1
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Knutsen EM, Konovalov DA. Accelerating segmentation of fossil CT scans through Deep Learning. Sci Rep 2024; 14:20943. [PMID: 39251621 PMCID: PMC11385573 DOI: 10.1038/s41598-024-71245-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 08/26/2024] [Indexed: 09/11/2024] Open
Abstract
Recent developments in Deep Learning have opened the possibility for automated segmentation of large and highly detailed CT scan datasets of fossil material. However, previous methodologies have required large amounts of training data to reliably extract complex skeletal structures. Here we present a method for automated Deep Learning segmentation to obtain high-fidelity 3D models of fossils digitally extracted from the surrounding rock, training the model with less than 1%-2% of the total CT dataset. This workflow has the capacity to revolutionise the use of Deep Learning to significantly reduce the processing time of such data and boost the availability of segmented CT-scanned fossil material for future research outputs. Our final Unet segmentation model achieved a validation Dice similarity of 0.96.
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Affiliation(s)
- Espen M Knutsen
- College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia.
- Queensland Museum Tropics, Townsville, QLD, 4810, Australia.
| | - Dmitry A Konovalov
- College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
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2
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Wright NL, Klompmaker AA, Petsios E. Exploring the preservation of a parasitic trace in decapod crustaceans using finite elements analysis. PLoS One 2024; 19:e0296146. [PMID: 38626153 PMCID: PMC11020947 DOI: 10.1371/journal.pone.0296146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/22/2024] [Indexed: 04/18/2024] Open
Abstract
The fossil record of parasitism is poorly understood, due largely to the scarcity of strong fossil evidence of parasites. Understanding the preservation potential for fossil parasitic evidence is critical to contextualizing the fossil record of parasitism. Here, we present the first use of X-ray computed tomography (CT) scanning and finite elements analysis (FEA) to analyze the impact of a parasite-induced fossil trace on host preservation. Four fossil and three modern decapod crustacean specimens with branchial swellings attributed to an epicaridean isopod parasite were CT scanned and examined with FEA to assess differences in the magnitude and distribution of stress between normal and swollen branchial chambers. The results of the FEA show highly localized stress peaks in reaction to point forces, with higher peak stress on the swollen branchial chamber for nearly all specimens and different forces applied, suggesting a possible shape-related decrease in the preservation potential of these parasitic swellings. Broader application of these methods as well as advances in the application of 3D data analysis in paleontology are critical to understanding the fossil record of parasitism and other poorly represented fossil groups.
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Affiliation(s)
- Nathan L. Wright
- Department of Geosciences, Baylor University, Waco, Texas, United States of America
| | - Adiël A. Klompmaker
- Department of Museum Research and Collections & Alabama Museum of Natural History, University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Elizabeth Petsios
- Department of Geosciences, Baylor University, Waco, Texas, United States of America
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3
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Łaska W, Rodríguez-Tovar FJ, Uchman A. New insights into endolithic palaeocommunity development in mobile hard substrate using CT imaging of bioeroded clasts from the Pliocene (Almería, SE Spain). THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2024; 111:8. [PMID: 38329546 DOI: 10.1007/s00114-024-01892-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/13/2024] [Accepted: 01/17/2024] [Indexed: 02/09/2024]
Abstract
Bioeroded carbonate clasts from a Pliocene shallow-marine succession of Almería (SE Spain, Betic Cordillera) were analysed with computed tomography (CT). This revealed the detailed 3D architecture of bioerosion structures hidden within and allowed for their ichnotaxonomic identification (14 ichnospecies of 5 ichnogenera) and quantification. Borings are produced by worms, mostly polychaetes and sipunculids dominated, followed by bivalves and lastly by sponges. The crosscutting relationship between the borings and their preservation characteristics points to a complex colonization history of the clasts with repeated bioerosive episodes interrupted by physical disturbances, including overturning and abrasion of the clasts followed by their recolonization. Our findings facilitated paleoenvironmental interpretation and can be compared to analogous modern-day ecological succession. The sharp dominance of worm borings - early successional species - may be related to frequent, periodic, physical disturbance that possibly prevented the cobble-dwelling macroboring community from being overtaken by sponges - late successional taxa. CT, hand sample and petrographic observations detected, aside from borings, other irregularly shaped pores which are interpreted to be generated by diagenetic processes including dolomitization, silicification and dissolution, representing an intraparticle moldic and moldic enlarged porosity. Boring porosity crosscutting the diagenetically altered grains suggests the later occurrence of bioerosion processes. Irregular shapes ranging from roughly spherical, elongate sub-polyhedral to amoeboid resemble morphologies produced by modern sponges. Moldic pores possibly acted as primary domiciles for boring sponges, which infested, altered and enlarged pre-existing pores as they grew (as happens in the modern), providing an example of how biological and non-biological processes interacted and together influenced endolithic palaeocommunity development.
