Hostname: page-component-cd9895bd7-fscjk Total loading time: 0 Render date: 2024-12-25T06:22:02.355Z Has data issue: false hasContentIssue false
  • English
  • Français

VIRTUAL PALEONTOLOGY—AN OVERVIEW

Published online by Cambridge University Press:  27 April 2017

Mark Sutton ,
Imran Rahman  and
Russell Garwood
Mark Sutton
Affiliation:
Department of Earth Sciences and Engineering, Imperial College London, London SW7 2BP, UK 〈m.sutton@imperial.ac.uk〉
Imran Rahman
Affiliation:
Oxford University Museum of Natural History, Oxford OX1 3PW, UK 〈imran.rahman@oum.ox.ac.uk〉
Russell Garwood
Affiliation:
School of Earth, Atmospheric and Environmental Sciences, The University of Manchester, Manchester, M13 9PL, UK 〈russell.garwood@manchester.ac.uk〉
Get access

Abstract

Virtual paleontology is the study of fossils through three-dimensional digital visualizations; it represents a powerful and well-established set of tools for the analysis and dissemination of fossil data. Techniques are divisible into tomographic (i.e., slice-based) and surface-based types. Tomography has a long predigital history, but the recent explosion of virtual paleontology has resulted primarily from developments in X-ray computed tomography (CT), and of surface-based technologies (e.g., laser scanning). Destructive tomographic methods include forms of physical-optical tomography (e.g., serial grinding); these are powerful but problematic techniques. Focused Ion Beam (FIB) tomography is a modern alternative for microfossils; it is also destructive but is capable of extremely high resolutions. Nondestructive tomographic methods include the many forms of CT, which are the most widely used data-capture techniques at present, but are not universally applicable. Where CT is inappropriate, other nondestructive technologies (e.g., neutron tomography, magnetic resonance imaging, optical tomography) can prove suitable. Surface-based methods provide portable and convenient data capture for surface topography and texture, and might be appropriate when internal morphology is not of interest; technologies include laser scanning, photogrammetry, and mechanical digitization. Reconstruction methods that produce visualizations from raw data are many and various; selection of an appropriate workflow will depend on many factors, but is an important consideration that should be addressed prior to any study. The vast majority of three-dimensional fossils can now be studied using some form of virtual paleontology, and barriers to broader adaptation are being eroded. Technical issues regarding data sharing remain problematic. Technological developments continue; those promising tomographic recovery of compositional data are of particular relevance to paleontology.

Type
Research Article
Information
The Paleontological Society Papers , Volume 22: Virtual Paleontology , September 2016 , pp. 1 - 20
Copyright
Copyright © 2017, The Paleontological Society 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Abel, R.L., Laurini, C., and Richter, M., 2012, A palaeobiologist’s guide to ‘virtual’ micro-CT preparation: Palaeontologia Electronica, v. 15, no. 2, 17 p.Google Scholar
Ager, D.V., 1965, Serial grinding techniques, in Kummel, B., and Raup, D., eds., Handbook of Palaeontological Techniques: San Francisco, California, Freeman, p. 212–224.Google Scholar
