[MORPHMET] A Step-by-Step Guide For Geometric Morphometrics Of Floral Symmetry

2018-10-10 Thread 'Yoland SAVRIAMA' via MORPHMET 


Dear colleagues,


I would like to attract your attention on this newly published paper.


SAVRIAMA, Y. (2018). A Step-by-Step Guide For Geometric Morphometrics Of 
Floral Symmetry. *Frontiers in Plant Science*, *9*, 1433.

https://doi.org/10.3389/fpls.2018.01433


A detailed guide for shape analysis of flowers with any type of symmetry 
using tpsdig2 (or equivalent) for data acquisition, R for data formatting 
and MorphoJ for visualisations. 

This is a practical translation of the theoretical and mathematical 
framework contained in Savriama & Klingenberg (2011).


Savriama, Y., & Klingenberg, C. P. (2011). Beyond bilateral symmetry: 
geometric morphometric methods for any type of symmetry. *BMC evolutionary 
biology*, *11*(1), 280.


Best wishes!

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[MORPHMET] Problem to export data from Landmak editor to MorphoJ

2018-10-10 Thread Maria Gracia Salamanca Garcia 
Dear morphometricians, 


I am doing geometric morphometric analysis to 3D scans (more than 100 scans), 
and I am using Landmark Editor. I have already placed all the landmarks in the 
same order and did all the correspondences. 

However, I am unable to export the data to MorphoJ. The software shows me a 
window that says 'The selected measures have inconsistent correspondences to 
the atlas', and then collapses.

I redid all the correspondences, tried different arrangements, but it keeps 
failing.

I am trying to export from ply to NTsys file.

Does someone knows how to fix this error or which is my mistake?

Thank you very much!

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[MORPHMET] New Book Announcement: A Course in Morphometrics for Biologists (Cambridge, University Press, 2018)

2018-10-10 Thread morphmet 

Posted on behalf of Dr. Bookstein...

Dear Morphmetters,

   I'm delighted to announce the publication of my latest
 book, A Course in Morphometrics for Biologists (Cambridge
 University Press, 2018).  There are very nice comments
 on the back cover from several of our colleagues, including
 Morphmet's own Dennis Slice.  Here's the blurb, from
 the first inside page:

 "This book builds a much-needed bridge between biostatistics
  and organismal biology by linking the arithmetic of statistical
  studies of organismal form to the biological inferences
  that may follow from it. It incorporates a cascade of
  new explanations of regression, correlation, covariance
  analysis, and principal components analysis, before
  applying these techniques to an increasingly common
  data resource: the description of organismal forms
  by sets of landmark point configurations. For each data set,
  multiple analyses are interpreted and compared for
  insight into the relation between the arithmetic of
  the measurements and the rhetoric of the subsequent
  biological explanations. The text includes examples
  that range broadly over growth, evolution, and disease.
  For graduate students and researchers alike, this book
  offers a unique consideration of the scientific context
  surrounding the analysis of form in today's biosciences."

  For those of you who have been intrigued by any of my recent
 papers -- on integration and the BE-PwV plot, on the serious
 problems with Procrustes analysis, on the many pathologies of
 principal components in GMM, or on the possible resolution of
 these problems via a new version of factor analysis --
 all of these topics are touched on here, and many, many others as well.

  Fred Bookstein

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[MORPHMET] Transmitting Science 3D Geometric Morphometrics course in Crete

2018-10-10 Thread soledad . esteban 

Dear colleagues,

 

The 8th edition of Transmitting science course "3D Geometric Morphometrics" has 
a few slots available.

 

Dates and Place: January 28th – February 1st, 2019, Crete (Greece)

 

Instructor: Dr Melissa Tallman (Grand Valley State University, USA).

Registration and more info: 
https://www.transmittingscience.org/courses/geometric-morphometrics/3d-geometric-morphometrics/




 

PROGRAM:

 

Types of data acquisition: Using a microscribe. Collecting CT scans & Surface 
Scans. - Demonstration of Stratovan Checkpoint.

 

Brief Review of Fundamentals of Morphometrics: - How to choose landmarks. - 
Generalized Procrustes Analysis. - Other types of alignment. - Thin plate 
spline warping. Processing Microscribe data. - Using DVLR to merge two views. - 
Using resample to resample a line. Using Landmark Editor to collect data on 
surfaces. - Sliding semi-landmarks (using R geomorph package).

 

- How to do a precision test on 3D data.

 

- Data exploration: PCA analyses: Using Morphologika. Using MorphoJ. 
Between-group PCAs. PCAs in Procrustes form space.

 

- Visualizing shape change: Using MorphoJ in conjunction with Landmark Editor. 
Making calculations and visualizing shape changes in PCA morphospace. 
Calculating PCA scores post hoc.

 

- Data exploration: Regressions. Visualizing change that is associated with 
size (MorphoJ). Removing change associated from size from your data (MorphoJ). 
Common allometric trajectories. Comparing vector directions. Extracting linear 
dimensions from 3D data and using them as covariates.

 

- Data exploration: PLS analyses. Using MorphoJ to mean center (or not). 
Visualizing shape change in Landmark editor.

 

- Data exploration: Phylogeny. Visualizing shape changes in MorphoJ along a 
tree. Importing covariates and visualizing shape change associated with 
taxonomy (using MorphoJ). Creating a phyomorphospace. Correcting for phylogeny 
in PCA.

 

- Data interpretations: Using mean configurations (PAST) and Procrustes 
distances. Minimum spanning trees. Variability within a sample (comparing 
fossil distributions to extant distributions).

 

- Retrodeformation.

 

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

  

Best wishes




Sole

Soledad De Esteban-Trivigno
Institut Català de Paleontologia Miquel Crusafont (ICP)

Campus de la Universitat Autònoma de Barcelona

Cerdanyola del Vallès (Barcelona). Spain

www.icp.cat
  
 

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RE: [MORPHMET] Problem to export data from Landmak editor to MorphoJ

2018-10-10 Thread Murat Maga 
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