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Affiliation(s)
- Weronika Łaska
- Faculty of Geography and Geology, Institute of Geological Sciences, Jagiellonian University, Gronostajowa 3a, 30-387, Kraków, Poland.
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland.
| | - Francisco J Rodríguez-Tovar
- Departamento de Estratigrafía y Paleontología, Facultad de Ciencias, Universidad de Granada, 18002, Granada, Spain
| | - Alfred Uchman
- Faculty of Geography and Geology, Institute of Geological Sciences, Jagiellonian University, Gronostajowa 3a, 30-387, Kraków, Poland
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4
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Kolmann MA, Nagesan RS, Andrews JV, Borstein SR, Figueroa RT, Singer RA, Friedman M, López-Fernández H. DiceCT for fishes: recommendations for pairing iodine contrast agents with μCT to visualize soft tissues in fishes. JOURNAL OF FISH BIOLOGY 2023; 102:893-903. [PMID: 36647819 DOI: 10.1111/jfb.15320] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 01/11/2023] [Indexed: 06/17/2023]
Abstract
Computed tomography (CT) scanning and other high-throughput three-dimensional (3D) visualization tools are transforming the ways we study morphology, ecology and evolutionary biology research beyond generating vast digital repositories of anatomical data. Contrast-enhanced chemical staining methods, which render soft tissues radio-opaque when coupled with CT scanning, encompass several approaches that are growing in popularity and versatility. Of these, the various diceCT techniques that use an iodine-based solution like Lugol's have provided access to an array of morphological data sets spanning extant vertebrate lineages. This contribution outlines straightforward means for applying diceCT techniques to preserved museum specimens of cartilaginous and bony fishes, collectively representing half of vertebrate species diversity. This study contrasts the benefits of using either aqueous or ethylic Lugol's solutions and reports few differences between these methods with respect to the time required to achieve optimal tissue contrast. It also explores differences in minimum stain duration required for different body sizes and shapes and provides recommendations for staining specimens individually or in small batches. As reported by earlier studies, the authors note a decrease in pH during staining with either aqueous or ethylic Lugol's. Nonetheless, they could not replicate the drastic declines in pH reported elsewhere. They provide recommendations for researchers and collections staff on how to incorporate diceCT into existing curatorial practices, while offsetting risk to specimens. Finally, they outline how diceCT with Lugol's can aid ichthyologists of all kinds in visualizing anatomical structures of interest: from brains and gizzards to gas bladders and pharyngeal jaw muscles.
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Affiliation(s)
- Matthew A Kolmann
- University of Michigan Museum of Paleontology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Biology, University of Louisville, Louisville, Kentucky, USA
| | - Ramon S Nagesan
- Department of Ecology & Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, Michigan, USA
| | - James V Andrews
- University of Michigan Museum of Paleontology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Samuel R Borstein
- Department of Ecology & Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, Michigan, USA
| | - Rodrigo Tinoco Figueroa
- University of Michigan Museum of Paleontology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Randal A Singer
- Department of Ecology & Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, Michigan, USA
| | - Matt Friedman
- University of Michigan Museum of Paleontology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Hernán López-Fernández
- Department of Ecology & Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, Michigan, USA
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5
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Clark EG, Jenkins KM, Brodersen CR. Back to life: Techniques for developing high-quality 3D reconstructions of plants and animals from digitized specimens. PLoS One 2023; 18:e0283027. [PMID: 36989314 PMCID: PMC10058149 DOI: 10.1371/journal.pone.0283027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/28/2023] [Indexed: 03/30/2023] Open
Abstract
Expanded use of 3D imaging in organismal biology and paleontology has substantially enhanced the ability to visualize and analyze specimens. These techniques have improved our understanding of the anatomy of many taxa, and the integration of downstream computational tools applied to 3D datasets have broadened the range of analyses that can be performed (e.g., finite element analyses, geometric morphometrics, biomechanical modeling, physical modeling using 3D printing). However, morphological analyses inevitably present challenges, particularly in fossil taxa where taphonomic or preservational artifacts distort and reduce the fidelity of the original morphology through shearing, compression, and disarticulation, for example. Here, we present a compilation of techniques to build high-quality 3D digital models of extant and fossil taxa from 3D imaging data using freely available software for students and educators. Our case studies and associated step-by-step supplementary tutorials present instructions for working with reconstructions of plants and animals to directly address and resolve common issues with 3D imaging data. The strategies demonstrated here optimize scientific accuracy and computational efficiency and can be applied to a broad range of taxa.
