SlicerMorph paper

Congrats to @smrolfe and @muratmaga for getting the SlicerMorph paper published! :+1: :+1: :+1:

Rolfe, S., Pieper, S., Porto, A., Diamond, K., Winchester, J., Shan, S., Kirveslahti, H., Boyer, D., Summers, A. and Maga, A.M. (2021), SlicerMorph: An open and extensible platform to retrieve, visualize and analyze 3D morphology. Methods in Ecology and Evolution. Accepted Author Manuscript. https://doi.org/10.1111/2041-210X.13669

https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.13669

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Very nice! I would recommend to explicitly designate this paper as the paper to cite when somebody uses SlicerMorph (add “How to cite” to SlicerMorph website). This makes it much easier to follow who uses SlicerMorph and for what, and it is also much more impressive to have one paper with 500 citations than 10 papers with 50 citations each. Users of course can cite additional papers, more specific to certain SlicerMorph features (e.g, if they use ALPACA then they should cite the SlicerMorph paper and the ALPACA paper).

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Congratulations for the great work

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Thank you all for our help. This wouldn’t be possible without the support of this wonderful group of people around the Slicer platform.

@lassoan We do have how to cite SlicerMorph on the github repo. These were pointing out to the more detailed preprint versions of the paper, but will update with the new DOIs. ALLPACA paper is is also accepted to MEE and should appear shortly.

I’ve opened the SlicerMorph website and searched for “cite” and nothing was found on the page. I have not thought about checking it in the repository’s readme file, and probably I’m not alone. It could be better to duplicate the “How to cite” instructions at both places. I would also recommend considering renaming “Citations” to “How to cite” (because citations may also mean a list of papers that cite SlicerMorph), highlight one single paper to be cited (to accumulate instead of disperse citations), and describe why it is important that they cite (makes it easier to demonstrate impact for securing further funding for development and maintenance).

Yeah, I think we will actually forward the slicermorph.org to the repo as oppose to the old github.io pages.

Good suggestion for the Citations, I will rename that to how to cite.

When I searched for SlicerMorph then I got https://slicermorph.github.io/ as the first hit. If you don’t want people to use this landing page then it might be better to remove it.

Can SlicerMorph also use the PCA results with a continuous variable such as age for the samples to perform a regression analysis such as that which can be performed in MorphJ?

SlicerMorph and MorphoJ serve different functions. SlicerMorph is a digitization and shape variance visualization tool, whereas MorphoJ is an analytical tool with some function specific to analysis of coordinate data.

At this point SlicerMorph does not feature any analysis features built on latent variables like PC scores. You have two options.

  1. You can explore the available linear model tools in Python, and use them within Slicer/SlicerMorph. We can possibly work with you, if you want to go down that route. These are some examples of packages that offer linear modeling and regression in Python.
  2. You can take the PCA output from SlicerMorph and use R/geomorph package to do your analysis. This tutorial shows the necessary steps

More general question then, as I would prefer to use the functionality of MorphoJ than reinventing the wheel myself with Python tools or with having to format the PCA outputs in R (which in and of itself is slow and cumbersome when doing GMM with landmarks). Does anyone know which files in 3D Slicer or SlicerMorph are responsible for defining the saving system for fiducial files? If so I can modify said file to save in the format necessary for MorphoJ for our purposes to be able to directly import them without all the rigmarole of altering each .fcsv file and then combining them for analysis.

İ (and probably an order of more magnitude more publications that use R based gmm tools for shape analysis instead of morphoj) respectfully disagree with your assessment of functionality of R gmm ecosystem. But if course you are free to do what you want to do.

i don’t think you want to modify the fcsv write functions and rebuild Slicer from scratch, as those would be undoubtedly more work. Fcsvs are simple csv files that you can open in excel and append each other if that’s what you want.

İ do not know what format morphoj expects.