Albani, A.E., Bengtson, S., Canfield, D.E., Bekker, A., Macchiarelli, R., Mazurier, A., Hammarlund, E.U., Boulvais, P., Dupuy, J.-J., Fontaine, C., Fürsich, F.T., Gauthier-Lafaye, F., Janvier, P., Javaux, E., Ossa Ossa, F., Pierson-Wickmann, A.-C., Riboulleau, A., Sardini, P., Vachard, D., Whitehouse, M., and Meunier, A., 2010, Large colonial organisms with coordinated growth in oxygenated environments 2.1 Gyr ago: Nature, v. 466, p. 100–104.CrossRefGoogle ScholarPubMed
Antcliffe, J.B., and Brasier, M.D., 2011, Fossils with little relief: Using lasers to conserve, image, and analyse the Ediacara biota, in Laflamme, M., Schiffbauer, J.D., and Dornbos, S.Q., eds., Quantifying the Evolution of Early Life: Numerical Approaches to the Evaluation of Fossils and Ancient Ecosystems: Dordrecht, The Netherlands, Springer, p. 223–240.CrossRefGoogle Scholar
Ascaso, C., Wierzchos, J., Corral, J.C., López, R., and Alonso, J., 2003, New applications of light and electron microscopic techniques for the study of microbiological inclusions in amber: Journal of Paleontology, v. 77, p. 1182–1192.2.0.CO;2>CrossRefGoogle Scholar
Bates, K.T., Rarity, F., Manning, P.L., Hodgetts, D., Vial, B., Oms, O., Galobart, A., and Gawthorpe, R.L., 2008, High-resolution LiDAR and photogrammetric survey of the Fumanya dinosaur tracksites (Catalonia): Implications for the conservation and interpretation of geological heritage sites: Journal of the Geological Society of London, v. 165, p. 115–127.CrossRefGoogle Scholar
Bates, K.T., Breithaupt, B.H., Falkingham, P.L., Matthews, N., Hodgetts, D., and Manning, P.K., 2009a, Integrated LiDAR and photogrammetric documentation of the Red Gulch dinosaur tracksite (Wyoming, USA), in Foss, S.E., Cavin, J.L., Brown, T., Kirkland, J.I., and Santucci, V.L., eds., Proceedings of the Eighth Conference on Fossil Resources: Salt Lake City, Utah Geological Survey, p. 101–103.Google Scholar
Bates, K.T., Manning, P.L., Hodgetts, D., and Sellers, W.I., 2009b, Estimating mass properties of dinosaurs using laser imaging and 3D computer modelling: PLoS ONE, v. 4(2), e4532, DOI: 10.1371/journal.pone.0004532.CrossRefGoogle ScholarPubMed
Béthoux, O., McBride, J., and Maul, C., 2004, Surface laser scanning of fossil insect wings: Palaeontology, v. 47, p. 13–19.CrossRefGoogle Scholar
Brasier, M.D., Antcliffe, J., Saunders, M., and Wacey, D., 2015, Changing the picture of Earth’s earliest fossils (3.5–1.9Ga) with new approaches and new discoveries: Proceedings of the National Academy of Sciences, v. 112, p. 4859–4864.CrossRefGoogle ScholarPubMed
Breithaupt, B.H., and Matthews, N.A., 2001, Preserving paleontological resources using photogrammetry and geographic information systems, in Harmon, D., ed., Crossing Boundaries in Park Management: Proceedings of the 11th Conference on Research and Resource Management in Parks and Public Lands: Hancock, Michigan, The George Wright Society, p. 62–70.Google Scholar
Briggs, D.E.G., Siveter, David J., Siveter, Derek J., and Sutton, M.D., 2008, Virtual fossils from a 425 million-year-old volcanic ash: American Scientist, v. 96, p. 474–481.CrossRefGoogle Scholar
Callaway, E., 2011, Fossil data enter the web period: Nature, v. 472, p. 150.CrossRefGoogle ScholarPubMed
Chapman, R.E., 1989, Computer assembly of serial sections, in Feldmann, M., Chapman, R., and Hannibal, J.T., eds., Paleotechniques: The Paleontological Society Special Publication, v. 4, p. 157–164.Google Scholar
Clark, N.D.L., Adams, C., Lawton, T., Cruickshank, A.R., and Woods, K., 2004, The Elgin marvel: Using magnetic resonance imaging to look at a mouldic fossil from the Permian of Elgin, Scotland, UK: Magnetic Resonance Imaging, v. 22, p. 269–273.CrossRefGoogle Scholar