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Affiliation(s)
- Elizabeth G Clark
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, California, United States of America
| | - Kelsey M Jenkins
- Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, United States of America
| | - Craig R Brodersen
- School of the Environment, Yale University, New Haven, Connecticut, United States of America
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6
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Hamm CA, Hampe O, Mews J, Günter C, Milke R, Witzmann F, Savic LJ, Hecht L, Meister S, Hamm B, Asbach P, Diekhoff T. Quantitative dual-energy CT as a nondestructive tool to identify indicators for fossilized bone in vertebrate paleontology. Sci Rep 2022; 12:16407. [PMID: 36180510 PMCID: PMC9525674 DOI: 10.1038/s41598-022-20707-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 09/16/2022] [Indexed: 11/08/2022] Open
Abstract
Dual-energy computed tomography (DECT) is an imaging technique that combines nondestructive morphological cross-sectional imaging of objects and the quantification of their chemical composition. However, its potential to assist investigations in paleontology has not yet been explored. This study investigates quantitative DECT for the nondestructive density- and element-based material decomposition of fossilized bones. Specifically, DECT was developed and validated for imaging-based calcium and fluorine quantification in bones of five fossil vertebrates from different geological time periods and of one extant vertebrate. The analysis shows that DECT material maps can differentiate bone from surrounding sediment and reveals fluorine as an imaging marker for fossilized bone and a reliable indicator of the age of terrestrial fossils. Moreover, the jaw bone mass of Tyrannosaurus rex showed areas of particularly high fluorine concentrations on DECT, while conventional CT imaging features supported the diagnosis of chronic osteomyelitis. These findings highlight the relevance of radiological imaging techniques in the natural sciences by introducing quantitative DECT imaging as a nondestructive approach for material decomposition in fossilized objects, thereby potentially adding to the toolbox of paleontological studies.
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Affiliation(s)
- Charlie A Hamm
- Department of Radiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany.
- Institute of Diagnostic Radiology and Neuroradiology, Greifswald University Hospital, Ferdinand-Sauerbruch-Straße, 17475, Greifswald, Germany.
| | - Oliver Hampe
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Invalidenstraße 43, 10115, Berlin, Germany
| | - Jürgen Mews
- Canon Medical Systems Europe BV, Global RDC, Zilverstraat 1, 2718RP, Zoetermeer, The Netherlands
| | - Christina Günter
- Institute for Geosciences, University of Potsdam, 14469, Potsdam, Germany
| | - Ralf Milke
- Institut für Geologische Wissenschaften, Freie Universität Berlin, Malteserstraße 74-100, 12249, Berlin, Germany
| | - Florian Witzmann
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Invalidenstraße 43, 10115, Berlin, Germany
| | - Lynn J Savic
- Department of Radiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lutz Hecht
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Invalidenstraße 43, 10115, Berlin, Germany
- Institut für Geologische Wissenschaften, Freie Universität Berlin, Malteserstraße 74-100, 12249, Berlin, Germany
| | - Sabine Meister
- Institut für Geologische Wissenschaften, Freie Universität Berlin, Malteserstraße 74-100, 12249, Berlin, Germany
| | - Bernd Hamm
- Department of Radiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Patrick Asbach
- Department of Radiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
| | - Torsten Diekhoff
- Department of Radiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117, Berlin, Germany
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7
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Rowe AJ, Rayfield EJ. The efficacy of computed tomography scanning versus surface scanning in 3D finite element analysis. PeerJ 2022; 10:e13760. [PMID: 36042861 PMCID: PMC9420411 DOI: 10.7717/peerj.13760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/29/2022] [Indexed: 01/17/2023] Open
Abstract
Finite element analysis (FEA) is a commonly used application in biomechanical studies of both extant and fossil taxa to assess stress and strain in solid structures such as bone. FEA can be performed on 3D structures that are generated using various methods, including computed tomography (CT) scans and surface scans. While previous palaeobiological studies have used both CT scanned models and surface scanned models, little research has evaluated to what degree FE results may vary when CT scans and surface scans of the same object are compared. Surface scans do not preserve the internal geometries of 3D structures, which are typically preserved in CT scans. Here, we created 3D models from CT scans and surface scans of the same specimens (crania and mandibles of a Nile crocodile, a green sea turtle, and a monitor lizard) and performed FEA under identical loading parameters. It was found that once surface scanned models are solidified, they output stress and strain distributions and model deformations comparable to their CT scanned counterparts, though differing by notable stress and strain magnitudes in some cases, depending on morphology of the specimen and the degree of reconstruction applied. Despite similarities in overall mechanical behaviour, surface scanned models can differ in exterior shape compared to CT scanned models due to inaccuracies that can occur during scanning and reconstruction, resulting in local differences in stress distribution. Solid-fill surface scanned models generally output lower stresses compared to CT scanned models due to their compact interiors, which must be accounted for in studies that use both types of scans.
