I am a beginner in Geometric Morphometrics and I am working with archaeological artefacts. I have these 3 doubts in regards to semilandmark building on TPS:
1. before placing the LM curve in all specimens, do I need to put all the pictures in the same scale using in tosDig, like we do for LMs?
2. The idea is to place 2 LMs in each object and then 14 semilandmarks in the contour. By watching the tutorial I realized that I wouldn’t need to put the 2 landmarks first, but only draw the semilandmarks curve all around each specimen, because later all these points are going to be transformed into landmarks in tpsUtil anyways — is that correct?
3. After converting the semilandmarks in landmarks on tpsUtil, how do I slide the semilandmarks of my specimens using TPSRelw? Is it only after the sliding step that the file will be ready to be used normally on MorphoJ? Then the protocol is the same as usual? — running the GPA, building classifiers, covariance matrix, PCA, etc etc?
Hi! I will try to help u in any way I can.
1. You can perfectly scale then in TPSDig with the scale option.
2. TPS does not differentiate between landmarks and semilandmarks, all points you place will be treated as landmarks. Be very careful as landmarks have to be placed in the same order in all specimens.
3. For sliding semilandmarks I personally use other programms as Viwebox, where you can work in 2D and 3D and its tools are wider. After that proccess you can easily export your raw coordinates and analyze them wherever you want. I use MorphoJ for that, it´s easy for beginners like us and the tools are more than ok.
Hi Verónica!
Thank you so much for your answers and good suggestions. They helped me a lot, indeed!
If u need any kinf of references for beginners tell me! I will be pleased to suggest some of which have helped me a lot when starting in this world...
That is very kind of you, Verónica! :) I will certainly ask you if I have more questions or need references! Kind regards
Hi Verónica Fernández-Navarro ,
Regarding your answer for my question #3:
3. For sliding semilandmarks I personally use other programms as Viwebox, where you can work in 2D and 3D and its tools are wider. After that proccess you can easily export your raw coordinates and analyze them wherever you want. I use MorphoJ for that, it´s easy for beginners like us and the tools are more than ok.
I used TPSRelw to do the semilandmark sliding, but I'm not sure how to save the file there in order to run it in MorphoJ. Do you happen to know it?
I link you here the guide I usually go for. Check the export data part!
http://www.morpho-tools.net/softwareguide/GM%20guide%20v4%20LMs.pdf
Also the answer by Zelditch herself:
https://www.researchgate.net/post/How_do_you_show_your_semilandmarks_in_tpsrelw_once_youve_completed_them_in_tpsdigs
Hey Verónica, these links are of great help! Thank you so much! Let me ask you: would you pass me your e-mail address? Mine is [email protected]
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