I am confused about setting a scale when you place landmarks on objects because I read that when you do landmark placement on tps you can set the scale. I thought setting scale was unnecessary since the landmark points will be aligned using Procrustes alignment which removes the element of size, hence, the actual shape, the geometric property of the structure, is captured and included in the analysis.
Sir Jasper,
You still need to set a scale for capturing images of your specimen. This is to ensure that all images are of the same size in order for the analysis to really remove the element of size in the process.
GM analysis like any traditional morphometric technique still computes the size. However, what makes GM analysis very unique is that you can compute the allometry immediately. Allometry allows the researchers to determine how size can contribute to SHAPE analysis. You may have the option to whether proceed in the analysis analysis with that kind of allometry, but of course this could be deal-breaker in some journals (reviewers) that have a certain threshold for allometry.
The GM process conducts SHAPE analysis but we need to take extra precautions in capturing images in order to remove the effect of size during the analysis.
I hope this was clear. Let me know if you have any more questions. LOL
The reason for setting the scale is to obtain information about size as well as shape. If you do not set the scale factor, centroid size will be in units of pixels
There might be additional reasons: although the aim ofshape analysis is indeed to remove size as a nuisance factor, you might need to rule out whether shape is dependent on it. So you might need to rule out allometry (dependence of shape on size), or to determine whether any allometric signal you find is static, sexual or ontogenetic for which you do indeed need the centroid sizes.
It can be confusing to call "size" a nuisance factor because, in shape analysis, the nuisance factor is "scale". If shape depends on size, that is information, not noise.
I see what you mean. Nevertheless, relative size is standardized as part of the generalized Procrustes procedure, which basically amounts to treating it as noise. In that respect, he seems to have a point, in that from a purely theoretical perspective, scaling is indeed optional (it doesn't matter if scale is removed in pixes or mm). However, since pixel size isn't a particularly informative variable, nor a standardized one (my pixels aren't your pixels), scaling does come warmly recommended. Does that sum it up about right?
My point really is simple. You do not need to set the scale factor in tpsDig to superimpose the data (they will be scaled even if you do not set the scale factor). I am not saying that scaling is optional, what is optional is setting the scale factor. Scaling is optional in another sense, although not one I intended--you have the option to work in size-and-shape space, if you wish. However, in context of the original question, the reason for setting the scale factor is to get centroid size in units other than pixels. The reason for my comment on terminology, above, is that the word "size" has more than one meaning in the morphometrics literature. Because of that ambiguity, it can be confusing to refer to "size" as a nuisance parameter. Similarly, it can be confusing to refer to scaling as "size-standardization" because size-standardization often refers to removing the variation in shape that is due to size. Allometric variation in shape remains in the data following a Procrustes superimposition because it is not a nuisance parameter. It is signal not noise.
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