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Affiliation(s)
- Andre J. Rowe
- School of Earth Sciences, University of Bristol, Bristol, United Kingdom
| | - Emily J. Rayfield
- School of Earth Sciences, University of Bristol, Bristol, United Kingdom
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8
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Tamborini M. A Plea for a New Synthesis: From Twentieth-Century Paleobiology to Twenty-First-Century Paleontology and Back Again. BIOLOGY 2022; 11:1120. [PMID: 35892976 PMCID: PMC9394316 DOI: 10.3390/biology11081120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/22/2022] [Accepted: 07/24/2022] [Indexed: 11/16/2022]
Abstract
In this paper, I will briefly discuss the elements of novelty and continuity between twentieth-century paleobiology and twenty-first-century paleontology. First, I will outline the heated debate over the disciplinary status of paleontology in the mid-twentieth century. Second, I will analyze the main theoretical issue behind this debate by considering two prominent case studies within the broader paleobiology agenda. Third, I will turn to twenty-first century paleontology and address five representative research topics. In doing so, I will characterize twenty-first century paleontology as a science that strives for more data, more technology, and more integration. Finally, I will outline what twenty-first-century paleontology might inherit from twentieth-century paleobiology: the pursuit of and plea for a new synthesis that could lead to a second paleobiological revolution. Following in the footsteps of the paleobiological revolution of the 1960s and 1970s, the paleobiological revolution of the twenty-first century would enable paleontologists to gain strong political representation and argue with a decisive voice at the "high table" on issues such as the expanded evolutionary synthesis, the conservation of Earth's environment, and global climate change.
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Affiliation(s)
- Marco Tamborini
- Department of Philosophy, Technische Universität Darmstadt, Marktplatz 15 (Residenzschloss), 64283 Darmstadt, Germany
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9
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Perricone V, Grun T, Raia P, Langella C. Paleomimetics: A Conceptual Framework for a Biomimetic Design Inspired by Fossils and Evolutionary Processes. Biomimetics (Basel) 2022; 7:biomimetics7030089. [PMID: 35892359 PMCID: PMC9326541 DOI: 10.3390/biomimetics7030089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/29/2022] [Accepted: 07/02/2022] [Indexed: 12/10/2022] Open
Abstract
In biomimetic design, functional systems, principles, and processes observed in nature are used for the development of innovative technical systems. The research on functional features is often carried out without giving importance to the generative mechanism behind them: evolution. To deeply understand and evaluate the meaning of functional morphologies, integrative structures, and processes, it is imperative to not only describe, analyse, and test their behaviour, but also to understand the evolutionary history, constraints, and interactions that led to these features. The discipline of palaeontology and its approach can considerably improve the efficiency of biomimetic transfer by analogy of function; additionally, this discipline, as well as biology, can contribute to the development of new shapes, textures, structures, and functional models for productive and generative processes useful in the improvement of designs. Based on the available literature, the present review aims to exhibit the potential contribution that palaeontology can offer to biomimetic processes, integrating specific methodologies and knowledge in a typical biomimetic design approach, as well as laying the foundation for a biomimetic design inspired by extinct species and evolutionary processes: Paleomimetics. A state of the art, definition, method, and tools are provided, and fossil entities are presented as potential role models for technical transfer solutions.
