmetry axis only to display the results...
Best,
Carmelo

--
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/

- End forwarded message -

- End forwarded message -

- End forwarded message -

Re: CSV to NTSYSpc conversion tool

[morphmet_moderator]

- Forwarded message from Sami Rabei  -

 Date: Thu, 12 Jun 2014 19:37:59 -0400
  From: Sami Rabei
  Reply-To: Sami Rabei
  Subject: Re: CSV to NTSYSpc conversion tool
  To: morphmet@morphometrics.org, mauro...@gmail.com

Thanks a lot
  
 Sami Rabei
--
With my Best Wishes
Sami Hussein Rabei (PhD)
Botany Department,
Faculty of Science,
Damietta University,
New Damietta , Post Box 34517
Damietta, Egypt.
 
Tel. Mobile: 002 0101 7895350
Tel. Work:   002 057 2403981 
Tel. Home:   002 057 2403108
Fax: 002 057 2403868
 
mailto: samira...@du.edu.eg
Researcher ID: G-9848-2012
ORCID: -0001-6042-5877
http://scholar.google.com/citations?user=GexZOhIJ=

   - Original Message -
 From: morphmet_modera...@morphometrics.org
 To: morphmet@morphometrics.org
 Sent: Thursday, June 12, 2014 3:32 PM
 Subject: CSV to NTSYSpc conversion tool

- Forwarded message from Mauro Cavalcanti  -

Date: Fri, 6 Jun 2014 14:50:03 -0400
From: Mauro Cavalcanti
Reply-To: Mauro Cavalcanti
Subject: CSV to NTSYSpc conversion tool
To: morphmet@morphometrics.org

 Dear ALL,

I have wrote a simple console-based C/C++ program to perform the conversion of 
comma-delimited files (CSV) into NTSYSpc data files.

The distribution package, including binary executables for GNU/Linux and 
MS-Windows, as well as the full source code of the program and an example data 
file, can be downloaded from my personal website: 
http://sites.google.com/site/maurobio/software

Hope this is useful.

Best regards,

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

- End forwarded message -

- End forwarded message -

One-Day NSF Grant Training Seminar at Columbia University

[morphmet_moderator]

- Forwarded message from Ashley Williams  -

 Date: Wed, 11 Jun 2014 13:16:52 -0400
  From: Ashley Williams
  Reply-To: Ashley Williams
  Subject: One-Day NSF Grant Training Seminar at Columbia University
  To: morphmet@morphometrics.org

TitleWriting & Designing NSF Proposals Workshop
 Writing Winning Grants for NSF
 July 01, 2014
8:30 a.m. - 4:30 p.m.
Columbia University
New York, NY

Sponsored by: The Grant Training Center

This one-day comprehensive workshop is geared for those who wish to submit 
winning research proposals to the National Science Foundation (NSF). It is 
taught by experienced faculty who have received various NSF grants and serve as 
evaluators on NSF review panels.

Participants will understand how to navigate the FastLane, focus on the key 
sections of successful proposals and demonstrate that their projects merit the 
excellence and innovation that bring them to the top of other submissions. All 
sessions engage the attendees in interactive exercises, writing, lectures and 
discussions so that all participants will leave the class understanding how to 
research, write and develop their specific project.

Areas to be covered include the:

1. Overall strategic plan of grant-writing
2. Types of awards and NSF funding, including what to look for in a grant 
application
3. Proposal preparation process and submission mechanisms
4. Characteristics, content and function of the various pieces of the proposal, 
including: hypothesis, methods, outcomes, broader implications, evaluation, 
timelines and budgets
5. Secret to organizing and writing “Merit Review Criteria”

Participants will learn how to:

1. Compose the pieces of an NSF Research Grant Proposal
2. Understand the inner workings of NSF’s Peer Review System and the rating 
scores
3. Develop and write the approach and “Broader Impacts” section
4. Package superior proposal submissions
5. Avoid the fatal flaws of a grant
6. Effectively write and approach resubmissions

Space is limited, and since this class fills-up quickly, it is on a first-come, 
first-serve basis.
Workshop Fee: $375.00 (including tuition, materials, certificate of completion, 
and continental breakfast)

To register: Click Here
Or call us toll free at (866)-704-7268 or (571) 257-8864

 
 Additionally, a Writing & Designing NIH Proposals Workshop is also going to be 
held at Columbia University, on July 02, 2014.
Get a discount of $155 on registration for both workshops (Call us for the 
discount):
Each person can register for either NIH or NSF for the price of $375. If a 
person registers for both, the price is $595 (discount of $155). *Please 
contact Grant Training Center for the discount code.
For participants who has already registered for the NIH, this discount also 
applies if you register for the NSF workshop.

REGISTER NOW!!

July 01, 2014
New York, NY "Writing & Designing NSF Proposals", Workshop
Columbia University
July 02, 2014
New York, NY "Writing & Designing NIH Proposals", Workshop
Columbia University
Can't make it??
Join us for an online webinar!
 June 10, 2014
8:30 - 4:30 pm (EST) "Writing &Designing NSF Proposals" Webinar

 Columbia University is not endorsing or sponsoring the activities conducted by 
The Grant Training Center.

You received this e-mail due to your institutional or organizational 
affiliation. If we sent this e-mail to you in error, and you wish not to 
receive any further e-mails from us, simply send us an email with the word  
unsubscribe as subject.

- End forwarded message -

Fwd: advertising for a PhD and postdoc position in morphometrics ofembryos

[morphmet_moderator]

Hey Dennis,

It would appear we have a request to have a position posted to 
morphometrics.org.  Is that possible?

-JS

- Forwarded message from isala...@mappi.helsinki.fi -

 Date: Tue, 10 Jun 2014 21:39:50 +0300
  From: isala...@mappi.helsinki.fi
  Reply-To: isala...@mappi.helsinki.fi
  Subject: advertising for a PhD and postdoc position in morphometrics 
ofembryos
  To: morphmet_modera...@morphometrics.org

I would like to bring to your attention a PhD position in 3D  
morphometrics of embryos in the Biotechnology Institute of the  
University of Helsinki. I would be very grateful if you can post that  
add in your webpage, morphometrics.org since this jobs requires a  
person interested in morphometrics. 

The announcement can be found below:

1.Job/ project description: Potsdoc or graduate position for a PhD in  
developmental morphometrics

The main objectives of the PhD project is to:

a) Develop mathematical tools for non-landmark morphometrics of whole  
embryos and adult bodies. 

b) Use those tools to test quantitatively classical comparative  
hypotheses in evolution and development (evo-devo). These hypotheses  
include the hour-glass model and the patterns of variation in  
different stages of development according to the type of development. 

c) Collect data, mostly 3D scans, of embryonic material. 

The project would involve working with different species and would  
involve collecting data with a CT-scanner and analyzing already  
existing data. 
The biotechnology institute includes a range of experimental  
biologitst working on several systems. The supervisor of the  
theoretical aspects will be Dr. Salazar-Ciudad but the PhD would  
include close collaboration with Jukka Jernvall group. This includes  
collaboration with developmental biologists, bioinformaticians,  
paleontologists and other evolutionary and systems biologists. The  
work may also include, optionally, collaboration, and spending some  
time, in Barcelona. 

2. Requirements:

The applicant must be a biologists, preferably with a strong  
background in either evolutionary biology, developmental biology or  
theoretical biology. Some knowledge of ecology, zoology, cell and  
molecular biology are also desirable. 

Bioinformaticians, systems biologists or computer biologists that do  
not have a degree in biology (e.g. Computer scientists, physicists or  
engineers) would not be considered (not replied). 

Programming skills or a willingness to acquire them is required. 

The most important requirement is a strong interest and motivation on  
science, morphological evolution and development. A capacity for  
creative and critical thinking is also desirable. 

3. Description of the position:

The fellowship will be for a period of up to 4 years (100% research  
work: no teaching involved). 

The purpose of the fellowship is research training leading to the  
successful completion of a PhD degree. 

Salary according to Finnish PhD student salaries (or postdoc)  
depending on the applicant. 

4. The application must include:

-Application letter including a statement of interests
-CV (summarizing degrees obtained, subjects included in degree and  
grades, average grade)

-Application should be send to Isaac Salazar-Ciudad by email:

isaac.sala...@helsinki.fi

Foreign applicants are advised to attach an explanation of their
University's grading system. Please remember that all documents should
be in English. 

5. Examples of recent publications by Isaac Salazar-Ciudad group. 

-Salazar-Ciudad I. Morphological evolution and embryonic developmental  
diversity in metazoa. Development. 2010 Feb;137(4):531-9. 

--Salazar-Ciudad I, Jernvall J. A computational model of teeth and the  
developmental origins of morphological variation. Nature. 2010 Mar  
25;464(7288):583-6. 

-Salazar-Ciudad I1, Marín-Riera M. Adaptive dynamics under  
development-based genotype-phenotype maps. 
Nature. 2013 May 16;497(7449):361-4. 

6. Interested candidates should check our group webpage:

http://www.biocenter.helsinki.fi/salazar/index.html

The deadline is 15 of August (although candidates may be selected before). 

Isaac Salazar-Ciudad: isaac.sala...@helsinki.fi

- End forwarded message -

Re: landmark configuration reflection

[morphmet_moderator]

- Forwarded message from GREG CAMPBELL  -

 Date: Tue, 10 Jun 2014 04:50:44 -0400
  From: GREG CAMPBELL
  Reply-To: GREG CAMPBELL
  Subject: Re: landmark configuration reflection
  To: "morphmet@morphometrics.org"

Dear Miguel: You cannot reflect your points.  Human faces are not symmetric (a 
quick search in Google Scholar or PubMed will show this).  I think I recall 
that there is less sexual selection for symmetry in human males, but strong 
sexual selection for symmetry in human females.  The sexual selection is never 
strong enough to produce exact symmetry in individuals.  

Anybody reviewing your paper for publication would immediately suspect your 
results, if you just mirror your landmarks. Either stick to left sides, or 
digitize both sides and examine the extent and direction of assymetry with 
genetic diversity, or between males/females.

Greg Campbel
The Naive Chemist

-
 From: "morphmet_modera...@morphometrics.org"
To: morphmet@morphometrics.org
Sent: Tuesday, 10 June 2014, 8:43
Subject: landmark configuration reflection

- Forwarded message from Miguel Eduardo Delgado Burbano  -

 Date: Thu, 5 Jun 2014 17:59:15 -0300
  From: Miguel Eduardo Delgado Burbano
  Reply-To: Miguel Eduardo Delgado Burbano
  Subject: landmark configuration reflection
  To: morphmet_modera...@morphometrics.org

Hi all

I am performing a 2D geometric morphometric study using human skulls. In a 
previous research I digitized several landmarks and semilandmarks in the right 
half of the face, but now I am trying to perform an analysis using the complete 
face (i.e both halfs), so in order to not digitized again perhaps I can reflect 
the right landmark configuration on the left side. Since the reflection is 
performed during the procrustes (GPA) perhaps a particular software allows to 
reflect the landmark configuration  TPS, MorphoJ, GeoMorph etc?? 

   any suggestions?

thank you in advance

best 

Miguel

- End forwarded message -

- End forwarded message -

Re: landmark configuration reflection

[morphmet_moderator]

- Forwarded message from Carmelo Fruciano  -

 Date: Tue, 10 Jun 2014 04:01:02 -0400
  From: Carmelo Fruciano 
  Reply-To: Carmelo Fruciano 
  Subject: Re: landmark configuration reflection
  To: morphmet@morphometrics.org

morphmet_modera...@morphometrics.org ha scritto:

>
> - Forwarded message from Miguel Eduardo Delgado Burbano  -
>
>  Date: Thu, 5 Jun 2014 17:59:15 -0300
>   From: Miguel Eduardo Delgado Burbano
>   Reply-To: Miguel Eduardo Delgado Burbano
>   Subject: landmark configuration reflection
>   To: morphmet_modera...@morphometrics.org
>
> Hi all
>
> I am performing a 2D geometric morphometric study using human  
> skulls. In a previous research I digitized several landmarks and  
> semilandmarks in the right half of the face, but now I am trying to  
> perform an analysis using the complete face (i.e both halfs), so in  
> order to not digitized again perhaps I can reflect the right  
> landmark configuration on the left side. Since the reflection is  
> performed during the procrustes (GPA) perhaps a particular software  
> allows to reflect the landmark configuration  TPS, MorphoJ, GeoMorph  
> etc?? 
>
>    any suggestions?

