Re: [MORPHMET] "high-throughput" 2D scanning using photo-scanner

[Carmelo Fruciano]

Dear Henry,
in addition to what Andrea suggested, I should mention that flatbed  
scanners have been already used also on fish and there are papers  
published on this.

An example is:
Herler, J., et al. (2007). "A simple technique for digital imaging of  
live and preserved small fish specimens." Cybium 31(1): 39-44.

Best,
Carmelo

henry wallace  ha scritto:


I am contemplating a project involving small insects.  Data would be pixel
areas or distances of head, thorax, abdomen.  2D measurements.  Large
numbers of specimens required.

With appendages removed, the insects would be mounted on a flat surface,
such as poster board or paper, which is then scanned using a desktop
scanner (photo-scanner).  Dozens could be scanned at single time and the
resulting images can be cropped for data gathering.

Was just wanting initial reactions and/or recommendations on the approach.

H.

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

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[MORPHMET] Alternatives to PLS or CCA

[Luis Mendoza]

Maybe a very basic question but I hope someone can help.

Discussion and use of different Canonical ordinarios methods (redundancy 
analysis RDA, canonical correspondence analysis CCA, linear discrimination 
análisis LDA, canonical correlation analysis CCorA, partial least squares 
PLS), to explicitly explore patterns of covariation or relationships 
 between 2 or more data sets, are common in the ecological literature.

However, in the case of geometric morphometrics, the methods most used or 
suggested 
 to explore relationships between a set of morphological variables and a 
set of other variables (environmental, ecogeographic, trophic), basically 
focus on symmetrical Canonical ordinarios methods as "Canonical correlation 
analysis" and mainly PLS analysis (after Rohlf & Corti, 2000).

Perhaps the explanation is very simple and is related to the properties of 
geometric morphometrics data. But I have severe doubts on the applicability 
(or not) the  asymmetric methods  (e.g. Redundancy analysis), which are 
very common and powerful in ecology, especially in cases in which 
environmental variables are assumed as explanatory variables and those who 
do not comply with the assumption of a linear relationship between 
environmental variables and morphological variables assumed in the PLS.

Thanks.

LUIS.

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[MORPHMET] New 3D geometric morphometrics paper

[Abby Drake]

3D morphometric analysis of fossil canid skulls contradicts the suggested
domestication of dogs during the late Paleolithic

Abby Grace Drake, Michael Coquerelle & Guillaume Colombeau

www.nature.com/srep/2015/150205/srep08299/full/srep08299.html

-- 
Abby Grace Drake, PhD

Biology Department
Skidmore College

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

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Re: [MORPHMET] 3D images - manipulation and registration?

[Stefan Schlager]

Hi Hildur,

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

Best
Stefan

On 04/02/15 14:22, Hildur Magnúsdóttir wrote:
> Hi everyone,
>
> I'm using geometric morphometrics to study variation in the shell
> morphology of the common whelk. I'm really interested in using 3D
> images as a basis for this study but I'm having problems with
> manipulation and registration (e.g. rigid registration) of my images
> prior to digitizing of landmarks.
>
> I'm using a MakerBot® Digitizer™ Desktop 3D Scanner for capturing the
> 3D images and it generates either .stl or .ply files that I read into
> the R for digitizing. My problem is that when I read those files into
> the R they are not all oriented in the same way inside the box in the
> rgl window, thus it is very hard to align them reliably so that the
> landmarks are truly comparable between individuals.
>
> So my question to you all is if you know of a method to align or
> register the 3D images before I read them into R? Or of a package in R
> that can perform this action?
>
> I would be very grateful for any advice on this,
>
> Hildur
>
>
> Hildur Magnúsdóttir
> PhD Student
> University of Iceland, Department of Life and Environmental Sciences
> and Hólar University College, Department of Aquaculture and Fish Biology
> Telephone: +354 823 2485
> -- 
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
> To unsubscribe from this group and stop receiving emails from it, send
> an email to morphmet+unsubscr...@morphometrics.org
> .

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Re: [MORPHMET] "high-throughput" 2D scanning using photo-scanner

[alcardini]

Hi Henry,
do you mean using a flat-bed scanner to take pics of 3D structures?
I've done that on marmot hemimandibles (papers with Nagorsen in my
webpage). You'll find the test of its accuracy here:
http://www.italian-journal-of-mammalogy.it/article/view/10993
It's one of the datasets in the study. Compared to 3D data, results
were pretty good and similar (only slightly worse) to those obtained
by taking pictures. However, this will be specific to the data and the
study hypothesis.