Croft, W.N., 1950, A parallel grinding instrument for the investigation of fossils by serial sections: Journal of Paleontology, v. 24, p. 693–698.Google Scholar
Donoghue, P.C.J., Bengtson, S., Dong, X., Gostling, N.J., Huldtgren, T., Cunningham, J.A., Yin, C., Yue, Z., Peng, F., and Stampanoni, M., 2006, Synchrotron X-ray tomographic microscopy of fossil embryos: Nature, v. 442, p. 680–683.CrossRefGoogle ScholarPubMed
Falkingham, P.L., 2012, Acquisition of high resolution 3D models using free, open-source, photogrammetric software: Palaeontologia Electronica, v. 15, no. 1, 15 p.Google Scholar
Galtier, J., and Phillips, T., 1999, The acetate peel technique, in Jones, T.P., and Rowe, N.P., eds., Fossil Plants and Spores: London, The Geological Society, p. 67–70.Google Scholar
Green, D.J., and Alemseged, Z., 2012, Australopithecus afarensis scapular ontogeny, function, and the role of climbing in human evolution: Science, v. 338, p. 514–517.CrossRefGoogle ScholarPubMed
Hagadorn, J.W., Xiao, S., Donoghue, P.C.J., Bengtson, S., Gostling, N.J., Pawlowska, M., Raff, E.C., Raff, R.A., Turner, F.R., Chongyu, Y., Zhou, C., Yuan, X., McFeely, M.B., Stampanoni, M., and Nealson, K.H., 2006, Cellular and subcellular structure of Neoproterozoic animal embryos: Science, v. 314, p. 291–294.CrossRefGoogle ScholarPubMed
Hammer, Ø., 1999, Computer-aided study of growth patterns in tabulate corals, exemplified by Catenipora heintzi from Ringerike, Oslo Region: Norsk Geologisk Tidsskrift, v. 79, p. 219–226.CrossRefGoogle Scholar
Hammer, Ø., Bengtson, S., Malzbender, T., and Gelb, D., 2002, Imaging fossils using reflectance transformation and interactive manipulation of virtual light sources: Palaeontologia Electronica, v. 5, no. 4, 9 p.Google Scholar
Haring, A., Exner, U., and Harzhauser, M., 2009, Surveying a fossil oyster reef using terrestrial laser scanning [abs.]: Geophysical Research Abstracts, v. 11, p. 10714.Google Scholar
Haubitz, B., Prokop, M., Doehring, W., Ostrom, J.H., and Wellnhofer, P., 1988, Computed tomography of Archaeopteryx : Palaeobiology, v. 14, p. 206–213.CrossRefGoogle Scholar
Haug, J.T., Briggs, D.E.G., and Haug, C., 2012, Morphology and function in the Cambrian Burgess Shale megacheiran arthropod Leanchoilia superlata and the application of a descriptive matrix: BMC Evolutionary Biology, v. 12, p. 162.CrossRefGoogle ScholarPubMed
Herbert, M.J., 1999, Computer-based serial section reconstruction, in Harper, D.A.T., ed., Numerical Palaeobiology: Computer-Based Modelling and Analysis of Fossils and their Distributions: Chichester, UK, Wiley, p. 93–126.Google Scholar
Hickman-Lewis, K., Garwood, R.J., Brasier, M.D., McLoughlin, N., Goral, T., Jiang, H., and Wacey, D., In press, Carbonaceous microstructures of the 3.46Ga stratiform ‘Apex chert,’ Chinaman Creek locality, Pilbara, Western Australia: Precambrian Research.Google Scholar
Kamenz, C., Dunlop, J.A., Scholtz, G., Kerp, H., and Hass, H., 2008, Microanatomy of Early Devonian book lungs: Biology Letters, v. 4, p. 212–215.CrossRefGoogle ScholarPubMed
Kearsley, A.T., Burchell, M.J., Graham, G.A., Hörz, F., Wozniakiewicz, P.A., and Cole, M.J., 2007, Cometary dust characteristics: Comparison of stardust craters with laboratory impacts: 38th Lunar and Planetary Science Conference, Houston: Houston, Texas, National Aeronautics and Space Administration, p. 1562.Google Scholar
Kermack, D.M., 1970, True serial-sectioning of fossil material: Biological Journal of the Linnean Society, v. 2, p. 47–53.CrossRefGoogle Scholar
