ForamJ – a tool for the reproducible, semi-automated analysis of foraminifera micro computed tomography datasets
ForamJ – a tool for the reproducible, semi-automated analysis of foraminifera micro computed tomography datasets
The application of micro-computed tomography (µCT) to foraminiferal test analysis has opened new avenues for high-resolution, non-destructive 3D characterisation of internal and external morphological features. However, existing workflows are typically limited by low throughput, manual segmentation, and reliance on proprietary software, constraining dataset reproducibility and scalability. Here we present ForamJ, an open-source ImageJ plugin developed specifically for the semi-automated, reproducible analysis of foraminiferal µCT datasets. ForamJ streamlines key stages of image processing, including test segmentation, infill removal, chamber isolation, and morphological quantification, with outputs tailored to established micropaleontological metrics. These include both calcite volume and chamber volumes, test surface area, inner and outer wall thickness, chamber centroid coordinates - parameters directly relevant to taxonomy, taphonomy, paleoecology, and biomineralisation processes. The plugin supports both single-sample and batch-processing workflows, enabling high-throughput analysis. Validation against manual segmentation performed in commercial software demonstrates ForamJ’s analytical fidelity. Two use cases are presented: (1) the assessment of species-specific morphological variability in ancient cosmopolitan benthic foraminifera genus Cibicidoides spp. and (2) quantification of trends in between multiple species of modern planktonic foraminifera. By embedding foraminifera-specific metrics into an accessible, reproducible, and extensible framework, ForamJ provides a dedicated digital toolset for advancing µCT-based test analysis in foraminiferal research.
Trend, Jacob
63f583e3-79be-4a5b-954a-10fb70fb1118
Alvarez-Borges, Fernando
5512cdfd-6ad3-475f-8aec-2fc767607314
Babila, Tali L.
a59f9473-d145-4d43-92c0-ea682f29fdcc
Trend, Jacob
63f583e3-79be-4a5b-954a-10fb70fb1118
Alvarez-Borges, Fernando
5512cdfd-6ad3-475f-8aec-2fc767607314
Babila, Tali L.
a59f9473-d145-4d43-92c0-ea682f29fdcc
Trend, Jacob, Alvarez-Borges, Fernando and Babila, Tali L.
(2026)
ForamJ – a tool for the reproducible, semi-automated analysis of foraminifera micro computed tomography datasets.
Scientific Reports.
(doi:10.1038/s41598-026-43276-3).
Abstract
The application of micro-computed tomography (µCT) to foraminiferal test analysis has opened new avenues for high-resolution, non-destructive 3D characterisation of internal and external morphological features. However, existing workflows are typically limited by low throughput, manual segmentation, and reliance on proprietary software, constraining dataset reproducibility and scalability. Here we present ForamJ, an open-source ImageJ plugin developed specifically for the semi-automated, reproducible analysis of foraminiferal µCT datasets. ForamJ streamlines key stages of image processing, including test segmentation, infill removal, chamber isolation, and morphological quantification, with outputs tailored to established micropaleontological metrics. These include both calcite volume and chamber volumes, test surface area, inner and outer wall thickness, chamber centroid coordinates - parameters directly relevant to taxonomy, taphonomy, paleoecology, and biomineralisation processes. The plugin supports both single-sample and batch-processing workflows, enabling high-throughput analysis. Validation against manual segmentation performed in commercial software demonstrates ForamJ’s analytical fidelity. Two use cases are presented: (1) the assessment of species-specific morphological variability in ancient cosmopolitan benthic foraminifera genus Cibicidoides spp. and (2) quantification of trends in between multiple species of modern planktonic foraminifera. By embedding foraminifera-specific metrics into an accessible, reproducible, and extensible framework, ForamJ provides a dedicated digital toolset for advancing µCT-based test analysis in foraminiferal research.
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Submitted date: 28 November 2025
Accepted/In Press date: 3 March 2026
e-pub ahead of print date: 24 March 2026
Identifiers
Local EPrints ID: 510561
URI: http://eprints.soton.ac.uk/id/eprint/510561
ISSN: 2045-2322
PURE UUID: 8fecb64e-fd00-4f9d-b139-5c17cb5c85a3
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Date deposited: 13 Apr 2026 16:53
Last modified: 14 Apr 2026 02:10
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Author:
Jacob Trend
Author:
Fernando Alvarez-Borges
Author:
Tali L. Babila
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