The 3D and 2D landmarks on photos of hemimandibles are provided as
suppl. info. Those of the scanned images are not but, as I said,
they're very similar to the photos. Anyway, I am happy to share those
too. Just need a spare moment to look for the data.


I was about to do this again myself on carabids but gave up as the
curator who gave me the specimens was not too happy about it.
For a macroevolutionary comparison, where differences are large, I
suspect the error may be relatively small. With very small specimens
there may be problems with resolution and with big ones there could be
issues with depth and, at least in carabids, with big ones their
curvature (e.g., pronotum and head relative to the abdomen) does not
make them ideal.
Curiously, my experience is that, at least with cheap scanners, the
old ones are better. They have more depth of field.

I am pretty sure that other people have done similar 'experiments'.
Good luck with your project.
Cheers

Andrea


On 03/02/2015, henry wallace  wrote:
> I am contemplating a project involving small insects.  Data would be pixel
> areas or distances of head, thorax, abdomen.  2D measurements.  Large
> numbers of specimens required.
>
> With appendages removed, the insects would be mounted on a flat surface,
> such as poster board or paper, which is then scanned using a desktop
> scanner (photo-scanner).  Dozens could be scanned at single time and the
> resulting images can be cropped for data gathering.
>
> Was just wanting initial reactions and/or recommendations on the approach.
>
> H.
>
> --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
>
> To unsubscribe from this group and stop receiving emails from it, send an
> email to morphmet+unsubscr...@morphometrics.org.
>


-- 
NO DOCX, XLSX AND PPTX, PLEASE!!!

COAUTHORS AND CONTRIBUTORS, PLEASE, FOR SHARING FILES, CONVERT THEM IN DOC,
XLS (UNLESS LONGER THAN 256 COLUMNS) AND PPT


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,
andrea.card...@uwa.edu.au

Webpage: http://sites.google.com/site/hymsfme/drandreacardini
and:
http://www.dscg.unimore.it/site/home/ricerca/aree-di-ricerca/evolution-taxonomy-and-forensics.html

Datasets:
http://ads.ahds.ac.uk/catalogue/archive/cerco_lt_2007/overview.cfm#metadata
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/

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[MORPHMET] "high-throughput" 2D scanning using photo-scanner

[henry wallace]

I am contemplating a project involving small insects.  Data would be pixel
areas or distances of head, thorax, abdomen.  2D measurements.  Large
numbers of specimens required.

With appendages removed, the insects would be mounted on a flat surface,
such as poster board or paper, which is then scanned using a desktop
scanner (photo-scanner).  Dozens could be scanned at single time and the
resulting images can be cropped for data gathering.

Was just wanting initial reactions and/or recommendations on the approach.

H.

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

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to morphmet+unsubscr...@morphometrics.org.

[MORPHMET] Postdoc position (MOCAP, 2 years France)

[Fab Indi]

Dear colleagues,
A post-doc position on Motion capture and analysis of the face is open for 2 
years at the University of Compiègne, Research Unit Biomechanics and 
Bioengineering (see doc attached). This project is part of the Sorbonne 
University Chair (Facile) for cranio-facial reconstruction for forensic.
Contact us for further informations,
Best wishes,

Fabrice Demeter
(fabrice.deme...@upmc.fr)
-

Qualifications required:
- Background in biomechanics
- Ability to collect and analyze experimental data
- Experience with motion capture and analysis (Vicon system/ Nexus 2)
- Experience with software for Medical image segmentation (Scan IP/ Simpleware)
- Excellent oral / written communication in English (French would be an 
advantage)
All information concerning the University of Technology of Compiègne and the 
Compiègne area can be found respectively under www.utc.fr and www.compiegne.fr
Please send your applications including your CV (including a publications list 
and a summary of the previous research experience, a cover letter, and a 
recommendation letter per email as soon as possible) to : Professor Frédéric 
Marin (frederic.ma...@utc.fr).

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[MORPHMET] 3D images - manipulation and registration?

[Hildur Magnúsdóttir]

Hi everyone,

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

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

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

I would be very grateful for any advice on this,

Hildur


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

-- 
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