Hi Miguel,
Normally these days when I have to do these reflections I use Matlab.  
For an older paper (Fruciano et al. 2011 - It J Zool) I think I used  
LMedit from the IMP package (it's been a while now). 
However, if your data is only on half of the face, I would perform the  
analysis only on half the face and then use reflection across a  
symmetry axis only to display the results... 
Best,
Carmelo

-- 
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/

- End forwarded message -

Re: landmark configuration reflection

[morphmet_moderator]

- Forwarded message from Tim Astrop  -

 Date: Tue, 10 Jun 2014 03:57:26 -0400
  From: Tim Astrop
  Reply-To: Tim Astrop
  Subject: Re: landmark configuration reflection
  To: morphmet@morphometrics.org

Hi Miguel!

I have not found a piece of GUI based software that will do this, however, I do 
have some code for the R package Geomorph that does landmark reflection on the 
x axis if you are interested?

Cheers

Tim

Tim Astrop PhD
 Department of Biology & Biochemistry

University of Bath
timastrop.wordpress.com

On 10 June 2014 08:43,   wrote:

- Forwarded message from Miguel Eduardo Delgado Burbano  -

 Date: Thu, 5 Jun 2014 17:59:15 -0300
  From: Miguel Eduardo Delgado Burbano
  Reply-To: Miguel Eduardo Delgado Burbano
  Subject: landmark configuration reflection
  To: morphmet_modera...@morphometrics.org

Hi all

I am performing a 2D geometric morphometric study using human skulls. In a 
previous research I digitized several landmarks and semilandmarks in the right 
half of the face, but now I am trying to perform an analysis using the complete 
face (i.e both halfs), so in order to not digitized again perhaps I can reflect 
the right landmark configuration on the left side. Since the reflection is 
performed during the procrustes (GPA) perhaps a particular software allows to 
reflect the landmark configuration  TPS, MorphoJ, GeoMorph etc?? 

   any suggestions?

thank you in advance

best 

Miguel

- End forwarded message -

- End forwarded message -

Re: Comparing svd() and prcomp() output from R

[morphmet_moderator]

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Thu, 12 Jun 2014 06:45:46 -0700
  From: morphmet_modera...@morphometrics.org
  Reply-To: morphmet_modera...@morphometrics.org
  Subject: Re: Comparing svd() and prcomp() output from R
  To: morphmet@morphometrics.org

- Forwarded message from Stefan Schlager  -

Date: Sun, 8 Jun 2014 08:29:16 -0400
From: Stefan Schlager 
Reply-To: Stefan Schlager 
Subject: Re: Fwd: Re: Comparing svd() and prcomp() output from R
To: morphmet@morphometrics.org

Hi Murat,

to get the same results, you need to:

a) center your data (as dennis slice pointed out) => gives identical PCs
b) divide the squared singular values by (sample size -1) => gives
identical eigenvalues

Best
Stefan

On 07/06/14 06:16, morphmet wrote:
>
>
>
>  Original Message 
> Subject: Re: Comparing svd() and prcomp() output from R
> Date: Fri, 6 Jun 2014 16:26:20 -0400
> From: Dennis E. Slice 
> To: morphmet@morphometrics.org
>
> I take it you are comparing svd(x) and prcomp(x) where x is your data
> matrix? prcomp() subtracts the mean. -ds
>
> On 6/6/14, 11:09 AM, morphmet_modera...@morphometrics.org wrote:
>>
>> - Forwarded message from "Maga, Murat"
>>  -
>>
>>   Date: Thu, 15 May 2014 18:54:15 -0400
>>From: "Maga, Murat" 
>>Reply-To: "Maga, Murat" 
>>Subject: Comparing svd() and prcomp() output from R
>>To: "'morphmet@morphometrics.org'" 
>>
>> Hi folks,
>>
>> This is really a R question, but perhaps someone can help me. 
>>
>> When I run svd() and prcomp() functions on my procrustes aligned
>> coordinates, I end up with an interesting situation, where the 1st
>> component from the prcomp() is identical to the 2nd component from
>> svd() and it keeps going with this shift. 
>>
>> The first component from SVD has a large variance attached to it. If
>> you remove that and recalculate the percentages, they are identical
>> to the variances explained by prcomp. 
>>
>> Any ideas what's happening?
>>
>> Thanks,
>> M
>>
>> CONFIDENTIALITY NOTICE: This e-mail message, including any
>> attachments, is for the sole use of the intended recipient(s) and may
>> contain confidential and privileged information protected by law. Any
>> unauthorized review, use, disclosure or distribution is prohibited. 
>> If you are not the intended recipient, please contact the sender by
>> reply e-mail and destroy all copies of the original message. 
>>
>> - End forwarded message -
>>
>>
>
>
>
>

- End forwarded message -

- End forwarded message -



signature.asc
Description: PGP signature

Average contours

[morphmet_moderator]

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Thu, 12 Jun 2014 06:40:34 -0700
  From: morphmet_modera...@morphometrics.org
  Reply-To: morphmet_modera...@morphometrics.org
  Subject: Average contours
  To: morphmet@morphometrics.org

- Forwarded message from "Pere M. Parés-Casanova" 
 -

Date: Sat, 7 Jun 2014 10:16:45 -0400
From: "Pere M. Parés-Casanova" 
Reply-To: "Pere M. Parés-Casanova" 
Subject: Average contours
To: morphmet@morphometrics.org

Dear morphometricians. 
I know it is quite simple, but how to "countour" a figure in order to
illustrate the total form, i.e., not considering only landmarks? Just for
superimposing the "standard" sample with landmarked samples. 
Thanks in advance!

Pere-Miquel

- End forwarded message -

- End forwarded message -

RE: ERROR IN TPSRELW

[morphmet_moderator]

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Wed, 11 Jun 2014 05:22:45 -0700
  From: morphmet_modera...@morphometrics.org
  Reply-To: morphmet_modera...@morphometrics.org
  Subject: RE: ERROR IN TPSRELW
  To: morphmet@morphometrics.org

- Forwarded message from "F. James Rohlf"  -

 Date: Fri, 6 Jun 2014 14:31:21 -0400
  From: "F. James Rohlf"
  Reply-To: ro...@life.bio.sunysb.edu
  Subject: RE: ERROR IN TPSRELW
  To: morphmet@morphometrics.org

It means that with < 3 landmarks you cannot analyze variation in shape. One or 
two landmarks is not sufficient to capture a shape.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -

F. James Rohlf, Distinguished Professor, Emeritus, Stony Brook University

The much revised 4th editions of Biometry and Statistical Tables are now 
available:

http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-rohlf

From: morphmet_modera...@morphometrics.org 
[mailto:morphmet_modera...@morphometrics.org]
Sent: Thursday, June 05, 2014 11:08 PM
To: morphmet@morphometrics.org
Subject: ERROR IN TPSRELW

- Forwarded message from eugy peró  -

Date: Thu, 15 May 2014 17:48:10 -0400
From: eugy peró
Reply-To: eugy peró
Subject: ERROR IN TPSRELW
To: "morphmet@morphometrics.org"

Hi!

What is the meaning of the message Error: cannot use < 3 landmarks in TPSRelw?

Sorry my english! Im from Argentina...

Thanks!

- End forwarded message -

- End forwarded message -

- End forwarded message -

CSV to NTSYSpc conversion tool

[morphmet_moderator]

- Forwarded message from Mauro Cavalcanti  -

 Date: Fri, 6 Jun 2014 14:50:03 -0400
  From: Mauro Cavalcanti 
  Reply-To: Mauro Cavalcanti 
  Subject: CSV to NTSYSpc conversion tool
  To: morphmet@morphometrics.org

Dear ALL,

I have wrote a simple console-based C/C++ program to perform the conversion of 
comma-delimited files (CSV) into NTSYSpc data files. 

The distribution package, including binary executables for GNU/Linux and 
MS-Windows, as well as the full source code of the program and an example data 
file, can be downloaded from my personal website: 
http://sites.google.com/site/maurobio/software

Hope this is useful. 

Best regards,

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

- End forwarded message -

Re: Comparing svd() and prcomp() output from R

[morphmet_moderator]

- Forwarded message from Marko Djurakic  -

 Date: Fri, 6 Jun 2014 09:25:03 -0400
  From: Marko Djurakic
  Reply-To: Marko Djurakic
  Subject: Re: Comparing svd() and prcomp() output from R
  To: morphmet@morphometrics.org

On 6.6.2014 11:09, morphmet_modera...@morphometrics.org wrote:

Hi folks,

This is really a R question, but perhaps someone can help me.

When I run svd() and prcomp() functions on my procrustes aligned coordinates, I 
end up with an interesting situation, where the 1st component from the prcomp() 
is identical to the 2nd component from svd() and it keeps going with this shift.

The first component from SVD has a large variance attached to it. If you remove 
that and recalculate the percentages, they are identical to the variances 
explained by prcomp.

Any ideas what's happening?

Thanks,
M

Hi,
I am not able to answer why did you obtain such shift between svd() and 
prcomp(), but below is a way how you can obtain identical results using those 
functions.

Probably you provided an incorrect input for svd(). Both prcomp() and svd() use 
the singular value decomposition to find eigenvectors and eigenvalues. However, 
functions differ regarding required inputs. prcomp() works on a matrix of 
Procrustes aligned coordinates (e.g rows are individuals and columns are 
x,y,(z) variables). If you want to obtain results using svd() you must provide 
covariance matrix of the CENTERED data rather than matrix of Procrustes aligned 
coordinates. If you do this accordingly, svd() will return eigenvalues and 
eigenvectors, and individual scores can be computed by multiplying eigenvectors 
with original data (matrix of the CENTERED data).

If you are interested here is David Polly's great tutorial that might help:
http://www.indiana.edu/~g562/PBDB2013/Day%203B%20-%20PCA%20and%20morphospace.pdf

Here I summarized svd() and prcomp() comparison:

## Load package, data, perform GPA, format Procrustes coordinates into two 
dimensional array (e.g rows are individuals and columns are x,y variables)
library (geomorph)
data (plethodon)                                               
coords 

Re: ERROR IN TPSRELW

[morphmet_moderator]

- Forwarded message from Jean-Pierre Dujardin  -

 Date: Fri, 6 Jun 2014 09:23:32 -0400
  From: Jean-Pierre Dujardin
  Reply-To: Jean-Pierre Dujardin
  Subject: Re: ERROR IN TPSRELW
  To: Morphmet

Con dos landmarks no es posible generar otra forma que la de una línea recta...
 On Jun 6, 2014 4:09 PM,   wrote:

- Forwarded message from eugy peró  -

 Date: Thu, 15 May 2014 17:48:10 -0400
  From: eugy peró
  Reply-To: eugy peró
  Subject: ERROR IN TPSRELW
To: "morphmet@morphometrics.org"

Hi!What is the meaning of the message Error: cannot use < 3 landmarks in 
TPSRelw?
Sorry my english! Im from Argentina...
Thanks!

