3DKMI: A MATLAB package to generate shape signatures from Krawtchouk moments and an application to species delimitation in planktonic foraminifera
The rapid and repeatable characterization of individual morphology has advanced automated taxonomic classification. The most direct study of evolutionary processes is, however, not from taxonomic description, but rather of the evolution of the traits that comprise individuals and define species. Rep...
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ftzenodo:oai:zenodo.org:12668293 2024-09-15T18:30:52+00:00 3DKMI: A MATLAB package to generate shape signatures from Krawtchouk moments and an application to species delimitation in planktonic foraminifera Lin, Huahua Zhang, Wenshu Mulqueeney, James Brombacher, Anieke Searle-Barnes, Alex Nixon, Mark Cai, Xiaohao Ezard, Thomas 2024-07-05 https://doi.org/10.5061/dryad.66t1g1k93 unknown Zenodo https://github.com/krawtchouk/Krawtchouk-Moment-Invariants https://krawtchouk.github.io/ https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.66t1g1k93 oai:zenodo.org:12668293 info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode Planktonic foraminifera Morphogenic segmentation 3D Krawtchouk moments info:eu-repo/semantics/other 2024 ftzenodo https://doi.org/10.5061/dryad.66t1g1k93 2024-07-27T06:21:12Z The rapid and repeatable characterization of individual morphology has advanced automated taxonomic classification. The most direct study of evolutionary processes is, however, not from taxonomic description, but rather of the evolution of the traits that comprise individuals and define species. Repeatable signatures of individual morphology are crucial for analyzing the response to selection at scale, and thus tracking evolutionary trajectories through time and across species boundaries. Here, we introduce our 3DKMI – an open-source MATLAB package designed for the study of morphology using three-dimensional (3D) Krawtchouk moment invariants. The volumetric features derived from the 3D images remain stable under translation, scaling, and rotation and, for an image of size 128x128x128 can be computed in less than 0.1 seconds. We applied our package as a case study on a collection of 300 X-ray computed tomography scans of planktonic foraminifera specimens across five species to (1) assess the invariance of the features under different transformations and (2) analyze morphological differences among species based on the extracted characteristics. We show that 3DKMI has the capacity to efficiently and repeatedly characterize the signatures of individual morphology. In the future, we hope that the 3D feature extraction technique 3DKMI will be widely applied to digital collections to advance research in ecology and evolution. Funding provided by: Natural Environment Research Council ROR ID: https://ror.org/02b5d8509 Award Number: NE/P019269/1 Other/Unknown Material Planktonic foraminifera Zenodo |
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ftzenodo |
language |
unknown |
topic |
Planktonic foraminifera Morphogenic segmentation 3D Krawtchouk moments |
spellingShingle |
Planktonic foraminifera Morphogenic segmentation 3D Krawtchouk moments Lin, Huahua Zhang, Wenshu Mulqueeney, James Brombacher, Anieke Searle-Barnes, Alex Nixon, Mark Cai, Xiaohao Ezard, Thomas 3DKMI: A MATLAB package to generate shape signatures from Krawtchouk moments and an application to species delimitation in planktonic foraminifera |
topic_facet |
Planktonic foraminifera Morphogenic segmentation 3D Krawtchouk moments |
description |
The rapid and repeatable characterization of individual morphology has advanced automated taxonomic classification. The most direct study of evolutionary processes is, however, not from taxonomic description, but rather of the evolution of the traits that comprise individuals and define species. Repeatable signatures of individual morphology are crucial for analyzing the response to selection at scale, and thus tracking evolutionary trajectories through time and across species boundaries. Here, we introduce our 3DKMI – an open-source MATLAB package designed for the study of morphology using three-dimensional (3D) Krawtchouk moment invariants. The volumetric features derived from the 3D images remain stable under translation, scaling, and rotation and, for an image of size 128x128x128 can be computed in less than 0.1 seconds. We applied our package as a case study on a collection of 300 X-ray computed tomography scans of planktonic foraminifera specimens across five species to (1) assess the invariance of the features under different transformations and (2) analyze morphological differences among species based on the extracted characteristics. We show that 3DKMI has the capacity to efficiently and repeatedly characterize the signatures of individual morphology. In the future, we hope that the 3D feature extraction technique 3DKMI will be widely applied to digital collections to advance research in ecology and evolution. Funding provided by: Natural Environment Research Council ROR ID: https://ror.org/02b5d8509 Award Number: NE/P019269/1 |
format |
Other/Unknown Material |
author |
Lin, Huahua Zhang, Wenshu Mulqueeney, James Brombacher, Anieke Searle-Barnes, Alex Nixon, Mark Cai, Xiaohao Ezard, Thomas |
author_facet |
Lin, Huahua Zhang, Wenshu Mulqueeney, James Brombacher, Anieke Searle-Barnes, Alex Nixon, Mark Cai, Xiaohao Ezard, Thomas |
author_sort |
Lin, Huahua |
title |
3DKMI: A MATLAB package to generate shape signatures from Krawtchouk moments and an application to species delimitation in planktonic foraminifera |
title_short |
3DKMI: A MATLAB package to generate shape signatures from Krawtchouk moments and an application to species delimitation in planktonic foraminifera |
title_full |
3DKMI: A MATLAB package to generate shape signatures from Krawtchouk moments and an application to species delimitation in planktonic foraminifera |
title_fullStr |
3DKMI: A MATLAB package to generate shape signatures from Krawtchouk moments and an application to species delimitation in planktonic foraminifera |
title_full_unstemmed |
3DKMI: A MATLAB package to generate shape signatures from Krawtchouk moments and an application to species delimitation in planktonic foraminifera |
title_sort |
3dkmi: a matlab package to generate shape signatures from krawtchouk moments and an application to species delimitation in planktonic foraminifera |
publisher |
Zenodo |
publishDate |
2024 |
url |
https://doi.org/10.5061/dryad.66t1g1k93 |
genre |
Planktonic foraminifera |
genre_facet |
Planktonic foraminifera |
op_relation |
https://github.com/krawtchouk/Krawtchouk-Moment-Invariants https://krawtchouk.github.io/ https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.66t1g1k93 oai:zenodo.org:12668293 |
op_rights |
info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.66t1g1k93 |
_version_ |
1810472408856920064 |