Ten recommendations for scanning foraminifera by X-ray computed tomography
<p>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...
Saved in:
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Copernicus Publications
2025-04-01
|
| Series: | Journal of Micropalaeontology |
| Online Access: | https://jm.copernicus.org/articles/44/107/2025/jm-44-107-2025.pdf |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850174644359790592 |
|---|---|
| author | A. Searle-Barnes A. Brombacher A. Brombacher O. Katsamenis O. Katsamenis K. Rankin M. Mavrogordato T. Ezard |
| author_facet | A. Searle-Barnes A. Brombacher A. Brombacher O. Katsamenis O. Katsamenis K. Rankin M. Mavrogordato T. Ezard |
| author_sort | A. Searle-Barnes |
| collection | DOAJ |
| description | <p>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 (<span class="inline-formula"><i>μ</i></span>CT) 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.</p>
<p>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 <span class="inline-formula"><i>μ</i></span>CT 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.</p>
<p>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.</p>
<p>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.</p> |
| format | Article |
| id | doaj-art-78cf0b4dbf8d4d3d8b022425e3c38819 |
| institution | OA Journals |
| issn | 0262-821X 2041-4978 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Copernicus Publications |
| record_format | Article |
| series | Journal of Micropalaeontology |
| spelling | doaj-art-78cf0b4dbf8d4d3d8b022425e3c388192025-08-20T02:19:37ZengCopernicus PublicationsJournal of Micropalaeontology0262-821X2041-49782025-04-014410711710.5194/jm-44-107-2025Ten recommendations for scanning foraminifera by X-ray computed tomographyA. Searle-Barnes0A. Brombacher1A. Brombacher2O. Katsamenis3O. Katsamenis4K. Rankin5M. Mavrogordato6T. Ezard7Ocean and Earth Science, University of Southampton, European Way, Southampton, SO14 3ZH, UKOcean and Earth Science, University of Southampton, European Way, Southampton, SO14 3ZH, UKNational Oceanography Centre, European Way, Southampton, SO14 3ZH, UKMicro-VIS X-ray Imaging Centre, University of Southampton, SO17 1BJ, UKInstitute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UKMicro-VIS X-ray Imaging Centre, University of Southampton, SO17 1BJ, UKMicro-VIS X-ray Imaging Centre, University of Southampton, SO17 1BJ, UKOcean and Earth Science, University of Southampton, European Way, Southampton, SO14 3ZH, UK<p>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 (<span class="inline-formula"><i>μ</i></span>CT) 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.</p> <p>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 <span class="inline-formula"><i>μ</i></span>CT 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.</p> <p>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.</p> <p>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.</p>https://jm.copernicus.org/articles/44/107/2025/jm-44-107-2025.pdf |
| spellingShingle | A. Searle-Barnes A. Brombacher A. Brombacher O. Katsamenis O. Katsamenis K. Rankin M. Mavrogordato T. Ezard Ten recommendations for scanning foraminifera by X-ray computed tomography Journal of Micropalaeontology |
| title | Ten recommendations for scanning foraminifera by X-ray computed tomography |
| title_full | Ten recommendations for scanning foraminifera by X-ray computed tomography |
| title_fullStr | Ten recommendations for scanning foraminifera by X-ray computed tomography |
| title_full_unstemmed | Ten recommendations for scanning foraminifera by X-ray computed tomography |
| title_short | Ten recommendations for scanning foraminifera by X-ray computed tomography |
| title_sort | ten recommendations for scanning foraminifera by x ray computed tomography |
| url | https://jm.copernicus.org/articles/44/107/2025/jm-44-107-2025.pdf |
| work_keys_str_mv | AT asearlebarnes tenrecommendationsforscanningforaminiferabyxraycomputedtomography AT abrombacher tenrecommendationsforscanningforaminiferabyxraycomputedtomography AT abrombacher tenrecommendationsforscanningforaminiferabyxraycomputedtomography AT okatsamenis tenrecommendationsforscanningforaminiferabyxraycomputedtomography AT okatsamenis tenrecommendationsforscanningforaminiferabyxraycomputedtomography AT krankin tenrecommendationsforscanningforaminiferabyxraycomputedtomography AT mmavrogordato tenrecommendationsforscanningforaminiferabyxraycomputedtomography AT tezard tenrecommendationsforscanningforaminiferabyxraycomputedtomography |