- End forwarded message -

- End forwarded message -

Fwd:

[morphmet_moderator]

- Forwarded message from La Lala  -

 Date: Fri, 6 Jun 2014 09:17:10 -0400
  From: La Lala
  Reply-To: La Lala
  Subject:
  To: morphmet@morphometrics.org

Hello Everyone,

I want to conduct growth studies on Larger benthic Foraminifera with 3D 
landmarks. Is there a way to place sliding landmarks in Amira? Or can anyone 
recommend other software (preferably free) for placing slinding landmarks? My 
surfaces usually consist of over 50 materials, so the programm should also be 
able to "switch on and of" materials.

Thanks in advance
Julia Wöger

Inst. f. Palaeontologie, Universität Wien

- End forwarded message -

Re: DinoXcope Use in GM - mhol...@berkeley.edu

[morphmet_moderator]

- Forwarded message from La Lala  -

 Date: Fri, 6 Jun 2014 09:02:21 -0400
  From: La Lala
  Reply-To: La Lala
  Subject: Re: DinoXcope Use in GM - mhol...@berkeley.edu
  To: morphmet@morphometrics.org

Hello Michael,

We are currently useing a Dinolite to take pictures of larger benthic 
Foraminifera to investigate their growth. I think the resolution of the 
pictures is very good compared to opther usb microscopes. However it is very 
difficult to focus and the measuring software that comes with the microscope is 
absolutely not reliable. It prooved very difficult to get halfway accurate 
measurements even with a scalebar. Our Foraminifera are all very flat and easy 
to photograph, but I would not recomend it for more complex shapes. I think a 
microscope with camera would be preferable in your case.

Julia Wöger

Inst. f. Palaeontologie, Universität Wien

2014-06-06 11:10 GMT+02:00  :

- Forwarded message from Michael Holmes  -

 Date: Sun, 18 May 2014 17:14:00 -0400
  From: Michael Holmes
Reply-To: Michael Holmes
  Subject: DinoXcope Use in GM - mhol...@berkeley.edu
  To: morphmet@morphometrics.org

Hello,  Has anyone used a Dino-lite DinXcope for morphometrics of small 
mandibles (mice, etc)?  Are they effective at capturing subtle landmarks such 
as the mental foramen?  If you've used them, what lighting source do you use?  
Thanks in advance.

--
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

- End forwarded message -

- End forwarded message -

RE: ERROR IN TPSRELW

[morphmet_moderator]

- Forwarded message from Markus Bastir  -

 Date: Fri, 6 Jun 2014 05:30:05 -0400
  From: Markus Bastir
  Reply-To: mbas...@mncn.csic.es
  Subject: RE: ERROR IN TPSRELW
  To: morphmet@morphometrics.org

Hola,

Esto significa que o bien usas configuraciones que tengan menos de 3 landmarks, 
y por tanto no se pueden procesar, o, más probable, que tienes un problema de 
formato de las matrices de landmarks y el software no lo puede leer 
correctamente. ¿Usas TPS o NTS format?

Un saludo
Markus

De: morphmet_modera...@morphometrics.org 
[mailto:morphmet_modera...@morphometrics.org]
Enviado el: viernes, 06 de junio de 2014 11:08
Para: morphmet@morphometrics.org
Asunto: ERROR IN TPSRELW

- Forwarded message from eugy peró  -

Date: Thu, 15 May 2014 17:48:10 -0400
From: eugy peró
Reply-To: eugy peró
Subject: ERROR IN TPSRELW
To: "morphmet@morphometrics.org"

Hi!

What is the meaning of the message Error: cannot use < 3 landmarks in TPSRelw?

Sorry my english! Im from Argentina...

Thanks!

- End forwarded message -

- End forwarded message -

RE: unbend function of tpsUtil

[morphmet_moderator]

- Forwarded message from "F. James Rohlf"  -

 Date: Fri, 6 Jun 2014 03:59:53 -0400
  From: "F. James Rohlf"
  Reply-To: ro...@life.bio.sunysb.edu
  Subject: RE: unbend function of tpsUtil
  To: morphmet@morphometrics.org

The tpsUtil software’s unbending function simply does a polynomial regression 
for the points. The SSresid is the residual SS from that regression, The R^2 
gives the squared multiple regression coefficient as a standardized measure of 
fit. The column b2 gives the value of the regression coefficient for the 
quadratic term. Probably only useful to tell you if the specimen was bending up 
or bending down.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -

F. James Rohlf, Distinguished Professor, Emeritus, Stony Brook University

The much revised 4th editions of Biometry and Statistical Tables are now 
available:

http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-rohlf

From: morphmet_modera...@morphometrics.org 
[mailto:morphmet_modera...@morphometrics.org]
Sent: Wednesday, June 04, 2014 8:06 PM
To: morphmet@morphometrics.org
Subject: unbend function of tpsUtil

- Forwarded message from "Litt, Margaret Aline"  -

Date: Wed, 14 May 2014 09:57:17 -0400
From: "Litt, Margaret Aline"
Reply-To: "Litt, Margaret Aline"
Subject: unbend function of tpsUtil
To: morphmet@morphometrics.org

Hello,

In the view listing panel for the unbend function of tps, what do the b^2 and 
SSResid values indicate about the fit?

Aline

mal...@mun.ca

- End forwarded message -

- End forwarded message -

landmark configuration reflection

[morphmet_moderator]

- Forwarded message from Miguel Eduardo Delgado Burbano  -

 Date: Thu, 5 Jun 2014 17:59:15 -0300
  From: Miguel Eduardo Delgado Burbano
  Reply-To: Miguel Eduardo Delgado Burbano
  Subject: landmark configuration reflection
  To: morphmet_modera...@morphometrics.org

Hi all

I am performing a 2D geometric morphometric study using human skulls. In a 
previous research I digitized several landmarks and semilandmarks in the right 
half of the face, but now I am trying to perform an analysis using the complete 
face (i.e both halfs), so in order to not digitized again perhaps I can reflect 
the right landmark configuration on the left side. Since the reflection is 
performed during the procrustes (GPA) perhaps a particular software allows to 
reflect the landmark configuration  TPS, MorphoJ, GeoMorph etc?? 

   any suggestions?

thank you in advance

best 

Miguel

- End forwarded message -

tpsSmall update - 1.29

[morphmet_moderator]

- Forwarded message from "F. James Rohlf"  -

 Date: Thu, 5 Jun 2014 17:43:25 -0400
  From: "F. James Rohlf" 
  Reply-To: ro...@life.bio.sunysb.edu
  Subject: tpsSmall update - 1.29
  To: morphmet@morphometrics.org

I have just uploaded to the SB morphometrics site a small update to tpsSmall. 
Thanks to Andrea Cardini for reporting the problem when using 3D landmarks. Now 
version 1.29. 

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -

F. James Rohlf, Distinguished Professor, Emeritus, Stony Brook University

The much revised 4th editions of Biometry and Statistical Tables are now 
available:

http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-rohlf

- End forwarded message -

New versions of Morpho (2.0.3-1) and Rvcg (0.8) now on CRAN

[morphmet_moderator]

- Forwarded message from Stefan Schlager  -

 Date: Thu, 5 Jun 2014 11:36:10 -0400
  From: Stefan Schlager 
  Reply-To: Stefan Schlager 
  Subject: New versions of  Morpho (2.0.3-1)  and Rvcg (0.8) now on CRAN
  To: morphmet@morphometrics.org

 Dear all,

I released a new version of Morpho (2.0.3-1) on CRAN. 
Changes and new features in Morpho are

  * added support for objects stored in a list in bindArr
  * made rotreverse an S3 function for matrices and mesh3d
  * fixed bug in slider3d if pairedLM != 0
  * fixed pooled within covariance matrix (covW) for single group entries
  * speed up rotonto, rotonmat by vectorizing
  * removed junk comments
  * added fix for weighted Grandmean in CVA (thanks to Anne-Beatrice Defour)
  * added check for empty patches and curves in cExtract (thanks to M. Friess 
for pointing that out)
  * added 'cutMeshPlane' and 'cutSpace' to cut a pointcloud/mesh into upper and 
lower part
  * added function 'solutionSpace' to calculate the basis of the solution space 
for Ax=b, with det(A)=0
  * minor changes in asymPermute (docu and table naming)
  * enabled multigroup support in asymPermute
  * added groupmean output in asymPermute
  * updateNormals: if no faces are present, mesh will be returned unchanged 
now. quadric faces are converted to triangular ones
  * add new function 'quad2trimesh' for converting quadric meshes into 
triangular meshes. 
  * made code in pcaplot3d easier to maintain by creating .pcaplot3d
  * assigned additional attributes to output of procSym

Changes and new features inRvcg:

  * improved memory footprint by using optional components
  * set defaults in vcgQEdecim to those in meshlab and updated docu
  * added helperfunction setRays
  * added vcgIsosurface to create meshes form 3D arrays (using value 
thresholding)
  * vcgClean now supports executing multiple cleaning operations in arbitrary 
sequences. 
  * fixed color handling in vcgClean
  * added handling of existing vertex colors in vcgIsolated
  * fixed colorimport in vcgImport
  * added option to merge close vertices in vcgClean and to report removed 
vertices
  * set borderchk to FALSE as default in vcgClost and vcgClostKD
  * added vcgKDtree to use kdtree search from vcglib on pointclouds. 

And, as always, you can track the ongoing development on github 
(https://github.com/zarquon42b) or sourceforge 
(https://sourceforge.net/projects/morpho-rpackage/)
and install it with the R-package "devtools" by issueing the command 
install_github("zarquon42b/Morpho") or install_github("zarquon42b/Rvcg") 
resepctively (please note that you need to install a compiler first)

All the best
Stefan

- End forwarded message -



signature.asc
Description: PGP signature

Re: Image database of plant leaves

[morphmet_moderator]

- Forwarded message from andrea cardini  -

 Date: Tue, 3 Jun 2014 05:29:10 -0400
  From: andrea cardini 
  Reply-To: andrea cardini 
  Subject: Re: Image database of plant leaves
  To: morphmet@morphometrics.org, morphmet@morphometrics.org

If you're happy with the landmark configuration, 
the one we used in Viscosi & Cardini, 2011, Plos One is online. 
Maybe you can check with the first author if he's happy to share the pics too. 

