ShapeRotator
- The quantification of complex morphological patterns typically involves comprehensive shape and size analyses, usually obtained by gathering morphological data from all the structures that capture the phenotypic diversity of an organism or object. Articulated structures are a critical component of overall phenotypic diversity, but data gathered from these structures are difficult to incorporate into modern analyses because of the complexities associated with jointly quantifying 3D shape in multiple structures. While there are existing methods for analyzing shape variation in articulated structures in two-dimensional (2D) space, these methods do not work in 3D, a rapidly growing area of capability and research. Here, we describe a simple geometric rigid rotation approach that removes the effect of random translation and rotation, enabling the morphological analysis of 3D articulated structures. Our method is based on Cartesian coordinates in 3D space, so it can be applied to any morphometric problem that also uses 3D coordinates (e.g.,The quantification of complex morphological patterns typically involves comprehensive shape and size analyses, usually obtained by gathering morphological data from all the structures that capture the phenotypic diversity of an organism or object. Articulated structures are a critical component of overall phenotypic diversity, but data gathered from these structures are difficult to incorporate into modern analyses because of the complexities associated with jointly quantifying 3D shape in multiple structures. While there are existing methods for analyzing shape variation in articulated structures in two-dimensional (2D) space, these methods do not work in 3D, a rapidly growing area of capability and research. Here, we describe a simple geometric rigid rotation approach that removes the effect of random translation and rotation, enabling the morphological analysis of 3D articulated structures. Our method is based on Cartesian coordinates in 3D space, so it can be applied to any morphometric problem that also uses 3D coordinates (e.g., spherical harmonics). We demonstrate the method by applying it to a landmark-based dataset for analyzing shape variation using geometric morphometrics. We have developed an R tool (ShapeRotator) so that the method can be easily implemented in the commonly used R package geomorph and MorphoJ software. This method will be a valuable tool for 3D morphological analyses in articulated structures by allowing an exhaustive examination of shape and size diversity.…
Author details: | Marta Vidal-GarciaORCiD, Lashi BandaraORCiD, J. Scott KeoghORCiD |
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DOI: | https://doi.org/10.1002/ece3.4018 |
ISSN: | 2045-7758 |
Pubmed ID: | https://pubmed.ncbi.nlm.nih.gov/29760906 |
Title of parent work (English): | Ecology and evolution |
Subtitle (English): | an R tool for standardized rigid rotations of articulated three-dimensional structures with application for geometric morphometrics |
Publisher: | Wiley |
Place of publishing: | Hoboken |
Publication type: | Article |
Language: | English |
Date of first publication: | 2018/04/15 |
Publication year: | 2018 |
Release date: | 2021/12/06 |
Tag: | articulation; morphology; motion correction; multi-modular morphology |
Volume: | 8 |
Issue: | 9 |
Number of pages: | 7 |
First page: | 4669 |
Last Page: | 4675 |
Funding institution: | Australian Research CouncilAustralian Research Council; Knut and Alice Wallenberg foundationKnut & Alice Wallenberg Foundation [KAW 2013.0322]; German Research Foundation (DFG)German Research Foundation (DFG) [SPP2026] |
Organizational units: | Mathematisch-Naturwissenschaftliche Fakultät / Institut für Mathematik |
DDC classification: | 5 Naturwissenschaften und Mathematik / 51 Mathematik / 510 Mathematik |
Peer review: | Referiert |
Publishing method: | Open Access / Gold Open-Access |
DOAJ gelistet | |
License (German): | CC-BY - Namensnennung 4.0 International |