Ketcham, R.A., and Carlson, W.D., 2001, Acquisition, optimization and interpretation of X-ray computed tomographic imagery: Applications to the geosciences: Computers & Geosciences, v. 27, p. 381–400.CrossRefGoogle Scholar
Kielan-Jaworowska, Z., Presley, R., and Poplin, C.A., 1986, The cranial vascular system in taeniolabidoid multituberculate mammals: Philosophical Transactions of the Royal Society of London, Series B, Biological Sciences, v. 313, p. 525–602.Google Scholar
Kraus, K., 2007, Photogrammetry: Geometry from Images and Laser Scans, 2nd edition., Berlin, Walter de Gruyter, 459 p.CrossRefGoogle Scholar
Laaß, M., and Schillinger, B., 2015, Reconstructing the auditory apparatus of therapsids by means of neutron tomography: Physics Procedia, v. 69, p. 628–635.CrossRefGoogle Scholar
Lichtenbelt, B., Crane, R., and Naqvi, S., 1998, Introduction to Volume Rendering: Upper Saddle River, New Jersey, Prentice Hall, 236 p.Google Scholar
Long, A.G., 1960, Stamnostoma huttonense gen. et sp. nov. a pteridosperm seed and cupule from the Calciferous Sandstone series of Berwickshire: Transactions of the Royal Society of Edinburgh, v. 64, p. 201–215.CrossRefGoogle Scholar
Lorensen, W.E., and Cline, H.E., 1987, Marching Cubes: A high resolution 3D surface construction algorithm: Computer Graphics, v. 21, p. 163–169.CrossRefGoogle Scholar
Lyons, P.D., Rioux, M., and Patterson, R.T., 2000, Application of a three-dimensional color laser scanner to paleontology: An interactive model of a juvenile Tylosaurus sp. basisphenoid-basioccipital: Palaeontologia Electronica, v. 3, no. 2, 16 p.Google Scholar
Ma, L., Taylor, K.G., Lee, P.D., Dobson, K.J., Dowey, P.J., and Courtois, L., 2016, Novel 3D centimetre-to nano-scale quantification of an organic-rich mudstone: The Carboniferous Bowland Shale, northern England: Marine and Petroleum Geology, v. 72, p. 193–205.CrossRefGoogle Scholar
Maisey, J.G., 1975, A serial sectioning technique for fossils and hard tissues: Curator, v. 18, p. 140–147.CrossRefGoogle Scholar
Mallison, H., Hohloch, A., and Pfretzschner, H., 2009, Mechanical digitizing for paleontology—New and improved techniques: Palaeontologia Electronica, v. 12, no. 2, 41 p.Google Scholar
Maloof, A.C., Rose, C.V., Beach, R., Samuels, B.M., Calmet, C.C., Erwin, D.H., Poirer, G.R., Yao, N., and Simons, F.J., 2010, Possible animal-body fossils in pre-Marinoan limestones from South Australia: Nature Geoscience, v. 3, p. 653–659.CrossRefGoogle Scholar
Mietchen, D., Aberhan, M., Manz, B., Hampe, O., Mohr, B., Neumann, C., and Volke, F., 2008, Three-dimensional magnetic resonance imaging of fossils across taxa: Biogeosciences, v. 5, p. 25–41.CrossRefGoogle Scholar
Muir-Wood, H.M., 1934, On the internal structure of some Mesozoic Brachiopoda: Philosophical Transactions of the Royal Society of London, Series B, v. 223, p. 511–567.Google Scholar
Orr, P.J., Siveter, Derek J., Briggs, D.E.G., Siveter, David J., and Sutton, M. D., 2000, A new arthropod from the Silurian Konservat-Lagerstätte of Herefordshire, UK: Proceedings of the Royal Society B, v. 267, p. 1497–1504.CrossRefGoogle ScholarPubMed
Phaneuf, M.W., 1999, Applications of focused ion beam microscopy to materials science specimens: Micron, v. 30, p. 277–288.CrossRefGoogle Scholar
Platt, B.F., Hasiotis, S.T., and Hirmas, D.R., 2010, Use of low-cost multistripe laser triangulation (MLT) scanning technology for three-dimensional quantitative paleoichnological and neoichnological studies: Journal of Sedimentary Research, v. 80, p. 590–610.CrossRefGoogle Scholar
