Dear Lydia,
I read quickly but the steps you wrote seem correct to me. Most of them
are also summarized in the guidelines I wrote a while ago:
https://europeanjournaloftaxonomy.eu/index.php/ejt/issue/view/1425
In the papers, you'll find some caveats about the statistical analyses
and visualization of superimposed data and the references to the papers
covering those issues.
I've not used CoordGen8 for ages and can't remember what it does precisely.
However, before importing the data in MorphoJ, I suggest you to rescale
the objects to their original centroid size (CS). Otherwise, that
information is lost in MorphoJ unless you import CS as a covariate. Be
careful, because MorphoJ (after redoing the superimposition) will show
you a CS variable regardless of whether you imported shape or form data.
In the first case, however, CS is just rounding error (1.00001, 0.9999
and the like). If you import form (i.e., rescaled superimposed data),
that's not an issue and you have the correct CS. Most of the time, you
want to analyze both shape, size and maybe allometry.
Rescaling is trivial: in xls, multiply each shape coordinates for the
corresponding CS. Alternatively, if you use TPSRelw, there should be an
option for rescaling. It used to be called "restore size" (more or less)
but possibly now it's Boas coordinates. Jim will correct me. I am not
sure and cannot check now, as I have a beta version installed which is a
bit different.
Good luck with the analysis!
Cheers
Andrea PS I think there's a later version of MorphoJ now.
On 09/07/2025 20:12, 'Lydia Irons' via Morphmet wrote:
Hi,
I’d like some input on whether I’m using various geometric morphometric
programs correctly or not. I’m a research technician working on a geometric
morphometric project on seed beetles, and I’ve mainly taught myself how to
use all these programs by reading various handbooks and such. Since there
are a lot of steps, I want to make sure I’m not missing anything or doing
something incorrectly. Here’s how I’ve been doing it, starting from placing
landmarks all the way to running statistical analyses:
1. I use tpsUtil32 to create a tps file of all the photos I want to
landmark using the “Build tps file from images” operation. I hit “Input”
and choose an image file from the folder where all my images are, then I
hit “Output” and create a name for the tps file. I then select “Setup” and
include all the images I need, then hit “ok”
2. Then I upload this file to tpsDig264 and place the landmarks first, then
the semilandmarks, for each specimen. I use the “Digitize landmarks” tool
for landmarks, and the “Draw background curves” tool for semilandmarks. I
make sure every specimen has the same number of landmarks and
semilandmarks, using the “Resample curve” option to keep the number of
semilandmarks consistent for each curve
3. Once I’m done landmarking, I open the tps file using Notepad and change
the number after “ID=” to the unique specimen IDs I’ve given to each
specimen
4. Then I use CoordGen8 and upload the tps file using the “load tps,
convert curves, create SLM proto” option. I save the protocol file, then do
a “SemiLandMark Alignment” and upload the protocol file to align all the
landmarks and semilandmarks. Then I hit “save all”
5. The resulting file then has to be formatted for MorphoJ, which involves
adding the specimen IDs to the beginning of each block of coordinates that
corresponds to that specimen, deleting the centroid size at the end of each
block of coordinates, making sure a paragraph mark separates each
specimen’s block of coordinates, and adding a comma followed by a space
between every number
6. Once the formatting is done, I upload this file to MorphoJ 1.07a by
selecting “create new dataset” and selecting the data as 2 dimensions,
selecting “yes” for object symmetry if applicable, and choosing the file
type as “text.” Then I click “new procrustes fit” and line up the landmarks
if there is object symmetry. I look for any outliers, generate a covariance
matrix, extract classifiers from my specimen ID, and run whatever analyses
I need to (PCA, CVA, ANOVA, etc.)
Are there any steps I’m missing or things I’m doing incorrectly?
Thank you in advance,
Lydia Irons
--
Andrea Cardini
E-mail address: alcard...@gmail.com, card...@unimo.it
WEBPAGE: https://sites.google.com/view/alcardini2/
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