Analysing planktonic foraminiferal growth in three dimensions with foram3D: an R package for automated trait measurements from CT scans
Foraminifera are one of the few taxa that preserve their entire ontogeny in their fossilised remains. Revealing this ontogeny through micro-computed tomography (CT) of fossil planktonic foraminifera has greatly improved our understanding of their life history and allows accurate quantification of to...
Published in: | Journal of Micropalaeontology |
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Copernicus Publications
2022
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ftnonlinearchiv:oai:noa.gwlb.de:cop_mods_00063281 2023-05-15T18:00:55+02:00 Analysing planktonic foraminiferal growth in three dimensions with foram3D: an R package for automated trait measurements from CT scans Brombacher, Anieke Searle-Barnes, Alex Zhang, Wenshu Ezard, Thomas H. G. 2022-11 electronic https://doi.org/10.5194/jm-41-149-2022 https://noa.gwlb.de/receive/cop_mods_00063281 https://noa.gwlb.de/servlets/MCRFileNodeServlet/cop_derivate_00062370/jm-41-149-2022.pdf https://jm.copernicus.org/articles/41/149/2022/jm-41-149-2022.pdf eng eng Copernicus Publications Journal of Micropalaeontology -- http://www.bibliothek.uni-regensburg.de/ezeit/?2053393 -- https://www.j-micropalaeontol.net/volumes.html -- http://jm.geoscienceworld.org/ -- 2041-4978 https://doi.org/10.5194/jm-41-149-2022 https://noa.gwlb.de/receive/cop_mods_00063281 https://noa.gwlb.de/servlets/MCRFileNodeServlet/cop_derivate_00062370/jm-41-149-2022.pdf https://jm.copernicus.org/articles/41/149/2022/jm-41-149-2022.pdf https://creativecommons.org/licenses/by/4.0/ uneingeschränkt info:eu-repo/semantics/openAccess CC-BY article Verlagsveröffentlichung article Text doc-type:article 2022 ftnonlinearchiv https://doi.org/10.5194/jm-41-149-2022 2022-11-07T00:12:05Z Foraminifera are one of the few taxa that preserve their entire ontogeny in their fossilised remains. Revealing this ontogeny through micro-computed tomography (CT) of fossil planktonic foraminifera has greatly improved our understanding of their life history and allows accurate quantification of total shell volume, growth rates and developmental constraints throughout an individual's life. Studies using CT scans currently mainly focus on chamber size, but the wealth of three-dimensional data generated by CT scans has the potential to reconstruct complete growth trajectories. Here we present an open-source R package to analyse growth in three-dimensional space. Using only the centroid xyz coordinates of every chamber, the functions determine the growth sequence and check that chambers are in the correct order. Once the order of growth has been verified, the functions calculate distances and angles between subsequent chambers, determine the total number of whorls and the number of chambers in the final whorl at the time each chamber was built, and, for the first time, quantify trochospirality. The applications of this package will enable repeatable analysis of large data sets and quantification of key taxonomic traits and ultimately provide new insights into the effects of ontogeny on evolution. Article in Journal/Newspaper Planktonic foraminifera Niedersächsisches Online-Archiv NOA Journal of Micropalaeontology 41 2 149 164 |
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English |
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article Verlagsveröffentlichung |
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article Verlagsveröffentlichung Brombacher, Anieke Searle-Barnes, Alex Zhang, Wenshu Ezard, Thomas H. G. Analysing planktonic foraminiferal growth in three dimensions with foram3D: an R package for automated trait measurements from CT scans |
topic_facet |
article Verlagsveröffentlichung |
description |
Foraminifera are one of the few taxa that preserve their entire ontogeny in their fossilised remains. Revealing this ontogeny through micro-computed tomography (CT) of fossil planktonic foraminifera has greatly improved our understanding of their life history and allows accurate quantification of total shell volume, growth rates and developmental constraints throughout an individual's life. Studies using CT scans currently mainly focus on chamber size, but the wealth of three-dimensional data generated by CT scans has the potential to reconstruct complete growth trajectories. Here we present an open-source R package to analyse growth in three-dimensional space. Using only the centroid xyz coordinates of every chamber, the functions determine the growth sequence and check that chambers are in the correct order. Once the order of growth has been verified, the functions calculate distances and angles between subsequent chambers, determine the total number of whorls and the number of chambers in the final whorl at the time each chamber was built, and, for the first time, quantify trochospirality. The applications of this package will enable repeatable analysis of large data sets and quantification of key taxonomic traits and ultimately provide new insights into the effects of ontogeny on evolution. |
format |
Article in Journal/Newspaper |
author |
Brombacher, Anieke Searle-Barnes, Alex Zhang, Wenshu Ezard, Thomas H. G. |
author_facet |
Brombacher, Anieke Searle-Barnes, Alex Zhang, Wenshu Ezard, Thomas H. G. |
author_sort |
Brombacher, Anieke |
title |
Analysing planktonic foraminiferal growth in three dimensions with foram3D: an R package for automated trait measurements from CT scans |
title_short |
Analysing planktonic foraminiferal growth in three dimensions with foram3D: an R package for automated trait measurements from CT scans |
title_full |
Analysing planktonic foraminiferal growth in three dimensions with foram3D: an R package for automated trait measurements from CT scans |
title_fullStr |
Analysing planktonic foraminiferal growth in three dimensions with foram3D: an R package for automated trait measurements from CT scans |
title_full_unstemmed |
Analysing planktonic foraminiferal growth in three dimensions with foram3D: an R package for automated trait measurements from CT scans |
title_sort |
analysing planktonic foraminiferal growth in three dimensions with foram3d: an r package for automated trait measurements from ct scans |
publisher |
Copernicus Publications |
publishDate |
2022 |
url |
https://doi.org/10.5194/jm-41-149-2022 https://noa.gwlb.de/receive/cop_mods_00063281 https://noa.gwlb.de/servlets/MCRFileNodeServlet/cop_derivate_00062370/jm-41-149-2022.pdf https://jm.copernicus.org/articles/41/149/2022/jm-41-149-2022.pdf |
genre |
Planktonic foraminifera |
genre_facet |
Planktonic foraminifera |
op_relation |
Journal of Micropalaeontology -- http://www.bibliothek.uni-regensburg.de/ezeit/?2053393 -- https://www.j-micropalaeontol.net/volumes.html -- http://jm.geoscienceworld.org/ -- 2041-4978 https://doi.org/10.5194/jm-41-149-2022 https://noa.gwlb.de/receive/cop_mods_00063281 https://noa.gwlb.de/servlets/MCRFileNodeServlet/cop_derivate_00062370/jm-41-149-2022.pdf https://jm.copernicus.org/articles/41/149/2022/jm-41-149-2022.pdf |
op_rights |
https://creativecommons.org/licenses/by/4.0/ uneingeschränkt info:eu-repo/semantics/openAccess |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.5194/jm-41-149-2022 |
container_title |
Journal of Micropalaeontology |
container_volume |
41 |
container_issue |
2 |
container_start_page |
149 |
op_container_end_page |
164 |
_version_ |
1766170191372222464 |