Poplin, C.M., and Ricqles, A. de, 1970, A technique of serial sectioning for the study of undecalcified fossils: Curator, v. 13, p. 7–20.CrossRefGoogle Scholar
Rahman, I.A., Adcock, K., and Garwood, R.J., 2012, Virtual fossils: A new resource for science communication in paleontology: Evolution: Education and Outreach, v. 5, p. 635–641.CrossRefGoogle Scholar
Rahman, I.A., Zamora, S., Falkingham, P.L., and Phillips, J.C., 2015, Cambrian cinctan echinoderms shed light on feeding in the ancestral deuterostome: Proceedings of the Royal Society, Series B, v. 282, art. 20151964, DOI: 10.1098/rspb.2015.1964.Google ScholarPubMed
Rayfield, E.J., 2007, Finite Element Analysis and understanding the biomechanics and evolution of living and fossil organisms: Annual Review of Earth and Planetary Sciences, v. 35, p. 541–576.CrossRefGoogle Scholar
Reingruber, H., Zankel, A., Mayrhofer, P., and Poelt, P., 2011, Quantitative characterization of microfiltration membranes by 3D reconstruction: Journal of Membrane Science, v. 372, p. 66–74.CrossRefGoogle Scholar
Remondino, F., Rizzi, A., Girardi, S., Petti, F.M., and Avanzini, M., 2010, 3D ichnology—Recovering digital 3D models of dinosaur footprints: The Photogrammetric Record, v. 25, p. 266–282.CrossRefGoogle Scholar
Rowe, T.B., Colbert, M., Ketcham, R.A., Maisano, J., and Owen, P., 2001, High-resolution X-ray computed tomography in vertebrate morphology: Journal of Morphology, v. 248, p. 277–278.Google Scholar
Salman, N., Yvinec, M., and Merigot, Q., 2010, Feature preserving mesh generation from 3D point clouds: Computer Graphics Forum, v. 29, p. 1623–1632.CrossRefGoogle Scholar
Schiffbauer, J.D., and Xiao, S., 2009, Novel application of focused ion beam electron microscopy (FIB-EM) in preparation and analysis of microfossil ultrastructures: A new view of complexity in early eukaryotic organisms: Palaios, v. 24, p. 616–626.CrossRefGoogle Scholar
Schiffbauer, J.D., and Xiao, S., 2011, Paleobiological applications of focused ion beam electron microscopy (FIB-EM): An ultrastructural approach to the (micro)fossil record, in Laflamme, M., Schiffbauer, J.D., and Dornbos, S.Q., eds., Quantifying the Evolution of Early Life: Numerical Approaches to the Evaluation of Fossils and Ancient Ecosystems: Dordrecht, The Netherlands, Springer, p. 321–354.CrossRefGoogle Scholar
Schopf, J.W., and Kudryavtsev, A.B., 2009, Confocal laser scanning microscopy and Raman imagery of ancient microscopic fossils: Precambrian Research, v. 173, p. 39–49.CrossRefGoogle Scholar
Schwarz, D., Vontobel, P.L., Eberhard, H., Meyer, C.A., and Bongartz, G., 2005, Neutron tomography of internal structures of vertebrate remains: A comparison with X-ray computed tomography: Paleontologia Electronica, v. 8, no. 2, 11 p.Google Scholar
Scott, A.C., and Hemsley, A.R., 1991, A comparison of new microscopical techniques for the study of fossil spore wall ultrastructure: Review of Palaeobotany and Palynology, v. 67, p. 133–139.CrossRefGoogle Scholar
Shi, C.S., Schopf, J.W., and Kudryavtsev, A.B., 2013, Characterization of the stem anatomy of the Eocene fern Dennstaedtiopsis aerenchymata (Dennstaedtiaceae) by use of confocal laser scanning microscopy: American Journal of Botany, v. 100, p. 1626–1640.CrossRefGoogle ScholarPubMed
Sollas, W.J., 1903, A method for the investigation of fossils by serial sections: Philosophical Transactions of the Royal Society of London, Series B, v. 196, p. 259–265.Google Scholar