Cheers

Andrea

At 09:04 03/06/2014, morphmet_modera...@morphometrics.org wrote:

>- Forwarded message from morphmet_modera...@morphometrics.org -
>
>Date: Mon, 02 Jun 2014 01:43:10 -0700
>From: morphmet_modera...@morphometrics.org
>Reply-To: morphmet_modera...@morphometrics.org
>Subject: Image database of plant leaves
>To: morphmet@morphometrics.org
>
>
>- Forwarded message from Ely Raz  -
>
>Date: Wed, 16 Apr 2014 17:14:43 -0400
>From: Ely Raz 
>Reply-To: Ely Raz 
>Subject: Image database of plant leaves
>To: morphmet@morphometrics.org
>
>Hi,
>
>
>I am looking for an image database of plant 
>leaves. If you know some please send me an email. 
>
>
>Thanks. 
>
>
>
>- End forwarded message -
>
>
>
>
>
>- End forwarded message -
>
>

Dr. Andrea Cardini
Researcher in Animal Biology, Dipartimento di 
Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, l.go S. Eufemia 19, 41121 Modena, Italy
Honorary Fellow, Centre for Anatomical and Human 
Sciences, University of Hull, Cottingham Road, 
Hull, HU6 7RX, UK & University of York, Heslington, York YO10 5DD, UK
Adjunct Associate Professor, Centre for Forensic 
Science , The University of Western Australia, 35 
Stirling Highway, Crawley WA 6009, Australia

E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: http://sites.google.com/site/hymsfme/drandreacardini
Summary of research interests at: 
http://www.dscg.unimore.it/site/home/ricerca/aree-di-ricerca/evolution-taxonomy-and-forensics.html

FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/issue/view/405
or full volume at: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf

Editorial board for:
Zoomorphology: 
http://www.springer.com/life+sciences/animal+sciences/journal/435
Journal of Zoological Systematics and 
Evolutionary Research: http://www.wiley.com/bw/journal.asp?ref=0947-5745&site=1
Hystrix, the Italian Journal of 
Mammalogy: http://www.italian-journal-of-mammalogy.it/ 

- End forwarded message -

Re: tps util and tpsdig2

[morphmet_moderator]

- Forwarded message from andrea cardini  -

 Date: Tue, 3 Jun 2014 05:02:13 -0400
  From: andrea cardini 
  Reply-To: andrea cardini 
  Subject: Re: tps util and tpsdig2
  To: morphmet@morphometrics.org

Gabriela, not sure if it may work for you. 
However, you can get landmark coordinates from 
pics also using ImageJ (which is multiplatform). 
It's won't be in the TPS format but format conversions are then pretty easy. 

I am using TPSDig using WINE in Linux. It's a 
long way but you can install Linux in VBox (or 
VMware) in your Mac and then run any of the TPS 
software from there without need to reboot your machine. 

Good luck

Andrea

At 10:40 02/06/2014, you wrote:

>- Forwarded message from morphmet_modera...@morphometrics.org -
>
>Date: Sun, 01 Jun 2014 00:41:50 -0700
>From: morphmet_modera...@morphometrics.org
>Reply-To: morphmet_modera...@morphometrics.org
>Subject: Re: tps util and tpsdig2
>To: morphmet@morphometrics.org
>
>
>- Forwarded message from "Gabriela N."  -
>
>Date: Wed, 16 Apr 2014 01:20:47 -0400
>From: "Gabriela N." 
>Reply-To: "Gabriela N." 
>Subject: Re: tps util and tpsdig2
>To: morphmet@morphometrics.org
>
>Please reply to: gna...@mlml.calstate.edu
>
>I am using the tps util and tpsdig2 on my 
>virtual machine on my Mac, but am having trouble 
>with my hard drive space starting to be limited 
>to the point of being unable to process any more pix. 
>
>I saw that there is a MacMorph software (by Mark 
>Spencer) for digitizing landmarks for Macs 
>available on the 
>http://life.bio.sunysb.edu/morph/Â 
>webpage, but no link for downloading this 
>software. It would be great if anyone has used a 
>mac version of tps util and tpsdig2 that works 
>for them to process my pix on my Mac. 
>
>Any help or guidance would be greatly appreciated!
>
>
>
>- End forwarded message -
>
>
>
>
>
>- End forwarded message -
>
>

Dr. Andrea Cardini
Researcher in Animal Biology, Dipartimento di 
Scienze Chimiche e Geologiche, Università di 
Modena e Reggio Emilia, l.go S. Eufemia 19, 41121 Modena, Italy
Honorary Fellow, Centre for Anatomical and Human 
Sciences, University of Hull, Cottingham Road, 
Hull, HU6 7RX, UK & University of York, Heslington, York YO10 5DD, UK
Adjunct Associate Professor, Centre for Forensic 
Science , The University of Western Australia, 35 
Stirling Highway, Crawley WA 6009, Australia

E-mail address: alcard...@gmail.com, andrea.card...@unimore.it
WEBPAGE: http://sites.google.com/site/hymsfme/drandreacardini
Summary of research interests at: 
http://www.dscg.unimore.it/site/home/ricerca/aree-di-ricerca/evolution-taxonomy-and-forensics.html

FREE Yellow BOOK on Geometric Morphometrics: 
http://www.italian-journal-of-mammalogy.it/issue/view/405
or full volume at: 
http://www.italian-journal-of-mammalogy.it/public/journals/3/issue_241_complete_100.pdf

Editorial board for:
Zoomorphology: 
http://www.springer.com/life+sciences/animal+sciences/journal/435
Journal of Zoological Systematics and 
Evolutionary Research: http://www.wiley.com/bw/journal.asp?ref=0947-5745&site=1
Hystrix, the Italian Journal of 
Mammalogy: http://www.italian-journal-of-mammalogy.it/ 

- End forwarded message -

geomorph 2.1

[morphmet_moderator]

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Sat, 07 Jun 2014 22:53:33 -0700
  From: morphmet_modera...@morphometrics.org
  Reply-To: morphmet_modera...@morphometrics.org
  Subject: geomorph 2.1
  To: morphmet@morphometrics.org

- Forwarded message from "Adams, Dean [EEOBS]"  -

 Date: Sun, 1 Jun 2014 08:42:01 -0400
  From: "Adams, Dean [EEOBS]" 
Reply-To: "Adams, Dean [EEOBS]" 
  Subject: geomorph 2.1
  To: "morphmet@morphometrics.org" 

 Hello all, 

 The latest version of geomorph is now up on the CRAN repository. This version 
contains enhanced 2D digitizing capabilities, as well as several new analytical 
functions for comparing regression slopes, and performing permutation tests 
using residual randomization. 

 In addition, geomorph now contains a set of analytical tools for performing 
various phylogenetic comparative methods on high-dimensional data (including 
shape). These tools include approaches for:

phylomorphospace visualization
comparing rates of multivariate evolution on phylogenies
phylogenetic partial least squares
phylogenetic signal (a multivariate version of Blomberg's Kappa)
PGLS for high-dimensional data

 References for all approaches are found in the man pages, along with examples. 

Regards,

 Dean 

--  
Dr. Dean C. 
Adams
Professor
Department of Ecology, Evolution, and Organismal
Biology
   Department of Statistics
Iowa State University
www.public.iastate.edu/~dcadams/
phone:
515-294-3834

- End forwarded message -

- End forwarded message -

cluster analysis advice

[morphmet_moderator]

- Forwarded message from "Schmidt, Eric"  -

 Date: Mon, 2 Jun 2014 16:34:35 -0400
  From: "Schmidt, Eric"
  Reply-To: "Schmidt, Eric"
  Subject: cluster analysis advice
  To: "morphmet@morphometrics.org"

I'd like to ask for some advice on using kinds of cluster analysis for a 
morphological data set.  Shape is not involved.  I have data on the weights of 
certain organs from numerous mice.  These included things like livers, spleens, 
hearts, and kidneys, dissected from adult mice.  One aim is to take the data 
and find modular patterns within them, without making any a priori hypotheses.  
I'd also do this with the body weight residuals of all the organs.   

 One method I will try is to do a PCA, using organ types as the variables.  If 
different organ types tend to group and cluster, perhaps those "clusters" could 
be used as a priori hypotheses in a PLS regression.  Another way to group 
organs might be to base clusters on germ layers, and do PLS.   However, I'd 
like some advice on a method or set of methods that will do a cluster analysis 
independent of an initial hypothesis.

 Thank you

 Eric
 Wash U

-

The materials in this email are private and may contain Protected Health 
Information. If you are not the intended recipient be advised that any 
unauthorized use, disclosure, copying, distribution or the taking of any action 
in reliance on the contents of this information is strictly prohibited. If you 
have received this email in error, please immediately notify the sender via 
return email.

- End forwarded message -

RE: Problems with TpsRegr df<1

[morphmet_moderator]

- Forwarded message from "F. James Rohlf"  -

 Date: Mon, 2 Jun 2014 14:28:58 -0400
  From: "F. James Rohlf" 
  Reply-To: ro...@life.bio.sunysb.edu
  Subject: RE: Problems with TpsRegr dfThat message means sample size is 
not adequate in relation to the number of shape variables. See the help file 
for the formula for the degrees of freedom. 

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -

F. James Rohlf, Distinguished Professor, Emeritus, Stony Brook University

The much revised 4th editions of Biometry and Statistical Tables are now 
available:

http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-rohlf

From: morphmet_modera...@morphometrics.org 
[mailto:morphmet_modera...@morphometrics.org] 
Sent: Sunday, June 01, 2014 10:41 PM
To: morphmet@morphometrics.org
Subject: Problems with TpsRegr df

Last call course Intro GMM, Barcelona, August 2014

[morphmet_moderator]

- Forwarded message from "soledad.esteban"  -

 Date: Thu, 29 May 2014 16:18:20 +0200
  From: "soledad.esteban"
  Reply-To: "soledad.esteban"
  Subject: Last call course Intro GMM, Barcelona, August 2014
  To: morphmet_modera...@morphometrics.org

Dear colleagues,
This is the last call for the course  "INTRODUCTION TO GEOMETRIC MORPHOMETRICS- 
5th edition". Only 5 places left!

INSTRUCTORS: Dr. Chris Klingenberg (University of Manchester, UK) and Dr. Jesús 
 Marugán (UAM, Spain). DATES: August 4-8, 2014; 38 teaching hours. 

PLACE:  Facilities of the Centre of Restauració i Interpretació Paleontologica, 
Els Hostalets de Pierola,  Barcelona (Spain). 

Organized by: Transmitting Science, the Institut Catalá de Paleontologia Miquel 
 Crusafont and the Council of Hostalets de Pierola. 

More information:  
http://www.transmittingscience.org/courses/gm/introduction-to-gm/  or  writing 
to cour...@transmittingscience.org 

This course is entitled to teach the main concepts of shape analysis based on  
landmark coordinates and its multivariate procedures, and how they can be put 
into practice across any biological discipline in which the phenotype (form) 
and  its variation are the principal sources of information. 

Please feel free to distribute this information between your colleagues if you  
consider it appropriate. 

With best regards 

Soledad De Esteban Trivigno
Investigadora del Institut Català de Paleontologia M. Crusafont (ICP) 
soledad.este...@icp.cat 
Mòdul ICP - Facultat de Biociències 
Campus de la Universitat Autònoma de Barcelona 
E-08193 Cerdanyola del Vallès 
www.icp.cat

- End forwarded message -

RE: csv to nts tool?

[morphmet_moderator]

- Forwarded message from "F. James Rohlf"  -

 Date: Wed, 28 May 2014 03:44:52 -0400
  From: "F. James Rohlf" 
  Reply-To: ro...@life.bio.sunysb.edu
  Subject: RE: csv to nts tool?
  To: morphmet@morphometrics.org

I could add such an option to tpsUtil but there would have to be some 
constraints on the format of the csv file. For example, the coordinates in the 
first two (or 3) columns and some way to know where the coordinates for one 
specimen left off and the next begins. 

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -

F. James Rohlf, Distinguished Professor, Emeritus, Stony Brook University

The much revised 4th editions of Biometry and Statistical Tables are now 
available:

http://www.whfreeman.com/Catalog/product/biometry-fourthedition-sokal

http://www.whfreeman.com/Catalog/product/statisticaltables-fourthedition-rohlf

From: morphmet_modera...@morphometrics.org 
[mailto:morphmet_modera...@morphometrics.org] 
Sent: Tuesday, May 27, 2014 8:04 AM
To: morphmet@morphometrics.org
Subject: csv to nts tool?

