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 |
---|---|
Main Authors: | , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Copernicus Publications
2022
|
Subjects: | |
Online Access: | https://doi.org/10.5194/jm-41-149-2022 https://doaj.org/article/db42dc6af63744f5b10069f6503a7df6 |
id |
ftdoajarticles:oai:doaj.org/article:db42dc6af63744f5b10069f6503a7df6 |
---|---|
record_format |
openpolar |
spelling |
ftdoajarticles:oai:doaj.org/article:db42dc6af63744f5b10069f6503a7df6 2023-05-15T18:00:54+02:00 Analysing planktonic foraminiferal growth in three dimensions with foram3D: an R package for automated trait measurements from CT scans A. Brombacher A. Searle-Barnes W. Zhang T. H. G. Ezard 2022-11-01T00:00:00Z https://doi.org/10.5194/jm-41-149-2022 https://doaj.org/article/db42dc6af63744f5b10069f6503a7df6 EN eng Copernicus Publications https://jm.copernicus.org/articles/41/149/2022/jm-41-149-2022.pdf https://doaj.org/toc/0262-821X https://doaj.org/toc/2041-4978 doi:10.5194/jm-41-149-2022 0262-821X 2041-4978 https://doaj.org/article/db42dc6af63744f5b10069f6503a7df6 Journal of Micropalaeontology, Vol 41, Pp 149-164 (2022) Geology QE1-996.5 article 2022 ftdoajarticles https://doi.org/10.5194/jm-41-149-2022 2022-12-30T19:44:42Z 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 x y z 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 Directory of Open Access Journals: DOAJ Articles Journal of Micropalaeontology 41 2 149 164 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Geology QE1-996.5 |
spellingShingle |
Geology QE1-996.5 A. Brombacher A. Searle-Barnes W. Zhang T. H. G. Ezard Analysing planktonic foraminiferal growth in three dimensions with foram3D: an R package for automated trait measurements from CT scans |
topic_facet |
Geology QE1-996.5 |
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 x y z 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 |
A. Brombacher A. Searle-Barnes W. Zhang T. H. G. Ezard |
author_facet |
A. Brombacher A. Searle-Barnes W. Zhang T. H. G. Ezard |
author_sort |
A. Brombacher |
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://doaj.org/article/db42dc6af63744f5b10069f6503a7df6 |
genre |
Planktonic foraminifera |
genre_facet |
Planktonic foraminifera |
op_source |
Journal of Micropalaeontology, Vol 41, Pp 149-164 (2022) |
op_relation |
https://jm.copernicus.org/articles/41/149/2022/jm-41-149-2022.pdf https://doaj.org/toc/0262-821X https://doaj.org/toc/2041-4978 doi:10.5194/jm-41-149-2022 0262-821X 2041-4978 https://doaj.org/article/db42dc6af63744f5b10069f6503a7df6 |
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_ |
1766170185869295616 |