Ten recommendations for scanning foraminifera by X-ray computed tomography

Abstract

Marine sediment cores uniquely provide a temporally high-resolution and well-preserved archive of foraminifera fossils, which are essential for understanding environmental, ecological, and evolutionary dynamics over geological timescales. Foraminifera preserve their entire ontogeny in their fossilized shells, and much of this life history remains hidden from view under a light microscope. X-ray microfocus computed tomography (μCT) imaging of individual foraminifera reveals internal chambers and pores that are traditionally hidden from view. Their volume, shape, and growth form foundations of oceanographic and environmental research.

Here, we present a set of 10 recommendations for the preparation and scanning of individual fossilized foraminifera using glue-, gel-, and solvent-free methods. We focus on the primary X-ray parameters of μCT imaging that a researcher can optimize according to their throughput, signal-to-noise ratio, and cost requirements to generate three-dimensional (3D; volumetric) datasets. We showcase the effect of these parameters on image quality through repeated scans on a single planktonic foraminifer that varied the X-ray beam power and energy, detector binning, number of projections, and exposure times.

In our case study, the highest beam power resulted in the widest contrast between the subject of interest and the background, allowing the easiest threshold-based segmentation of the object and aiding computers in automated feature extraction.

The values of these parameters can exhibit significant variability across individuals, based on the specific needs of the study, the equipment used, and the unique attributes of the samples under consideration. Our motivation with this paper is to share our experience and offer a foundation for similar studies.

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Identifiers

ORCID for Alex Searle-Barnes: orcid.org/0000-0003-0389-7717

ORCID for Anieke Brombacher: orcid.org/0000-0003-2310-047X

ORCID for Orestis Katsamenis: orcid.org/0000-0003-4367-4147

ORCID for Kathryn Rankin: orcid.org/0000-0002-8458-1038

ORCID for Thomas Ezard: orcid.org/0000-0001-8305-6605

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