- Forwarded message from morphmet_modera...@morphometrics.org -

Date: Tue, 20 May 2014 22:18:43 -0700
From: morphmet_modera...@morphometrics.org
Reply-To: morphmet_modera...@morphometrics.org
Subject: csv to nts tool?
To: morphmet@morphometrics.org

- Forwarded message from morphmet_modera...@morphometrics.org -

Date: Wed, 14 May 2014 22:32:49 -0700
From: morphmet_modera...@morphometrics.org
Reply-To: morphmet_modera...@morphometrics.org
Subject: csv to nts tool?
To: morphmet@morphometrics.org

- Forwarded message from morphmet_modera...@morphometrics.org -

Date: Sun, 11 May 2014 20:51:43 -0700
From: morphmet_modera...@morphometrics.org
Reply-To: morphmet_modera...@morphometrics.org
Subject: csv to nts tool?
To: morphmet@morphometrics.org

- Forwarded message from morphmet_modera...@morphometrics.org -

Date: Thu, 08 May 2014 21:49:17 -0700
From: morphmet_modera...@morphometrics.org
Reply-To: morphmet_modera...@morphometrics.org
Subject: csv to nts tool?
To: morphmet@morphometrics.org

- Forwarded message from morphmet_modera...@morphometrics.org -

Date: Mon, 05 May 2014 17:56:21 -0700
From: morphmet_modera...@morphometrics.org
Reply-To: morphmet_modera...@morphometrics.org
Subject: csv to nts tool?
To: morphmet@morphometrics.org

- Forwarded message from morphmet_modera...@morphometrics.org -

Date: Sun, 04 May 2014 16:39:30 -0700
From: morphmet_modera...@morphometrics.org
Reply-To: morphmet_modera...@morphometrics.org
Subject: csv to nts tool?
To: morphmet@morphometrics.org

- Forwarded message from morphmet_modera...@morphometrics.org -

Date: Sat, 03 May 2014 08:11:54 -0700
From: morphmet_modera...@morphometrics.org
Reply-To: morphmet_modera...@morphometrics.org
Subject: csv to nts tool?
To: morphmet@morphometrics.org

- Forwarded message from morphmet_modera...@morphometrics.org -

Date: Thu, 01 May 2014 17:56:22 -0700
From: morphmet_modera...@morphometrics.org
Reply-To: morphmet_modera...@morphometrics.org
Subject: csv to nts tool?
To: morphmet@morphometrics.org

- Forwarded message from morphmet_modera...@morphometrics.org -

Date: Thu, 01 May 2014 09:00:27 -0700
From: morphmet_modera...@morphometrics.org
Reply-To: morphmet_modera...@morphometrics.org
Subject: csv to nts tool?
To: morphmet@morphometrics.org

- Forwarded message from William Ary  -

Date: Tue, 8 Apr 2014 22:23:58 -0400
From: William Ary 
Reply-To: William Ary 
Subject: csv to nts tool?
To: morphmet@morphometrics.org

Hello all-

A friend wants to use Geomorph, but his digitized landmark files are exported 
from Aviso (CT image processing software) in csv format. Is there a conversion 
utility to go from csv to nts or tps? I checked the SUNY morphometrics page and 
saw several conversion tools but they all go the other way from nts to csv. 

Does a csv to nts file converter exist?

Thank you

Will Ary

- End forwarded message -

- End forwarded message -

- End forwarded message -

- End forwarded message -

- End forwarded message -

- End forwarded message -

- End forwarded message -

- End forwarded message -

- End forwarded message -

- End forwarded message -

- End forwarded message -

Re: csv to nts tool?

[morphmet_moderator]

- Forwarded message from Mauro Cavalcanti  -

 Date: Tue, 27 May 2014 16:04:40 -0400
  From: Mauro Cavalcanti 
  Reply-To: Mauro Cavalcanti 
  Subject: Re: csv to nts tool?
  To: morphmet@morphometrics.org

Hi,

Being myself the author of one of the NTS to CVS conversion software available 
on the SUNY server, I can only tell you that it would be exceedingly easy to 
write a small utility for doing the opposite, that is converting from CVS to 
NTS. If there are interest in this, I could write such a program, but I am 
under the impression that this can be easily done with the geomorph R package 
(read a dataset stored in csv format and then write this dataset to disk using 
a geomorph function). 

Hope this helps. 

Cheers,

2014-05-27 15:03 GMT-03:00  :

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Tue, 20 May 2014 22:18:43 -0700
  From: morphmet_modera...@morphometrics.org
Reply-To: morphmet_modera...@morphometrics.org
  Subject: csv to nts tool?
  To: morphmet@morphometrics.org

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Wed, 14 May 2014 22:32:49 -0700
  From: morphmet_modera...@morphometrics.org
Reply-To: morphmet_modera...@morphometrics.org
  Subject: csv to nts tool?
  To: morphmet@morphometrics.org

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Sun, 11 May 2014 20:51:43 -0700
  From: morphmet_modera...@morphometrics.org
Reply-To: morphmet_modera...@morphometrics.org
  Subject: csv to nts tool?
  To: morphmet@morphometrics.org

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Thu, 08 May 2014 21:49:17 -0700
  From: morphmet_modera...@morphometrics.org
Reply-To: morphmet_modera...@morphometrics.org
  Subject: csv to nts tool?
  To: morphmet@morphometrics.org

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Mon, 05 May 2014 17:56:21 -0700
  From: morphmet_modera...@morphometrics.org
Reply-To: morphmet_modera...@morphometrics.org
  Subject: csv to nts tool?
  To: morphmet@morphometrics.org

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Sun, 04 May 2014 16:39:30 -0700
  From: morphmet_modera...@morphometrics.org
Reply-To: morphmet_modera...@morphometrics.org
  Subject: csv to nts tool?
  To: morphmet@morphometrics.org

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Sat, 03 May 2014 08:11:54 -0700
  From: morphmet_modera...@morphometrics.org
Reply-To: morphmet_modera...@morphometrics.org
  Subject: csv to nts tool?
  To: morphmet@morphometrics.org

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Thu, 01 May 2014 17:56:22 -0700
  From: morphmet_modera...@morphometrics.org
Reply-To: morphmet_modera...@morphometrics.org
  Subject: csv to nts tool?
  To: morphmet@morphometrics.org

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Thu, 01 May 2014 09:00:27 -0700
  From: morphmet_modera...@morphometrics.org
Reply-To: morphmet_modera...@morphometrics.org
  Subject: csv to nts tool?
  To: morphmet@morphometrics.org

- Forwarded message from William Ary  -

 Date: Tue, 8 Apr 2014 22:23:58 -0400
  From: William Ary 
Reply-To: William Ary 
  Subject: csv to nts tool?
  To: morphmet@morphometrics.org

Hello all-

A friend wants to use Geomorph, but his digitized landmark files are exported 
from Aviso (CT image processing software) in csv format. Is there a conversion 
utility to go from csv to nts or tps? I checked the SUNY morphometrics page and 
saw several conversion tools but they all go the other way from nts to csv. 

Does a csv to nts file converter exist?

Thank you

Will Ary

- End forwarded message -

- End forwarded message -

- End forwarded message -

- End forwarded message -

- End forwarded message -

- End forwarded message -

- End forwarded message -

- End forwarded message -

- End forwarded message -

- End forwarded message -

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

- End forwarded message -

GMM, Oak leaf form, Help

[morphmet_moderator]

- Forwarded message from Mustapha LATEB  -

 Date: Thu, 22 May 2014 11:04:00 -0400
  From: Mustapha LATEB
  Reply-To: Mustapha LATEB
  Subject: GMM, Oak leaf form, Help
  To: "morphmet@morphometrics.org"

Dear,

 
I'm a student working on Leafs morphology of Oak hybrids.
I have followed the protocol of Vincenzo Viscosi and Andrea Cardini.
 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0025630

The Aim of my study :
In my study area there is only two described Hybrides in the literature. I 
would like to check by using GMM, if there is other hybrids.

I would like make a clusters of the sampled trees without separating them on 
differentes populations and compare the typical leaf form of each groupe with 
the botanical discription.

I have a sample of 84 trees, where I have selected 10 leaves per tree with 
repitition (then I got 20 images/ tree). I have digitized 11 landmarks per 
leave for the 84 trees, as specified in the Protocol,

My question is:
Could you please, show me the next steps in order to make an unsupervised 
classification or other techniques to define groups of trees. 

Thank you in advance
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
Mustapha LATEB

Magister student at UMMTO, Algeria &Master of Science student at MAICh, Greece 
Phone: +30 6994997057 
Skype: Mus.Lat

- End forwarded message -

DinoXcope Use in GM - mhol...@berkeley.edu

[morphmet_moderator]

- Forwarded message from Michael Holmes  -

 Date: Sun, 18 May 2014 17:14:00 -0400
  From: Michael Holmes
  Reply-To: Michael Holmes
  Subject: DinoXcope Use in GM - mhol...@berkeley.edu
  To: morphmet@morphometrics.org

Hello,  Has anyone used a Dino-lite DinXcope for morphometrics of small 
mandibles (mice, etc)?  Are they effective at capturing subtle landmarks such 
as the mental foramen?  If you've used them, what lighting source do you use?  
Thanks in advance.

--
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

- End forwarded message -

ERROR IN TPSRELW

[morphmet_moderator]

- Forwarded message from eugy peró  -

 Date: Thu, 15 May 2014 17:48:10 -0400
  From: eugy peró
  Reply-To: eugy peró
  Subject: ERROR IN TPSRELW
  To: "morphmet@morphometrics.org"

Hi!What is the meaning of the message Error: cannot use < 3 landmarks in 
TPSRelw?
Sorry my english! Im from Argentina...
Thanks!

- End forwarded message -

Comparing svd() and prcomp() output from R

[morphmet_moderator]

- Forwarded message from "Maga, Murat"  -

 Date: Thu, 15 May 2014 18:54:15 -0400
  From: "Maga, Murat" 
  Reply-To: "Maga, Murat" 
  Subject: Comparing svd() and prcomp() output from R
  To: "'morphmet@morphometrics.org'" 

Hi folks,

This is really a R question, but perhaps someone can help me. 

When I run svd() and prcomp() functions on my procrustes aligned coordinates, I 
end up with an interesting situation, where the 1st component from the prcomp() 
is identical to the 2nd component from svd() and it keeps going with this 
shift. 

The first component from SVD has a large variance attached to it. If you remove 
that and recalculate the percentages, they are identical to the variances 
explained by prcomp. 

Any ideas what's happening?

