Automated segmentation of synchrotron-scanned fossils
Computed tomography has revolutionised the study of the internal three-dimensional structure of fossils. Historically, fossils typically spent years in preparation to be freed from the enclosing rock. Now, X-ray and synchrotron tomography reveal structures that are otherwise invisible, and data acqu...
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| Format: | Article |
| Language: | English |
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Pensoft Publishers
2025-03-01
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| Series: | Fossil Record |
| Online Access: | https://fr.pensoft.net/article/139379/download/pdf/ |
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| author | Melanie A. D. During Jordan K. Matelsky Fredrik K. Gustafsson Dennis F. A. E. Voeten Donglei Chen Brock A. Wester Konrad P. Kording Per E. Ahlberg Thomas B. Schön |
| author_facet | Melanie A. D. During Jordan K. Matelsky Fredrik K. Gustafsson Dennis F. A. E. Voeten Donglei Chen Brock A. Wester Konrad P. Kording Per E. Ahlberg Thomas B. Schön |
| author_sort | Melanie A. D. During |
| collection | DOAJ |
| description | Computed tomography has revolutionised the study of the internal three-dimensional structure of fossils. Historically, fossils typically spent years in preparation to be freed from the enclosing rock. Now, X-ray and synchrotron tomography reveal structures that are otherwise invisible, and data acquisition can be fast. However, manual segmentation of these 3D volumes can still take months to years. This is especially challenging for resource-poor teams, as scanning may be free, but the computing power and (AI-assisted) segmentation software required to handle the resulting large data sets are complex to use and expensive. Here we present a free, browser-based segmentation tool that reduces computational overhead by splitting volumes into small chunks, allowing processing on low-memory, inexpensive hardware. Our tool also speeds up collaborative ground-truth generation and 3D visualisation, all in-browser. We developed and evaluated our pipeline on various open-data scans of differing contrast, resolution, textural complexity, and size. Our tool successfully isolated the Thrinaxodon and Broomistega pair from an Early Triassic burrow. It isolated cranial bones from the Cretaceous acipenseriform Parapsephurus willybemisi on both 45.53 µm and 13.67 µm resolution (voxel size) scanning data. We also isolated bones of the Middle Triassic sauropterygian Nothosaurus and a challenging scan of a squamate embryo inside an egg dating back to the Early Cretaceous. Our tool reliably reproduces expert-supervised segmentation at a fraction of the time and cost, offering greater accessibility than existing tools. Beyond the online tool, all our code is open source, enabling contributions from the palaeontology community to further this emerging machine-learning ecosystem. |
| format | Article |
| id | doaj-art-800d211e9fb6471a9d9d5ed65885a3c9 |
| institution | DOAJ |
| issn | 2193-0074 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Pensoft Publishers |
| record_format | Article |
| series | Fossil Record |
| spelling | doaj-art-800d211e9fb6471a9d9d5ed65885a3c92025-08-20T02:59:52ZengPensoft PublishersFossil Record2193-00742025-03-0128110311410.3897/fr.28.e139379139379Automated segmentation of synchrotron-scanned fossilsMelanie A. D. During0Jordan K. Matelsky1Fredrik K. Gustafsson2Dennis F. A. E. Voeten3Donglei Chen4Brock A. Wester5Konrad P. Kording6Per E. Ahlberg7Thomas B. Schön8Uppsala UniversityUniversity of PennsylvaniaKarolinska InstitutetUppsala UniversityUppsala UniversityJohns Hopkins University Applied Physics LaboratoryUniversity of PennsylvaniaUppsala UniversityUppsala UniversityComputed tomography has revolutionised the study of the internal three-dimensional structure of fossils. Historically, fossils typically spent years in preparation to be freed from the enclosing rock. Now, X-ray and synchrotron tomography reveal structures that are otherwise invisible, and data acquisition can be fast. However, manual segmentation of these 3D volumes can still take months to years. This is especially challenging for resource-poor teams, as scanning may be free, but the computing power and (AI-assisted) segmentation software required to handle the resulting large data sets are complex to use and expensive. Here we present a free, browser-based segmentation tool that reduces computational overhead by splitting volumes into small chunks, allowing processing on low-memory, inexpensive hardware. Our tool also speeds up collaborative ground-truth generation and 3D visualisation, all in-browser. We developed and evaluated our pipeline on various open-data scans of differing contrast, resolution, textural complexity, and size. Our tool successfully isolated the Thrinaxodon and Broomistega pair from an Early Triassic burrow. It isolated cranial bones from the Cretaceous acipenseriform Parapsephurus willybemisi on both 45.53 µm and 13.67 µm resolution (voxel size) scanning data. We also isolated bones of the Middle Triassic sauropterygian Nothosaurus and a challenging scan of a squamate embryo inside an egg dating back to the Early Cretaceous. Our tool reliably reproduces expert-supervised segmentation at a fraction of the time and cost, offering greater accessibility than existing tools. Beyond the online tool, all our code is open source, enabling contributions from the palaeontology community to further this emerging machine-learning ecosystem.https://fr.pensoft.net/article/139379/download/pdf/ |
| spellingShingle | Melanie A. D. During Jordan K. Matelsky Fredrik K. Gustafsson Dennis F. A. E. Voeten Donglei Chen Brock A. Wester Konrad P. Kording Per E. Ahlberg Thomas B. Schön Automated segmentation of synchrotron-scanned fossils Fossil Record |
| title | Automated segmentation of synchrotron-scanned fossils |
| title_full | Automated segmentation of synchrotron-scanned fossils |
| title_fullStr | Automated segmentation of synchrotron-scanned fossils |
| title_full_unstemmed | Automated segmentation of synchrotron-scanned fossils |
| title_short | Automated segmentation of synchrotron-scanned fossils |
| title_sort | automated segmentation of synchrotron scanned fossils |
| url | https://fr.pensoft.net/article/139379/download/pdf/ |
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