Stensiö, E.A., 1927, The Downtonian and Devonian vertebrates of Spitzbergen: Skrifter om Svalbard og Nordishavet, v. 12, 391 p.Google Scholar
Stoinski, S., 2011, From a skeleton to a 3D dinosaur, in Elewa, A.M.T., ed., Computational Paleontology: Berlin, Springer, p. 147–164.CrossRefGoogle Scholar
Strasser, B.J., 2008, GenBank—Natural history in the 21st century?: Science, v. 322, p. 537–538.CrossRefGoogle Scholar
Sutton, M.D., 2008, Tomographic techniques for the study of exceptionally preserved fossils: Proceedings of the Royal Society, Series B, v. 275, p. 1587–1593.Google Scholar
Sutton, M.D., Briggs, D.E.G., Siveter, David J., and Siveter, Derek J., 2001a, An exceptionally preserved vermiform mollusc from the Silurian of England: Nature, v. 410, p. 461–463.CrossRefGoogle ScholarPubMed
Sutton, M.D., Briggs, D.E.G., Siveter, David J., and Siveter, Derek J., 2001b, Methodologies for the visualization and reconstruction of three-dimensional fossils from the Silurian Herefordshire Lagerstätte: Palaeontologia Electronica, v. 4, no. 1, 17 p.Google Scholar
Sutton, M.D., Garwood, R.J., Siveter, David J., and Siveter, Derek J., 2012, SPIERS and VAXML: A software toolkit for tomographic visualisation, and a format for virtual specimen interchange: Palaeontologia Electronica, v. 15, no. 2, 14 p.Google Scholar
Sutton, M.D., Rahman, I.A., and Garwood, R.J., 2014, Techniques for Virtual Palaeontology: Oxford, UK, Wiley-Blackwell, 208 p.Google Scholar
Tafforeau, P., Boistel, R., Boller, E., Bravin, A., Brunet, M., Chaimanee, Y., Cloetens, P., Feist, M., Hoszowska, J., Jaeger, J.-J., Kay, R.F., Lazzari, V., Marivaux, L., Nel, A., Nemoz, C., Thibault, X., Vignaud, P., and Zabler, S., 2006, Applications of X-ray synchrotron microtomography for non-destructive 3D studies of paleontological specimens: Applied Physics A, v. 83, p. 195–202.CrossRefGoogle Scholar
Tate, J.R., and Cann, C.E., 1982, High-resolution computed tomography for the comparative study of fossil and extant bone: American Journal of Physical Anthropology, v. 58, p. 67–73.CrossRefGoogle ScholarPubMed
Uchic, M.D., Holzer, L., Inkson, B.J., Principe, E.L., and Munroe, P., 2007, Three-dimensional microstructural characterization using focused ion beam tomography: MRS Bulletin, v. 32, p. 408–416.CrossRefGoogle Scholar
Volkert, C.A., and Minor, A.M., 2007, Focused ion beam microscopy and micromachining: MRS Bulletin, v. 32, p. 389–399.CrossRefGoogle Scholar
Wacey, D., Menon, S., Green, L., Gerstmann, D., Kong, C., Mcloughlin, N., Saunders, M., and Brasier, M., 2012, Taphonomy of very ancient microfossils from the ~3400 Ma Strelley Pool Formation and ~1900 Ma Gunflint Formation: New insights using a focused ion beam: Precambrian Research, v. 220–221, p. 234–250.CrossRefGoogle Scholar
Watters, W.A., and Grotzinger, J.P., 2001, Digital reconstruction of calcified early metazoans, terminal Proterozoic Nama Group, Namibia: Paleobiology, v. 27, p. 159–171.2.0.CO;2>CrossRefGoogle Scholar
Wilhite, R., 2003, Digitizing large fossil skeletal elements for three-dimensional applications: Palaeontologia Electronica, v. 5, no. 2, 10 p.Google Scholar
Winkler, B., 2006, Applications of neutron radiography and neutron tomography: Reviews in Mineralogy and Geochemistry, v. 63, p. 459–471.CrossRefGoogle Scholar
Zhang, G., Tsou, Y., and Rosenberger, A.L., 2000, Reconstruction of the Homunculus skull using a combined scanning and stereolithography process: Rapid Prototyping Journal, v. 6, p. 267–275.CrossRefGoogle Scholar