Thanks,
M

CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for 
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- End forwarded message -

Calling papers for June 2014

[morphmet_moderator]

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Wed, 04 Jun 2014 02:50:38 -0700
  From: morphmet_modera...@morphometrics.org
  Reply-To: morphmet_modera...@morphometrics.org
  Subject: Calling papers for June 2014
  To: morphmet@morphometrics.org

- Forwarded message from Asian Online Journals  -

 Date: Wed, 30 Apr 2014 05:23:57 -0400
  From: Asian Online Journals 
  Reply-To: Asian Online Journals 
  Subject: Calling papers for June 2014
  To: morphmet@morphometrics.org

Apologies for possible multiple posting

Call for Papers
 Greetings from Asian Online Journals!
 The Asian Online Journals welcomes research scholars and scientists from 
different domains in its sphere of Open Access publication. Through the 
incorporation of scientific researchers and industrial practitioners; Call for 
papers by Asian Online Journals becomes another achievement of its contribution 
towards the success of scientific research, social infrastructure and 
industrial advancement. 
 The purpose of Call for Papers is to distribute original scientific research, 
facts, and knowledge through broad assortment of journals in the fields of 
Computing, Information Systems, Engineering, Technology, Business, Management, 
Social Sciences, Humanities, Pharmacy, Nursing, Medical Sciences, Applied 
Sciences, Mathematics, Education, Agriculture, Food Sciences, and so on. Asian 
Online Journals always seek to publish an unbiased and balanced mix of high 
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PENCIL Publication of Biological Sciences (Call For Paper)

[morphmet_moderator]

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Wed, 04 Jun 2014 02:52:46 -0700
  From: morphmet_modera...@morphometrics.org
  Reply-To: morphmet_modera...@morphometrics.org
  Subject: PENCIL Publication of Biological Sciences (Call For Paper)
  To: morphmet@morphometrics.org

- Forwarded message from ppbsjour...@gmail.com -

Date: Mon, 5 May 2014 01:54:00 -0400
From: ppbsjour...@gmail.com
Reply-To: ppbsjour...@gmail.com
Subject: PENCIL Publication of Biological Sciences (Call For Paper)
To: pencilpressmanuscri...@gmail.com

Dear Researcher,

PENCIL Publication of Biological Sciences (PPBS) is currently accepting 
manuscripts for publication. PPBS seeks to bridge the gap between the 
Biological Sciences, thus creating a free one-stop shop for papers in related 
disciplines. We publish high-quality manuscripts in all areas of research in 
the Biological Sciences including:

Biotechnology, Biochemistry, Microbiology, Cell Biology, Genetics, Plant 
Biology, Animal Biology, Immunology, Bioinformatics, Biostatistics, Molecular 
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and Behavioral Biology etc. 

Papers published at PENCIL Academic Press are peer reviewed. Manuscripts are 
published within 3 weeks of submission in any of our journals with one (1) 
issue published monthly. 

The following types of papers are considered for publication:
1) Research articles. 2) Reviews and Case reports. 

We also publish articles in five other prestigious journals, namely:

PENCIL Publication of Agricultural Sciences, 
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*Click on the link below To View Published Articles, Read Instructions for 
Authors and Submit an Article:

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Submit your manuscript as an email attachment to
ppbsjour...@gmail.com

Kind regards,
Prof. Yalin
Editor PPBS
http://www.pencilacademicpress.org

- End forwarded message -

- End forwarded message -

trouble with Morphologika

[morphmet_moderator]

- Forwarded message from "Lewis, Dr. Donald"  -

 Date: Thu, 15 May 2014 13:38:53 -0500
  From: "Lewis, Dr. Donald"
  Reply-To: "Lewis, Dr. Donald"
  Subject: trouble with Morphologika
  To: morphmet_modera...@morphometrics.org

All,

After years of using Morphologika, I couldn’t open it today, and got a message 
when I clicked on the shortcut that it was to do with my version of Windows 7.

I’ve always been using Windows 7.

Any ideas? Is there an update to Morphologika?

What is the latest version, and can someone provide a link?

Thanks for the help.

Don Lewis

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- End forwarded message -

unbend function of tpsUtil

[morphmet_moderator]

- Forwarded message from "Litt, Margaret Aline"  -

 Date: Wed, 14 May 2014 09:57:17 -0400
  From: "Litt, Margaret Aline" 
  Reply-To: "Litt, Margaret Aline" 
  Subject: unbend function of tpsUtil
  To: morphmet@morphometrics.org

Hello,

In the view listing panel for the unbend function of tps, what do the b^2 and 
SSResid values indicate about the fit?

Aline
mal...@mun.ca

- End forwarded message -

RE: corresponding landmarks for pollinators and plants

[morphmet_moderator]

- Forwarded message from Javier Santos  -

 Date: Wed, 7 May 2014 05:45:57 -0400
  From: Javier Santos
  Reply-To: Javier Santos
  Subject: RE: corresponding landmarks for pollinators and plants
  To: Morphmet

Hello Jenny,
 
I find very interesting your study. May I make a suggestion on how to proceed 
with your experimental setup. Maybe you could use semilandmarks to make the 
outline shapes of your respective plant and animal structures, and then try to 
perform a two-block PLS to see the covariation between both landmark 
configurations. I do not know the exact hypothesis of your research, but I 
think this would be a good beginning.  When doing the latter it might be 
interesting for you to combine the matching LMs as type1 LMs with your semiLM 
in the outline shapes. I hope this helps.
 
 
Kind regards,
 
Javier Santos Santos
  jssan...@mncn.csic.es

PhD student

Integrative Biogeography and Global Change Group
  - Museo Nacional de Ciencias Naturales (MNCN-CSIC)
  http://www.ibiochange.mncn.csic.es/

Associated Researcher @ Evolutionary Morphology of Vertebrates Lab
  - Universiteit Gent
  http://www.fun-morph.ugent.be/
 

-
From: morphmet_modera...@morphometrics.org
To: morphmet@morphometrics.org
Subject: Re: corresponding landmarks for pollinators and plants
Date: Sun, 13 Apr 2014 19:37:17 -0700

- Forwarded message from Karl Fetter  -

 Date: Tue, 1 Apr 2014 15:48:21 -0400
  From: Karl Fetter
Reply-To: Karl Fetter
  Subject: Re: corresponding landmarks for pollinators and plants
  To: morphmet@morphometrics.org

What are the questions you want to ask? What are the components of shape that 
you think determine the biology of your system? Is the geometric arrangement of 
anthers important? Are the flowers asymmetrical? Where does pollination happen? 
Where are the nectar glands located.

What are the 3 landmarks you've considered?

Karl

On Tue, Apr 1, 2014 at 3:26 PM,   wrote:

- Forwarded message from morphmet_modera...@morphometrics.org -

Date: Tue, 01 Apr 2014 00:52:31 -0700
  From: morphmet_modera...@morphometrics.org
Reply-To: morphmet_modera...@morphometrics.org
  Subject: corresponding landmarks for pollinators and plants
  To: morphmet@morphometrics.org

- Forwarded message from "Hazlehurst, Jenny A"  -

 Date: Tue, 18 Mar 2014 18:18:49 -0400
  From: "Hazlehurst, Jenny A"
Reply-To: "Hazlehurst, Jenny A"
  Subject: corresponding landmarks for pollinators and plants
  To: "morphmet@morphometrics.org"

Hi there, I am trying to devise a plan to conduct an analysis of match between 
hummingbird bill shape and pollinated flower shape using a landmark-based 
analysis. I have been able to identify 3 landmarks that match between flowers 
and birds, but as this is not enough to generate principal warps or a PCA I'm 
not sure how to proceed. I'm new to this and could use some general pointers on 
how to make this unusual comparison. 

Thanks! 

Reply to: jhazl...@tulane.edu

- End forwarded message -

- End forwarded message -

- End forwarded message -

- End forwarded message -

Re: tps util and tpsdig2

[morphmet_moderator]

- Forwarded message from ERIK NAVARRO  -

 Date: Wed, 23 Apr 2014 13:28:27 -0400
  From: ERIK NAVARRO
  Reply-To: ERIK NAVARRO
  Subject: Re: tps util and tpsdig2
  To: morphmet@morphometrics.org

Hi Gabriela, 

I read your question and I have tried to understand your problem. First, I 
mention that I also work with programs TPS via virtual machine "Parallels" with 
"Windows XP" installed and have not had any problems with the management. I 
guess your case is that all your pictures and files are stored in the virtual 
machine. I comment you that you can save all your images in a folder on your 
Mac and work it from there to create your file “.TPS" and collect the 
landmarks. So you would not have the problem of space on your “Windows” hard 
drive. Also, I send you a file with a brief introduction to collecting 
landmarks that can be of help. 

Moreover, I tell you that I'm using the "TPSRelw" to the consensus of my 
geometries. My problem is that I can not open the file “.TPS" and tells me that 
I can not read the coordinates. My question is do you use "TPSRelw" in your 
virtual machine? If so, what version do you have? and Do you have the same 
problem with reading the file “.TPS"? 

Stay aware of your comments and I hope mine can help you with your analysis. 

Greetings. 

Erik J. Navarro S.
Estudiante de maestria en Biología Marina
Laboratorio de Genética
ICMyL Unidad Académica Mazatlán
UNAM
Mazatlán, Sinaloa. Mexico

El 22/04/2014, a las 22:37, morphmet_modera...@morphometrics.org escribió:

- Forwarded message from "Gabriela N."  -

Date: Mon, 7 Apr 2014 23:19:21 -0400
From: "Gabriela N."
Reply-To: "Gabriela N."
Subject: tps util and tpsdig2
To: morphmet@morphometrics.org

I am using the tps util and tpsdig2 on my virtual machine on my Mac, but am 
having trouble with my hard drive space starting to be limited to the point of 
being unable to process any more pix.

I saw that there is a MacMorph software (by Mark Spencer) for digitizing 
landmarks for Macs available on the http://life.bio.sunysb.edu/morph/webpage, 
but no link for downloading this software. It would be great if anyone has used 
a mac version of tps util and tpsdig2 that works for them to process my pix on 
my Mac.

Any help or guidance would be greatly appreciated!

-- 
Gabriela NavasIchthyology Lab
Moss Landing Marine Laboratories
8272 Moss Landing Road
Moss Landing, Ca 95039

- End forwarded message -

- End forwarded message -

Re: tps util and tpsdig2

[morphmet_moderator]

- Forwarded message from Jose Tavera  -

 Date: Wed, 23 Apr 2014 12:44:13 -0400
  From: Jose Tavera
  Reply-To: Jose Tavera
  Subject: Re: tps util and tpsdig2
  To: morphmet@morphometrics.org

Hi Gabriela,

I have used TPSdig2 and TPSUtil the latest version on my mac. I use the virtual 
machine software Parallels v5.0. and Windows XP. So far I have not had any 
problems and I have open files of at least 400 good quality pix. However You 
can always add more usable memory to your virtual machine, I have 1 GB of ram 
and a few GB of hard disk allocated to my windows partition as I only use it 
for TPS software. Is not much but I hope it helps

Jose

On Tue, Apr 22, 2014 at 9:37 PM,   wrote:

- Forwarded message from "Gabriela N."  -

 Date: Mon, 7 Apr 2014 23:19:21 -0400
  From: "Gabriela N."
Reply-To: "Gabriela N."
  Subject: tps util and tpsdig2
  To: morphmet@morphometrics.org

I am using the tps util and tpsdig2 on my virtual machine on my Mac, but am 
having trouble with my hard drive space starting to be limited to the point of 
being unable to process any more pix.

 I saw that there is a MacMorph software (by Mark Spencer) for digitizing 
landmarks for Macs available on the http://life.bio.sunysb.edu/morph/ webpage, 
but no link for downloading this software. It would be great if anyone has used 
a mac version of tps util and tpsdig2 that works for them to process my pix on 
my Mac.

Any help or guidance would be greatly appreciated!

--
Gabriela NavasIchthyology Lab
Moss Landing Marine Laboratories
8272 Moss Landing Road
Moss Landing, Ca 95039

- End forwarded message -

- End forwarded message -

Re: tps util and tpsdig2

[morphmet_moderator]

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Tue, 03 Jun 2014 00:10:34 -0700
  From: morphmet_modera...@morphometrics.org
  Reply-To: morphmet_modera...@morphometrics.org
  Subject: Re: tps util and tpsdig2
  To: morphmet@morphometrics.org

- Forwarded message from Emma Sherratt  -

 Date: Wed, 23 Apr 2014 08:47:02 -0400
  From: Emma Sherratt
Reply-To: Emma Sherratt
  Subject: Re: tps util and tpsdig2
  To: Morphmet

Gabriela,

There are other options for Mac to collect 2D landmark data from image files.
ImageJ http://imagej.nih.gov/ij/ has inbuilt landmark digitising options. And 
you can also write a macro to help automate your specific task.
A more suped up version of ImageJ is FIJI http://fiji.sc/Fiji

Geomorph R package cran.r-project.org/web/packages/geomorph/ has the function 
digitze2d that reads in a jpeg file and prompts the suer to digitize landmarks, 
which are then saved as a NTS file.

