The University of Southampton
University of Southampton Institutional Repository

Analysing planktonic foraminiferal growth in three dimensions with foram3D: an R package for automated trait measurements from CT scans

Analysing planktonic foraminiferal growth in three dimensions with foram3D: an R package for automated trait measurements from CT scans
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 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.
0262-821X
149-164
Brombacher, Anieke
2a4bbb84-4743-4a36-973b-4ad2bf743154
Searle-Barnes, Alex
27cd9e5f-9a76-4d3d-8c88-0d3d0b1fad63
Zhang, Wenshu
cfa69116-bc11-4ca4-8444-07037f4aeab9
Ezard, Thomas
a143a893-07d0-4673-a2dd-cea2cd7e1374
Brombacher, Anieke
2a4bbb84-4743-4a36-973b-4ad2bf743154
Searle-Barnes, Alex
27cd9e5f-9a76-4d3d-8c88-0d3d0b1fad63
Zhang, Wenshu
cfa69116-bc11-4ca4-8444-07037f4aeab9
Ezard, Thomas
a143a893-07d0-4673-a2dd-cea2cd7e1374

Brombacher, Anieke, Searle-Barnes, Alex, Zhang, Wenshu and Ezard, Thomas (2022) Analysing planktonic foraminiferal growth in three dimensions with foram3D: an R package for automated trait measurements from CT scans. Journal of Micropalaeontology, 41 (2), 149-164. (doi:10.5194/jm-41-149-2022).

Record type: Article

Abstract

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.

Text
jm-41-149-2022 - Version of Record
Available under License Creative Commons Attribution.
Download (2MB)

More information

Accepted/In Press date: 30 September 2022
Published date: 1 November 2022

Identifiers

Local EPrints ID: 472181
URI: http://eprints.soton.ac.uk/id/eprint/472181
ISSN: 0262-821X
PURE UUID: 5a52408a-f6ba-4442-9ba4-d1c0e53fe48d
ORCID for Anieke Brombacher: ORCID iD orcid.org/0000-0003-2310-047X
ORCID for Alex Searle-Barnes: ORCID iD orcid.org/0000-0003-0389-7717
ORCID for Thomas Ezard: ORCID iD orcid.org/0000-0001-8305-6605

Catalogue record

Date deposited: 28 Nov 2022 18:20
Last modified: 29 Nov 2022 02:52

Export record

Altmetrics

Contributors

Author: Wenshu Zhang
Author: Thomas Ezard ORCID iD

Download statistics

Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.

View more statistics

Atom RSS 1.0 RSS 2.0

Contact ePrints Soton: eprints@soton.ac.uk

ePrints Soton supports OAI 2.0 with a base URL of http://eprints.soton.ac.uk/cgi/oai2

This repository has been built using EPrints software, developed at the University of Southampton, but available to everyone to use.

We use cookies to ensure that we give you the best experience on our website. If you continue without changing your settings, we will assume that you are happy to receive cookies on the University of Southampton website.

×