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Affiliation(s)
- Valentina Perricone
- Department of Engineering, University of Campania Luigi Vanvitelli, Via Roma 29, 81031 Aversa, Italy
- Correspondence:
| | - Tobias Grun
- Department of Invertebrate Palaeontology, University of Florida, Florida Museum, Dickinson Hall, Gainesville, FL 32611, USA;
| | - Pasquale Raia
- Department of Earth Sciences, Environment and Resources, University of Naples Federico II, Via Vicinale Cupa Cintia 26, 80126 Napoli, Italy;
| | - Carla Langella
- Department of Architecture and Industrial Design, University of Campania Luigi Vanvitelli, Via San Lorenzo, 81031 Aversa, Italy;
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10
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Gatesy SM, Manafzadeh AR, Bishop PJ, Turner ML, Kambic RE, Cuff AR, Hutchinson JR. A proposed standard for quantifying 3-D hindlimb joint poses in living and extinct archosaurs. J Anat 2022; 241:101-118. [PMID: 35118654 PMCID: PMC9178381 DOI: 10.1111/joa.13635] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 12/02/2021] [Accepted: 01/09/2022] [Indexed: 01/10/2023] Open
Abstract
The last common ancestor of birds and crocodylians plus all of its descendants (clade Archosauria) dominated terrestrial Mesozoic ecosystems, giving rise to disparate body plans, sizes, and modes of locomotion. As in the fields of vertebrate morphology and paleontology more generally, studies of archosaur skeletal structure have come to depend on tools for acquiring, measuring, and exploring three‐dimensional (3‐D) digital models. Such models, in turn, form the basis for many analyses of musculoskeletal function. A set of shared conventions for describing 3‐D pose (joint or limb configuration) and 3‐D kinematics (change in pose through time) is essential for fostering comparison of posture/movement among such varied species, as well as for maximizing communication among scientists. Following researchers in human biomechanics, we propose a standard methodological approach for measuring the relative position and orientation of the major segments of the archosaur pelvis and hindlimb in 3‐D. We describe the construction of anatomical and joint coordinate systems using the extant guineafowl and alligator as examples. Our new standards are then applied to three extinct taxa sampled from the wider range of morphological, postural, and kinematic variation that has arisen across >250 million years of archosaur evolution. These proposed conventions, and the founding principles upon which they are based, can also serve as starting points for measuring poses between elements within a hindlimb segment, for establishing coordinate systems in the forelimb and axial skeleton, or for applying our archosaurian system more broadly to different vertebrate clades.
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Affiliation(s)
- Stephen M Gatesy
- Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, Rhode Island, USA
| | - Armita R Manafzadeh
- Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, Rhode Island, USA
| | - Peter J Bishop
- Structure and Motion Laboratory, Department of Comparative Biomedical Sciences, Royal Veterinary College, Hatfield, UK.,Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Geosciences Program, Queensland Museum, Brisbane, Queensland, Australia
| | - Morgan L Turner
- Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, Rhode Island, USA.,Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Robert E Kambic
- Department of Biology, Hood College, Frederick, Maryland, USA
| | - Andrew R Cuff
- Structure and Motion Laboratory, Department of Comparative Biomedical Sciences, Royal Veterinary College, Hatfield, UK.,Human Anatomy Resource Centre, University of Liverpool, Liverpool, UK
| | - John R Hutchinson
- Structure and Motion Laboratory, Department of Comparative Biomedical Sciences, Royal Veterinary College, Hatfield, UK
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11
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Olroyd SL, LeBlanc ARH, Araújo R, Angielczyk KD, Duhamel A, Benoit J, Amaral M. Histology and μCT reveal the unique evolution and development of multiple tooth rows in the synapsid Endothiodon. Sci Rep 2021; 11:16875. [PMID: 34413357 PMCID: PMC8377087 DOI: 10.1038/s41598-021-95993-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/27/2021] [Indexed: 02/07/2023] Open
Abstract
Several amniote lineages independently evolved multiple rows of marginal teeth in response to the challenge of processing high fiber plant matter. Multiple tooth rows develop via alterations to tooth replacement in captorhinid reptiles and ornithischian dinosaurs, but the specific changes that produce this morphology differ, reflecting differences in their modes of tooth attachment. To further understand the mechanisms by which multiple tooth rows can develop, we examined this feature in Endothiodon bathystoma, a member of the only synapsid clade (Anomodontia) to evolve a multi-rowed marginal dentition. We histologically sampled Endothiodon mandibles with and without multiple tooth rows as well as single-rowed maxillae. We also segmented functional and replacement teeth in µ-CT scanned mandibles and maxillae of Endothiodon and several other anomodonts with 'postcanine' teeth to characterize tooth replacement in the clade. All anomodonts in our sample displayed a space around the tooth roots for a soft tissue attachment between tooth and jaw in life. Trails of alveolar bone indicate varying degrees of labial migration of teeth through ontogeny, often altering the spatial relationships of functional and replacement teeth in the upper and lower jaws. We present a model of multiple tooth row development in E. bathystoma in which labial migration of functional teeth was extensive enough to prevent resorption and replacement by newer generations of teeth. This model represents another mechanism by which multiple tooth rows evolved in amniotes. The multiple tooth rows of E. bathystoma may have provided more extensive contact between the teeth and a triturating surface on the palatine during chewing.