Emma

  __
    (\   .-.   .-.   /_")
 \\_//^\\_//^\\_//
      `"`   `"`   `"`
Emma Sherratt, PhD.Postdoctoral Fellow in department of Ecology,
Evolution, and Organismal Biology
Iowa State University
Ames IA 50014
sherr...@iastate.edu
www.emmasherratt.com

On 22 April 2014 23:37,   wrote:

- Forwarded message from "Gabriela N."  -

 Date: Mon, 7 Apr 2014 23:19:21 -0400
  From: "Gabriela N."
Reply-To: "Gabriela N."
  Subject: tps util and tpsdig2
  To: morphmet@morphometrics.org

I am using the tps util and tpsdig2 on my virtual machine on my Mac, but am 
having trouble with my hard drive space starting to be limited to the point of 
being unable to process any more pix.

 I saw that there is a MacMorph software (by Mark Spencer) for digitizing 
landmarks for Macs available on the http://life.bio.sunysb.edu/morph/ webpage, 
but no link for downloading this software. It would be great if anyone has used 
a mac version of tps util and tpsdig2 that works for them to process my pix on 
my Mac.

Any help or guidance would be greatly appreciated!

--
Gabriela NavasIchthyology Lab
Moss Landing Marine Laboratories
8272 Moss Landing Road
Moss Landing, Ca 95039

- End forwarded message -

- End forwarded message -

- End forwarded message -

MorphoJ update

[morphmet_moderator]

- Forwarded message from Chris Klingenberg  -

 Date: Mon, 21 Apr 2014 12:52:55 -0400
  From: Chris Klingenberg 
  Reply-To: Chris Klingenberg 
  Subject: MorphoJ update
  To: morphmet@morphometrics.org

Dear morphometricians

I have just uploaded the new version 1.06b of MorphoJ to the web site. 

As usual, the program can be downloaded from the MorphoJ web page:
http://www.flywings.org.uk/MorphoJ_page.htm

This release contains a bug fix in the test for hypotheses of modularity 
(Modularity: Evaluate Hypothesis). The bug concerned the option to 
compute random partitions of the landmarks into spatially contiguous 
subsets. The algorithm for this particular option in previous versions 
contained a bug that led to erroneous sets of partitions and thus 
distributions of RV coefficients (for very large numbers of random 
partitions, this distribution did not necessarily approximate the 
distribution for the full enumeration of partitions). In the present 
version, this algorithm has been replaced by a simpler one that does not 
contain this error. However, the simpler algorithm will check for many 
more partitions of landmarks whether they are spatially contiguous or 
not. If there are many subsets of landmarks or if the adjacency graph is 
weakly connected (relatively few edges by comparison with the number of 
landmarks), the algorithm can take a lot of computation time. In this 
situation, consider to use a smaller number of random partitions first 
to see how long it takes. Adding further links to the adjacency graph 
will help to speed up computaions. 
For the same procedure, a minor addition is a new item in the pop-up 
menu for the diagrams with the distribution of RV coefficients. This new 
command allows the user to change the size of the arrow that indicates 
the RV coefficient for the hypothesis of modularity. 

A minor bug was fixed in the program that imports phylogenies from Nexus 
files (Import Phylogeny File). In the new version, all underscores in 
taxon and node names are converted to spaces already in the initial 
import of the Nexus file. This corresponds to the rule for Nexus files, 
and the change therefore ensures that MorphoJ handles taxon names in the 
way other programs do (or at least should). 
Some further bugs related to phylogenies were also fixed, affecting the 
permutation test and graphical output when the symmetric component of 
centroid size (left-right averages for structures with matching 
symmetry) is mapped onto a phylogeny. 

Best wishes,
Chris

-- 

***
Christian Peter Klingenberg
Faculty of Life Sciences
University of Manchester
Michael Smith Building
Oxford Road
Manchester M13 9PT
United Kingdom

Web site: http://www.flywings.org.uk
E-mail: c...@manchester.ac.uk
Phone: +44 161 2753899
Skype: chris_klingenberg
***

- End forwarded message -

Re: tps util and tpsdig2

[morphmet_moderator]

- Forwarded message from Fatih Mangıt  -

 Date: Wed, 23 Apr 2014 05:33:01 -0400
  From: Fatih Mangıt
  Reply-To: Fatih Mangıt
  Subject: Re: tps util and tpsdig2
  To: morphmet@morphometrics.org

TPS series seems to works fine with WineBottler. 
On 23 Nis 2014, at 07:37, morphmet_modera...@morphometrics.org wrote:

- Forwarded message from "Gabriela N."  -

Date: Mon, 7 Apr 2014 23:19:21 -0400
From: "Gabriela N."
Reply-To: "Gabriela N."
Subject: tps util and tpsdig2
To: morphmet@morphometrics.org

I am using the tps util and tpsdig2 on my virtual machine on my Mac, but am 
having trouble with my hard drive space starting to be limited to the point of 
being unable to process any more pix.

I saw that there is a MacMorph software (by Mark Spencer) for digitizing 
landmarks for Macs available on the http://life.bio.sunysb.edu/morph/webpage, 
but no link for downloading this software. It would be great if anyone has used 
a mac version of tps util and tpsdig2 that works for them to process my pix on 
my Mac.

Any help or guidance would be greatly appreciated!

-- 
Gabriela NavasIchthyology Lab
Moss Landing Marine Laboratories
8272 Moss Landing Road
Moss Landing, Ca 95039

- End forwarded message -

- End forwarded message -

Invitation to submit/ recommend manuscripts

[morphmet_moderator]

- Forwarded message from "J. Zoo Biol."  -

 Date: Sat, 19 Apr 2014 02:12:38 -0400
  From: "J. Zoo Biol."
  Reply-To: "J. Zoo Biol."
  Subject: Invitation to submit/ recommend manuscripts
  To: morphmet

New Page 2

JOURNAL OF

ZOO BIOLOGY

CALL FOR PAPERS
Online Submission
Submit your article

  You are cordially invited to submit or recommend papers to Journal of Zoo 
Biology, a fast track peer-reviewed and open access academic journal published 
by ESci Journals Publishing, which is one of the largest open access journal 
publishers around the world. To date ESci Journals have been indexed by many 
important databases.

  Journal of Zoo Biology is using online article submission, review and 
tracking system for quality and quick review processing. Journal provides rapid 
publication of research article. After 30 days Rapid Review Process by the 
editorial board members or outside experts, an accepted paper will be placed 
under In Press within 24 hours and will be published in the next issue. Click 
below tab to submit your manuscript.

ONLINE SUBMISSION
  or send your manuscript to zoob...@escijournals.net

  ESci Journals are open access - international journals. Researchers worldwide 
will have full access to all the articles published online and be able to 
download them with zero subscription fee. Moreover, the influence of your 
research will rapidly expand once you become an OA author, because an OA 
article has more chances to be used and cited than does one that plods through 
the subscription barriers of traditional publishing model.

  Journal of Zoo Biology is an open access peer-reviewed international journal 
publishes original as well as extended version of the published research. Aim 
of the journal is to undertake and promote relevant high quality zoological 
research, encouraging and rewarding excellence in the performance. It also 
promotes co-ordination, collaboration and co-operation between different fields 
of zoology. Journal covers a wide range of natural science topics. Besides 
taxonomy and systematics of various animal groups, papers dealing with 
embryology, histology, physiology, behavioral ecology, medical and agricultural 
entomology, fisheries, terrestrial and marine ecology, evolution, geography, 
paleontology, general zoology are accepted for publication.

  For more detailed information, please visit: www.escijournals.net/JZB Papers 
are expected to be submitted at "Article Submission" section in the above 
website. Feel free to contact us if you have any questions about the journal. 
You are more than welcome to keep us updated on the latest focuses of your 
academic interest and inquiries.

 JOIN EDITORIAL/REVIEW BOARD

  ESci Journals Publishing is seeking to recruit engaged and enthusiastic 
subject editors and reviewers for Journal of Zoo Biology to manage editorial 
processes and to guide its development as an academic journals. ESci Journals 
Publishing invites qualified individual or team applications from various 
specializations of Zoology and applied aspects for editorial review board of 
the journal. It is an excellent opportunity for an ambitious and focused 
individual with solid editorial experience to edit an exciting journal in ESci 
Journals Publishing portfolio.

  If you are interested in serving as a member of the editorial review board, 
kindly send us your resume to  zoob...@escijournals.net
   
   Click here if you don't want to receive further messages from ESci Journals 
Publishing.
  

- End forwarded message -

Image database of plant leaves

[morphmet_moderator]

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Mon, 02 Jun 2014 01:43:10 -0700
  From: morphmet_modera...@morphometrics.org
  Reply-To: morphmet_modera...@morphometrics.org
  Subject: Image database of plant leaves
  To: morphmet@morphometrics.org

- Forwarded message from Ely Raz  -

 Date: Wed, 16 Apr 2014 17:14:43 -0400
  From: Ely Raz 
  Reply-To: Ely Raz 
Subject: Image database of plant leaves
  To: morphmet@morphometrics.org

Hi,

I am looking for an image database of plant leaves. If you know some please 
send me an email. 

Thanks. 

- End forwarded message -

- End forwarded message -

Software: geomorph 2.0 for R

[morphmet_moderator]

- Forwarded message from "Adams, Dean [EEOBS]"  -

 Date: Wed, 16 Apr 2014 14:57:11 -0400
  From: "Adams, Dean [EEOBS]"
  Reply-To: "Adams, Dean [EEOBS]"
  Subject: Software: geomorph 2.0 for R
  To: "morphmet@morphometrics.org"

 Folks,

The newest version of geomorph is now available. Version 2.0 has many internal 
enhancements, as well as several new functions and options.  The latest version 
may be found at:  http://cran.r-project.org/web/packages/geomorph/index.html

A full list of changes is available on our blog (http://www.geomorph.net/ ), 
but the major highlights include:

1: Methods for combining morphometrics and phylogenetic comparative biology: 
This includes new methods for evaluating phylogenetic signal (multivariate 
Kappa), phylogenetic PLS, comparing multivariate rates of evolution, and 
visualizing phylomorphospace

2: Estimating missing landmarks using either the thin-plate spline or 
multivariate multiple regression

3: Enhanced 3D visualizations, including warping of surface meshes to visualize 
shape changes.

Thanks,

Dean and the geomorph team

--

Dr. Dean C. Adams

Professor

Department of Ecology, Evolution, and Organismal Biology

   Department of Statistics

Iowa State University

Ames, Iowa, 50011

www.public.iastate.edu/~dcadams/

phone: 515-294-3834

From: emma.sherr...@gmail.com [mailto:emma.sherr...@gmail.com] On Behalf Of 
Emma Sherratt
Sent: Wednesday, April 16, 2014 12:50 PM
To: Adams, Dean [EEOBS]
Cc: Otarola-Castillo, Erik  (eotarolacasti...@fas.harvard.edu)
Subject: Re: geomorph 2.0

The mac binary is up now, as are the blog posts and I update the Project 
description on the blog to match all the new functions.

Emma

  __

    (\   .-.   .-.   /_")

 \\_//^\\_//^\\_//

      `"`   `"`   `"`

Emma Sherratt, PhD.

