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 -- You received this message because you are subscribed to the Google Groups "Morphmet" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion visit https://groups.google.com/d/msgid/morphmet2/90d8291b-838e-41b1-affd-550808c1a962n%40googlegroups.com.
