general morphometric protocol
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General morphometric protocol. Four simple steps to morphometric success. Four steps. Data acquisition – images and landmarks Remove shape variation and generate shape variables – superimposition and TPS - PowerPoint PPT PresentationTRANSCRIPT
General morphometric protocol
Four simple steps to morphometric success
Four steps
• Data acquisition – images and landmarks• Remove shape variation and generate shape
variables – superimposition and TPS• Perform statistical analyses to test biological
hypotheses – standard multivariate analysis and resampling methods
• Produce graphical depiction of results – deformation grids, statistical plots, etc.
Data acquisition - images
• Transferring 3D to 2D depiction• Many ways to go wrong• Three things that don’t matter
– Location in plane– Scale– Rotation
Problems to avoid
• Paralax – pitch and roll• “bendiness” – look for straight lines and
include points on these lines• Articulated structures – can incorporate in
analysis or remove as noise, but easiest to avoid problem in beginning
Avoiding image problems
• Standardize image acquisition procedure• Independent quality check
Digitizing landmarks
• Homology• Type 1, 2, and 3 - sliding semilandmarks• Order is critical• Checking for errors and outliers• Symmetrical structures
Step two – remove nonshape variation and generate shape
variables
• 3 types of nonshape variation – relative position, scale, rotation
• Remove by a process called superimposition via generalized Procrustes analysis or GPA
Variation in images
Translation
Rotation
Scaling
Only shape variation left
Generate shape variables
Thin plate spline
Generates non-affine and affine components referred to as partial warps and uniform components
Affine and non-affine shape change
Shape coordinates
• Partial warps come in X and Y pairs, (2p-4)• Uniform components also a pair, X and Y• Combined referred to as the W (weight)
matrix• Scores are coordinates of a point along
partial warp axes• Nonsingular data matrix for multivariate
analysis of shape
Relative warps
• Can use PCA on W matrix to generate relative warp scores and use these as data matrix
• Useful for visualization of major axis of shape variation