Techniques for Virtual Palaeontology

Mark Sutton is a Senior Lecturer at Imperial College, London, UK specializing in Palaeozoic invertebrate palaeobiology and in three-dimensional visualization techniques. He is the primary author of the SPIERS software suite for palaeontological 3D reconstruction. Imran Rahman is a Research Fellow at The University of Bristol, UK.  He specializes in the origin and early evolution of echinoderms, and uses virtual palaeontology to study the form and function of fossil taxa. Russell Garwood is an 1851 Royal Commission Research Fellow based at The University of Manchester, UK. He uses X-ray techniques to study fossils, primarily early terrestrial arthropods. He is the secondary author of the SPIERS software suite.

• Acknowledgements viii1 Introduction and History 11.1 Introduction 11.2 Historical Development 41.2.1 Physical-Optical Tomography in the 20th Century 41.2.2 The CT Revolution 61.2.3 Modern Physical-Optical Tomography 71.2.4 Other Modern Tomographic Techniques 81.2.5 Surface-Based Techniques 91.2.6 Historical Summary 102 Destructive Tomography 142.1 Introduction 142.2 Physical-Optical Tomography 162.2.1 Approaches to Surface Exposure 162.2.2 Approaches to Imaging 192.2.3 Other Considerations for Methodology 232.2.4 Case Studies of Methodology 272.3 Focused Ion Beam Tomography 342.3.1 History 342.3.2 Principles and Practicalities 342.3.3 Examples in Palaeontology 362.3.4 Summary 373 Non-Destructive Tomography 413.1 Introduction 413.2 X-Ray Computed Tomography 423.2.1 Introduction to CT 423.2.2 History 433.2.3 X-Rays and Matter 463.2.4 X-Ray Microtomography 513.2.5 Medical Scanners 613.2.6 Lab-Based Nanotomography (Nano-CT) 633.2.7 Synchrotron Tomography 663.2.8 Tomographic Reconstruction 703.2.9 Artefacts 743.2.10 Phase-Contrast Tomography 783.2.11 Scanning Considerations 823.2.12 The Future: Three-Dimensional Elemental Mapping 833.2.13 Case Studies of Methodology 853.3 Neutron Tomography 893.3.1 History 903.3.2 Principles and Practicalities 903.3.3 Examples in Palaeontology 923.3.4 Summary 933.4 Magnetic Resonance Imaging 943.4.1 History 943.4.2 Principles and Practicalities 943.4.3 Examples in Palaeontology 963.4.4 Summary 973.5 Optical Tomography: Serial Focusing 983.5.1 History 983.5.2 Principles and Practicalities 983.5.3 Examples in Palaeontology 1013.5.4 Other Approaches 1023.5.5 Summary 1034 Surface-Based Methods 1154.1 Introduction 1154.2 Laser Scanning 1164.2.1 History 1164.2.2 Principles and Practicalities 1174.2.3 Case Studies of Methodology 1204.3 Photogrammetry 1224.3.1 History 1224.3.2 Principles and Practicalities 1224.3.3 Case Study of Methodology 1244.4 Mechanical Digitization 1255 Digital Visualization 1305.1 Introduction 1305.2 Reconstructing Tomographic Data 1325.2.1 Registered Tomographic Datasets 1325.2.2 Registration 1345.2.3 Vector Surfacing 1355.2.4 Volume Reconstructions 1375.3 Reconstructing Surface Data 1425.4 Visualization Methodologies 1425.4.1 Introduction 1425.4.2 Visualizing Triangle Meshes 1435.4.3 Direct Volume Rendering 1475.4.4 Direct Point-Cloud Rendering 1485.5 Software and Formats 1495.5.1 Reconstruction and Visualization Software 1495.5.2 Data Formats and File Formats 1525.6 Case Studies 1555.6.1 The Herefordshire Lagerstätte (Isosurfacing; SPIERS; Physical-Optical) 1555.6.2 Caecilian Amphibians (Isosurfacing; Amira; Synchrotron CT) 1595.6.3 Neoproterozoic Problematica (Vector Surfacing; Scripting; Physical-Optical) 1606 Applications beyond Visualization 1656.1 Introduction 1656.2 Geometric Morphometrics 1666.3 Dental Microwear Texture Analysis 1676.4 Biomechanical Modelling 1686.4.1 Finite-Element Analysis 1686.4.2 Multibody Dynamics Analysis 1716.4.3 Body-Size Estimation 1726.4.4 Computational Fluid Dynamics 173References 174Further Reading/Resources 1767 Summary 1777.1 Introduction 1777.2 Summary of Data-Capture Methodologies 1787.3 Recommendations for Method Selection 1827.4 Developments and Trends 1847.5 Concluding Remarks 187Index 188