Postdoctoral Fellow in department of Ecology,

Evolution, and Organismal Biology

Iowa State University

Ames IA 50014

sherr...@iastate.edu
www.emmasherratt.com

On 16 April 2014 10:52, Emma Sherratt  wrote:

Erik,

Also, as per Dean's request, I have given the blog a makeover to mark the new 
version. I have two posts waiting for when the Mac binary is completed - one 
highlighting the new version and one giving more details on the new 3D viz. 

Emma

  __

    (\   .-.   .-.   /_")

 \\_//^\\_//^\\_//

      `"`   `"`   `"`

Emma Sherratt, PhD.

Postdoctoral Fellow in department of Ecology,

Evolution, and Organismal Biology

Iowa State University

Ames IA 50014

sherr...@iastate.edu
www.emmasherratt.com

On 16 April 2014 10:49, Adams, Dean [EEOBS]  wrote:

Erik,

Geomorph 2.0 tarball and Windows build are up on CRAN.  I suggest you give it a 
careful look. Emma and I undertook a major overhaul, resulting in quite a few 
new functions, options, etc. and a serious cleaning/streamlining of the code 
and help files.

 

Dean

--

Dr. Dean C. Adams

Professor

Department of Ecology, Evolution, and Organismal Biology

   Department of Statistics

Iowa State University

Ames, Iowa, 50011

www.public.iastate.edu/~dcadams/

phone: 515-294-3834

 

- End forwarded message -

RE: New Website - For users beginning with morphometricanalysisusingMorphoJ

[morphmet_moderator]

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Sun, 01 Jun 2014 00:40:51 -0700
  From: morphmet_modera...@morphometrics.org
  Reply-To: morphmet_modera...@morphometrics.org
  Subject: RE: New Website - For users beginning with 
morphometricanalysisusingMorphoJ
  To: morphmet@morphometrics.org

- Forwarded message from "Lewis, Dr. Donald"  -

Date: Mon, 14 Apr 2014 14:58:45 -0400
From: "Lewis, Dr. Donald" 
Reply-To: "Lewis, Dr. Donald" 
Subject: RE: New Website - For users beginning with morphometric 
analysisusingMorphoJ
To: morphmet@morphometrics.org

Emma,
Please re-send the hyperlink. 
Don Lewis

-Original Message-
From: morphmet_modera...@morphometrics.org 
[mailto:morphmet_modera...@morphometrics.org] 
Sent: Tuesday, April 08, 2014 10:06 PM
To: morphmet@morphometrics.org
Subject: New Website - For users beginning with morphometric 
analysisusingMorphoJ

- Forwarded message from Emma Chance  
-

Date: Sun, 30 Mar 2014 07:47:03 -0400
From: Emma Chance 
Reply-To: Emma Chance 
Subject: New Website - For users beginning with morphometric analysis 
usingMorphoJ
To: "morphmet@morphometrics.org" 

Dear all, 
My name is Emma Chance and I am a final year student at the University of 
Manchester working on my dissertation project. I have created a website to help 
people beginning or switching to using MorphoJ, for analysing geometric 
morphometric data, get started with fewer difficulties and have a greater 
understanding into the rationale and purpose behind a few of the key 
statistical analyses. 
I would really appreciate it if you could take a look at my website, and spend 
no longer than 5 minutes of your time to answer a quick survey about how useful 
you have found my resource and any improvements that I could make. 

Thank you very much for your time. 
Kind regards, 
Emma Chance

- End forwarded message -

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- End forwarded message -

Problems with TpsRegr df<1

[morphmet_moderator]

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Sun, 01 Jun 2014 00:42:53 -0700
  From: morphmet_modera...@morphometrics.org
  Reply-To: morphmet_modera...@morphometrics.org
  Subject: Problems with TpsRegr df

Re: tps util and tpsdig2

[morphmet_moderator]

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Sun, 01 Jun 2014 00:41:50 -0700
  From: morphmet_modera...@morphometrics.org
  Reply-To: morphmet_modera...@morphometrics.org
  Subject: Re: tps util and tpsdig2
  To: morphmet@morphometrics.org

- Forwarded message from "Gabriela N."  -

 Date: Wed, 16 Apr 2014 01:20:47 -0400
  From: "Gabriela N."
Reply-To: "Gabriela N."
  Subject: Re: tps util and tpsdig2
  To: morphmet@morphometrics.org

Please reply to: gna...@mlml.calstate.edu

I am using the tps util and tpsdig2 on my virtual machine on my Mac, but am 
having trouble with my hard drive space starting to be limited to the point of 
being unable to process any more pix.

I saw that there is a MacMorph software (by Mark Spencer) for digitizing 
landmarks for Macs available on the http://life.bio.sunysb.edu/morph/ webpage, 
but no link for downloading this software. It would be great if anyone has used 
a mac version of tps util and tpsdig2 that works for them to process my pix on 
my Mac.

Any help or guidance would be greatly appreciated!

- End forwarded message -

- End forwarded message -

Phd positions available: Iowa State University

[morphmet_moderator]

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Tue, 22 Apr 2014 21:40:28 -0700
  From: morphmet_modera...@morphometrics.org
  Reply-To: morphmet_modera...@morphometrics.org
  Subject: Phd positions available: Iowa State University
  To: morphmet@morphometrics.org

- Forwarded message from "Adams, Dean [EEOBS]"  -

 Date: Tue, 8 Apr 2014 16:08:57 -0400
  From: "Adams, Dean [EEOBS]"
Reply-To: "Adams, Dean [EEOBS]"
  Subject: Phd positions available: Iowa State University
  To: "morphmet@morphometrics.org"

 Hello all,

 PhD positions are now available in my lab.  Current research foci include the 
interface between morphometrics and phylogenetic comparative biology, 
morphological evolution in animals with an emphasis on vertebrates, and 
investigations of the tempo and mode of evolutionary change.

 Prospective graduate students interested in geometric morphometrics, 
macroevolution, microevolution, and evolutionary theory are encouraged to 
apply. Successful applicants may develop an independent research project within 
these areas, or one that complements or extends other research in the lab. For 
more information about the research in our lab please visit our website:

 http://www.public.iastate.edu/~dcadams/

 Interested candidates should contact Dr. Dean Adams at dcad...@iastate.edu.

 Dean

 --

 Dr. Dean C. Adams

 Professor

 Department of Ecology, Evolution, and Organismal Biology

    Department of Statistics

 Iowa State University

 Ames, Iowa, 50011

 www.public.iastate.edu/~dcadams/

 phone: 515-294-3834

- End forwarded message -

- End forwarded message -

Re: Large Felid Skull Scan?

[morphmet_moderator]

- Forwarded message from morphmet_modera...@morphometrics.org -

 Date: Thu, 01 May 2014 09:01:17 -0700
  From: morphmet_modera...@morphometrics.org
  Reply-To: morphmet_modera...@morphometrics.org
  Subject: Re: Large Felid Skull Scan?
  To: morphmet@morphometrics.org

- Forwarded message from m...@uw.edu -

Date: Tue, 8 Apr 2014 23:48:50 -0400
  From: m...@uw.edu
Reply-To: m...@uw.edu
  Subject: Re: Large Felid Skull Scan?
  To: "morphmet@morphometrics.org"

Digimorph?
http://digimorph.org/specimens/Panthera_pardus/

From: morphmet_modera...@morphometrics.org
Sent: ‎Tuesday‎, ‎April‎ ‎8‎, ‎2014 ‎8‎:‎06‎ ‎PM
To: morphmet@morphometrics.org

- Forwarded message from Abby Drake  -

 Date: Sun, 30 Mar 2014 10:36:22 -0400
  From: Abby Drake
  Reply-To: Abby Drake
  Subject: Large Felid Skull Scan?
  To: morphmet@morphometrics.org

Hello All!

I am looking for a digital scan of a large felid skull (Lion, Tiger, Leopard, 
Jaguar...). It doesn't have to be CT, a surface scan would be fine. My only 
requirement is that the scan is of the cranium only without the lower jaw 
attached. Any help would be greatly appreciated!

Best Wishes,
Abby

--
Abby Grace Drake, PhD

Biology Department
Skidmore College

Phone: 508.981.2783
Skype: abby.drake
Website: http://www.skidmore.edu/academics/biology/adrake.htm

- End forwarded message -

- End forwarded message -

- End forwarded message -

RE: Primate MRI/high quality CT

[morphmet_moderator]

- Forwarded message from Elen Feuerriegel  -

 Date: Mon, 14 Apr 2014 03:50:55 -0400
  From: Elen Feuerriegel
  Reply-To: Elen Feuerriegel
  Subject: RE: Primate MRI/high quality CT
  To: "morphmet@morphometrics.org"

 Hello Murat, 

 Yes, I have tried KUPRI and they do have scans of interest to me but they are 
not good enough quality for the type of work I'd like to do. Thank you for the 
suggestion, though.

 Elen

 Elen Feuerriegel | PhD Candidate | School of Archaeology and Anthropology | 
College of Arts and Social Sciences | A. D. Hope Building | Australian National 
University | Canberra, A.C.T. Australia 0200 |

-
From: morphmet_modera...@morphometrics.org
Sent: 14 April 2014 09:06
To: morphmet@morphometrics.org
Subject: RE: Primate MRI/high quality CT  

- Forwarded message from Murat Maga  -

Date: Tue, 1 Apr 2014 15:36:56 -0400
From: Murat Maga
Reply-To: Murat Maga
Subject: RE: Primate MRI/high quality CT
To: morphmet@morphometrics.org

  Have you tried Kyoto collection?

 http://dmm.pri.kyoto-u.ac.jp/dmm/WebGallery/index.html

   From: morphmet_modera...@morphometrics.org 
[mailto:morphmet_modera...@morphometrics.org]
Sent: Tuesday, April 01, 2014 12:29 PM
To: morphmet@morphometrics.org
Subject: Primate MRI/high quality CT

- Forwarded message from Elen Feuerriegel  -

Date: Tue, 18 Mar 2014 18:30:28 -0400
From: Elen Feuerriegel
Reply-To: Elen Feuerriegel
Subject: Primate MRI/high quality CT
To: "morphmet@morphometrics.org"

   Hello all,

 Would anyone be able to direct me to a good source for high quality CT or MRI 
of extant hominoids? Or someone willing to share data? If possible, free of 
charge or low cost for access would be best.

 I'm particularly interested in performing "digital dissections" of the upper 
limb using imaging software such as Mimics in lieu of actually being able to 
access wet specimens. I've already downloaded a bunch of CT from KUPRI and 
NESPOS but I'm finding that the scans aren't giving me the level of detail that 
I need. Any help anyone could give me would be greatly appreciated.

 Many thanks,

 Elen Feuerriegel

 u5137...@uds.anu.edu.au

  Elen Feuerriegel | PhD Candidate | School of Archaeology and Anthropology | 
College of Arts and Social Sciences | A. D. Hope Building | Australian National 
University | Canberra, A.C.T. Australia 0200 |

- End forwarded message -

- End forwarded message -

- End forwarded message -

Large Felid Skull Scan?

[morphmet_moderator]

- Forwarded message from Brian Corner  -

 Date: Sun, 13 Apr 2014 09:23:37 -0400
  From: Brian Corner 
  Reply-To: Brian Corner 
  Subject: Large Felid Skull Scan?
  To: morphmet_modera...@morphometrics.org

Try U Texas Digital morph repository (http://www.digimorph.org/ ) or US 
national Museum of Natural History (http://3d.si.edu/)

Brian D Corner PhD. 

- End forwarded message -