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Affiliation(s)
| | - Aaron R H LeBlanc
- Centre for Oral, Clinical & Translational Sciences, King's College London, London, UK
| | - Ricardo Araújo
- Instituto de Plasmas e Fusão Nuclear, Universidade de Lisboa, Lisbon, Portugal
| | - Kenneth D Angielczyk
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, USA
| | - Aliénor Duhamel
- Evolutionary Studies Institute, School of Geosciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Julien Benoit
- Evolutionary Studies Institute, School of Geosciences, University of the Witwatersrand, Johannesburg, South Africa
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12
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Cunningham JA. The use of photogrammetric fossil models in palaeontology education. Evolution 2021; 14:1. [PMID: 33456644 PMCID: PMC7804905 DOI: 10.1186/s12052-020-00140-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 12/24/2020] [Indexed: 11/16/2022]
Abstract
Photogrammetry allows overlapping photographs of fossils to be taken and converted into photo-realistic three-dimensional (3-D) digital models. These models offer potential advantages in teaching palaeontology: they are cheap to produce, can be easily shared and allow the study of rare and delicate specimens. Here I describe approaches for using photogrammetric models in the teaching and learning of palaeontology. Little is known about how students perceive these models and whether they find them valuable in their learning. To address this, first-year university students taught using both fossil specimens and digital models were surveyed about their experience through an anonymous online survey. Most students found that the digital models were easy to use, helped them understand anatomy and were more useful than studying photographs. However, most did not see the models as a substitute for studying real fossils and felt they could learn more from physical models. Digital models are a useful addition to palaeontological education that can supplement real fossils and allow palaeontological education to take place in circumstances where handling of specimens is not possible.
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Hu Y, Limaye A, Lu J. Three-dimensional segmentation of computed tomography data using Drishti Paint: new tools and developments. ROYAL SOCIETY OPEN SCIENCE 2020; 7:201033. [PMID: 33489265 PMCID: PMC7813226 DOI: 10.1098/rsos.201033] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/24/2020] [Indexed: 05/14/2023]
Abstract
Computed tomography (CT) has become very widely used in scientific and medical research and industry for its non-destructive and high-resolution means of detecting internal structure. Three-dimensional segmentation of computed tomography data sheds light on internal features of target objects. Three-dimensional segmentation of CT data is supported by various well-established software programs, but the powerful functionalities and capabilities of open-source software have not been fully revealed. Here, we present a new release of the open-source volume exploration, rendering and three-dimensional segmentation software, Drishti v. 2.7. We introduce a new tool for thresholding volume data (i.e. gradient thresholding) and a protocol for performing three-dimensional segmentation using the 3D Freeform Painter tool. These new tools and workflow enable more accurate and precise digital reconstruction, three-dimensional modelling and three-dimensional printing results. We use scan data of a fossil fish as a case study, but our procedure is widely applicable in biological, medical and industrial research.
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Affiliation(s)
- Yuzhi Hu
- Department of Applied Mathematics, Research School of Physics, Australian National University, Canberra, ACT 2601, Australia
- Research School of Earth Sciences, Australian National University, Canberra, ACT 2601, Australia
| | - Ajay Limaye
- National Computational Infrastructure, Building 143, Corner of Ward Road and Garran Road, Ward Rd, Canberra, ACT 2601, Australia
| | - Jing Lu
- Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, People's Republic of China
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Kozikowski P. Extracting Three-dimensional Information from SEM Images by Means of Photogrammetry. Micron 2020; 134:102873. [PMID: 32339977 DOI: 10.1016/j.micron.2020.102873] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/03/2020] [Accepted: 04/03/2020] [Indexed: 12/21/2022]
Abstract
Optical photogrammetry software has been applied to scanning electron microscope images to obtain 3D models and quantitative data on carbon particles and graphite nanoparticles. Image acquisition has been automated by the use of external macro software. Mesh data has been reconstructed from a number of images taken at multiple sample stage tilt angles with a supplementary measurement of TEM grids for method validation. This 3D model has been scaled and processed to obtain values such as the volume, height and surface area of the samples and has been quantitatively compared to 2D measurements.
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Affiliation(s)
- Paweł Kozikowski
- Central Institute for Labour Protection, National Research Institute, ul. Czerniakowska 16, 00-701, Warsaw, Poland.
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15
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Marcé-Nogué J, Liu J. Evaluating fidelity of CT based 3D models for Zebrafish conductive hearing system. Micron 2020; 135:102874. [PMID: 32388237 DOI: 10.1016/j.micron.2020.102874] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/04/2020] [Accepted: 04/05/2020] [Indexed: 01/25/2023]
Abstract
The zebrafish Weberian apparatus is an emerging model for human conductive hearing system. Their Weberian apparatus comprises minute bones and ligamentary links, and conducts sound pressure transmission from the gas bladder to inner ear through four pairs of Weberian ossicles along the vertebral column. We herein present a methodological study using MicroCT to image the Weberian apparatus for biomechanical and morphological analysis. The aim of this work is to evaluate computational models generated from multiple MicroCT scans with different parameters, to identify the most feasible scan combination for practical (minimized scan time) yet accurate (relative to highest resolution) biomechanical simulations. We segmented and created 3D models from CT scan image stacks at 4.64 μm, 5.05 μm, 9.30 μm and 13.08 μm voxel resolutions, respectively. Then, we used geometric morphometrics analysis to quantify inter-model shape differences, as well as a series of finite element modal and harmonic analyses to simulate auditory signal vibrations. Relative to the highest resolution and most accurate model, the Model 9.30 is closest in overall geometry and biomechanical behavior of all lower resolution models. The differences in resolution and quality of the CT substantially affect the segmentation and reconstruction process of the three-dimensional model of the ossicles, and the subsequent analyses. We conclude that scan voxel resolution is a key factor influencing outcomes of biomechanical simulations of delicate and minute structures, especially when studying the harmonic response of minute ossicles connected by ligaments using finite element modeling. Furthermore, contrast variations in CT images as determined by x-ray power and scan speed, also affect fidelity in 3D models and simulation outcomes.
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Affiliation(s)
- Jordi Marcé-Nogué
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, NY, USA; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Juan Liu
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, NY, USA.
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Tamborini M. Technoscientific approaches to deep time. STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE 2020; 79:57-67. [PMID: 32072926 DOI: 10.1016/j.shpsa.2019.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 02/14/2019] [Accepted: 03/05/2019] [Indexed: 06/10/2023]
Abstract
In this paper, I argue that in order to understand the process behind the knowledge production in the historical sciences, we should change our theoretical focus slightly to consider the historical sciences as technoscientific disciplines. If we investigate the intertwinement of technology and theory, we can provide new insights into historical scientific knowledge production, preconditions, and aims. I will provide evidence for my claim by showing the central features of paleontological and paleobiological data practices of the nineteenth and twentieth centuries. In order to work with something that is imperfect and incomplete (the fossil record), paleontologists used different technological devices. These devices process, extract, correct, simulate, and eventually present paleontological explananda. Therefore, the appearance of anatomical features of non-manipulable fossilized organisms, phenomena such as mass-extinctions, or the life-like display of extinct specimens in a museum's hall, depend both on the correct use of technological devices and on the interplay between these devices and theories. Consequently, in order to capture its underlying epistemology, historical sciences should be analyzed and investigated against other technoscientific disciplines such as chemistry, synthetic biology, and nanotechnology, and not necessarily only against classical experimental sciences. This approach will help us understand how historical scientists can obtain their epistemic access to deep time.
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Affiliation(s)
- Marco Tamborini
- Institut für Philosophie, Technische Universität Darmstadt, Karolinenplatz 5, 64289, Darmstadt, Germany.
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17
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Benoit J, Legendre LJ, Tabuce R, Obada T, Mararescul V, Manger P. Brain evolution in Proboscidea (Mammalia, Afrotheria) across the Cenozoic. Sci Rep 2019; 9:9323. [PMID: 31249366 PMCID: PMC6597534 DOI: 10.1038/s41598-019-45888-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/07/2019] [Indexed: 12/12/2022] Open
Abstract
As the largest and among the most behaviourally complex extant terrestrial mammals, proboscideans (elephants and their extinct relatives) are iconic representatives of the modern megafauna. The timing of the evolution of large brain size and above average encephalization quotient remains poorly understood due to the paucity of described endocranial casts. Here we created the most complete dataset on proboscidean endocranial capacity and analysed it using phylogenetic comparative methods and ancestral character states reconstruction using maximum likelihood. Our analyses support that, in general, brain size and body mass co-evolved in proboscideans across the Cenozoic; however, this pattern appears disrupted by two instances of specific increases in relative brain size in the late Oligocene and early Miocene. These increases in encephalization quotients seem to correspond to intervals of important climatic, environmental and faunal changes in Africa that may have positively selected for larger brain size or body mass.
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Affiliation(s)
- Julien Benoit
- Evolutionary Studies Institute (ESI), University of the Witwatersrand, Braamfontein, 2050, Johannesburg, South Africa.
| | - Lucas J Legendre
- Jackson School of Geosciences, The University of Texas at Austin, 2275 Speedway Stop C9000, Austin, TX, United States
| | - Rodolphe Tabuce
- Institut des Sciences de L'Evolution de Montpellier, Université Montpellier 2, Place Eugène Batillon, F-34095 Montpellier, cedex 05, Montpellier, France
| | - Theodor Obada
- Academy of Sciences of Moldova, Institute of Zoology, Chişinău, Moldova
| | | | - Paul Manger
- School of Anatomical Sciences, University of the Witwatersrand, 7 York Road, Parktown, 2193, Johannesburg, South Africa
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Moya-Costa R, Cuenca-Bescós G, Bauluz B. Protocol for the reconstruction of micromammals from fossils. Two case studies: The skulls of Beremendia fissidens and Dolinasorex glyphodon. PLoS One 2019; 14:e0213174. [PMID: 30893322 PMCID: PMC6426217 DOI: 10.1371/journal.pone.0213174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 02/15/2019] [Indexed: 11/25/2022] Open
Abstract
We have developed a protocol for reconstructing 3D models of the skulls of extinct species of small mammals. For the first time, the reconstruction uses fragments of fossils from a mixture of different specimens and from related extant species. We use free software and commercial computers to make the process reproducible and usable for the scientific community. We present a semi-quantitative protocol to face the problem of making 3D reconstructions of fossil species that are incomplete in the fossil record and/or represented by a mixture of different individuals, as usually occurs with small vertebrates. Therefore this approach is useful when no complete skull is available. The protocol combines the use of microCT scan technology with a subsequent computer treatment using different software tools for 3D reconstruction from microCT and 3D design and printing (e.g. Fiji, SPIERS, Meshlab, Meshmixer) in a defined order. This kind of free and relatively simple software, plus the detailed description, makes this protocol practicable for researchers who do not necessarily have great deal of experience in working with 3D. As an example, we have performed virtual reconstructions of the skulls of two species of insectivore small mammals (Eulipotyphla): Beremendia fissidens and Dolinasorex glyphodon. The resulting skulls, plus models of the extant shrews Blarina brevicauda, Neomys fodiens, Crocidura russula and Sorex coronatus, make it possible to compare characteristics that can only be observed by means of microCT 3D reconstructions, and given the characteristics of the material, using this protocol. Among the characters we can compare are the position of the mandibles, the spatial relations among all the teeth, the shape of the snout and, in general, all parameters related with the anatomy of the rostrum. Moreover, these reconstructions can be used in different types of context: for anatomical purposes, especially to see internal features or characteristics at whole-skull scale, for bioengineering, animation, or other techniques that need a digital model.
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Affiliation(s)
- Raquel Moya-Costa
- Aragosaurus-IUCA, Department of Earth Sciences, University of Zaragoza, Zaragoza, Spain
| | - Gloria Cuenca-Bescós
- Aragosaurus-IUCA, Department of Earth Sciences, University of Zaragoza, Zaragoza, Spain
| | - Blanca Bauluz
- Aragosaurus-IUCA, Department of Earth Sciences, University of Zaragoza, Zaragoza, Spain
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Landi F, O’Higgins P. Applying Geometric Morphometrics to Digital Reconstruction and Anatomical Investigation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1171:55-71. [DOI: 10.1007/978-3-030-24281-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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APPLICATIONS OF THREE-DIMENSIONAL BOX MODELING TO PALEONTOLOGICAL FUNCTIONAL ANALYSIS. ACTA ACUST UNITED AC 2017. [DOI: 10.1017/scs.2017.11] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
AbstractFunctional analysis through computer modeling can inform on how extinct organisms moved and fed, allowing us to test long-standing paleobiological hypotheses. Many such studies are based on digital models derived from computed tomography or surface scanning, but these methods are not appropriate for all fossils. Here, we show that box modeling—3-D modeling of complex shapes based on simple objects—can be used to reconstruct the morphology of various fossil specimens. Moreover, the results of computational functional analyses utilizing such models are very similar to those for models derived from tomographic or surface-based techniques. Box modeling is more broadly applicable than alternative methods for digitizing specimens; hence, there is great potential for this approach in paleontological functional analysis. Possible applications include large-scale comparative studies, analyses of hypothetical morphologies, and virtually restoring incomplete/distorted specimens.
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