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Techniques for Virtual Palaeontology

ISBN: 978-1-118-59113-0
208 pages
January 2014, Wiley-Blackwell
Techniques for Virtual Palaeontology (1118591135) cover image

Description

Virtual palaeontology, the use of interactive three-dimensional digital models as a supplement or alternative to physical specimens for scientific study and communication, is rapidly becoming important to advanced students and researchers. Using non-invasive techniques, the method allows the capture of large quantities of useful data without damaging the fossils being studied

Techniques for Virtual Palaeontology guides palaeontologists through the decisions involved in designing a virtual palaeontology workflow and gives a comprehensive overview, providing discussions of underlying theory, applications, historical development, details of practical methodologies, and case studies. Techniques covered include physical-optical tomography (serial sectioning), focused ion beam tomography, all forms of X-ray CT, neutron tomography, magnetic resonance imaging, optical tomography, laser scanning, and photogrammetry. Visualization techniques and data/file formats are also discussed in detail.

Readership: All palaeontologists and students interested in three-dimensional visualization and analysis.

New Analytical Methods in Earth and Environmental Science

Because of the plethora of analytical techniques now available, and the acceleration of technological advance, many earth scientists find it difficult to know where to turn for reliable information on the latest tools at their disposal, and may lack the expertise to assess the relative strengths or limitations of a particular technique. This new series will address these difficulties by providing accessible introductions to important new techniques, lab and field protocols, suggestions for data handling and interpretation, and useful case studies. The series represents an invaluable and trusted source of information for researchers, advanced students and applied earth scientists wishing to familiarise themselves with emerging techniques in their field.

All titles in this series are available in a variety of full-colour, searchable eBook formats. Titles are also available in an enhanced eBook edition which may include additional features such as DOI linking, high resolution graphics and video.

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Table of Contents

Acknowledgements viii

1 Introduction and History 1

1.1 Introduction 1

1.2 Historical Development 4

1.2.1 Physical-Optical Tomography in the 20th Century 4

1.2.2 The CT Revolution 6

1.2.3 Modern Physical-Optical Tomography 7

1.2.4 Other Modern Tomographic Techniques 8

1.2.5 Surface-Based Techniques 9

1.2.6 Historical Summary 10

2 Destructive Tomography 14

2.1 Introduction 14

2.2 Physical-Optical Tomography 16

2.2.1 Approaches to Surface Exposure 16

2.2.2 Approaches to Imaging 19

2.2.3 Other Considerations for Methodology 23

2.2.4 Case Studies of Methodology 27

2.3 Focused Ion Beam Tomography 34

2.3.1 History 34

2.3.2 Principles and Practicalities 34

2.3.3 Examples in Palaeontology 36

2.3.4 Summary 37

3 Non-Destructive Tomography 41

3.1 Introduction 41

3.2 X-Ray Computed Tomography 42

3.2.1 Introduction to CT 42

3.2.2 History 43

3.2.3 X-Rays and Matter 46

3.2.4 X-Ray Microtomography 51

3.2.5 Medical Scanners 61

3.2.6 Lab-Based Nanotomography (Nano-CT) 63

3.2.7 Synchrotron Tomography 66

3.2.8 Tomographic Reconstruction 70

3.2.9 Artefacts 74

3.2.10 Phase-Contrast Tomography 78

3.2.11 Scanning Considerations 82

3.2.12 The Future: Three-Dimensional Elemental Mapping 83

3.2.13 Case Studies of Methodology 85

3.3 Neutron Tomography 89

3.3.1 History 90

3.3.2 Principles and Practicalities 90

3.3.3 Examples in Palaeontology 92

3.3.4 Summary 93

3.4 Magnetic Resonance Imaging 94

3.4.1 History 94

3.4.2 Principles and Practicalities 94

3.4.3 Examples in Palaeontology 96

3.4.4 Summary 97

3.5 Optical Tomography: Serial Focusing 98

3.5.1 History 98

3.5.2 Principles and Practicalities 98

3.5.3 Examples in Palaeontology 101

3.5.4 Other Approaches 102

3.5.5 Summary 103

4 Surface-Based Methods 115

4.1 Introduction 115

4.2 Laser Scanning 116

4.2.1 History 116

4.2.2 Principles and Practicalities 117

4.2.3 Case Studies of Methodology 120

4.3 Photogrammetry 122

4.3.1 History 122

4.3.2 Principles and Practicalities 122

4.3.3 Case Study of Methodology 124

4.4 Mechanical Digitization 125

5 Digital Visualization 130

5.1 Introduction 130

5.2 Reconstructing Tomographic Data 132

5.2.1 Registered Tomographic Datasets 132

5.2.2 Registration 134

5.2.3 Vector Surfacing 135

5.2.4 Volume Reconstructions 137

5.3 Reconstructing Surface Data 142

5.4 Visualization Methodologies 142

5.4.1 Introduction 142

5.4.2 Visualizing Triangle Meshes 143

5.4.3 Direct Volume Rendering 147

5.4.4 Direct Point-Cloud Rendering 148

5.5 Software and Formats 149

5.5.1 Reconstruction and Visualization Software 149

5.5.2 Data Formats and File Formats 152

5.6 Case Studies 155

5.6.1 The Herefordshire Lagerstätte (Isosurfacing; SPIERS; Physical-Optical) 155

5.6.2 Caecilian Amphibians (Isosurfacing; Amira; Synchrotron CT) 159

5.6.3 Neoproterozoic Problematica (Vector Surfacing; Scripting; Physical-Optical) 160

6 Applications beyond Visualization 165

6.1 Introduction 165

6.2 Geometric Morphometrics 166

6.3 Dental Microwear Texture Analysis 167

6.4 Biomechanical Modelling 168

6.4.1 Finite-Element Analysis 168

6.4.2 Multibody Dynamics Analysis 171

6.4.3 Body-Size Estimation 172

6.4.4 Computational Fluid Dynamics 173

References 174

Further Reading/Resources 176

7 Summary 177

7.1 Introduction 177

7.2 Summary of Data-Capture Methodologies 178

7.3 Recommendations for Method Selection 182

7.4 Developments and Trends 184

7.5 Concluding Remarks 187

Index 188

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Author Information

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.

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Reviews

“The authors have produced a well-organized volume that is easily accessible to both professionals and nonprofessionals and will likely be cited as an introductory source as virtual technologies in paleontology continue to emerge.”  (The Quarterly Review of Biology, 1 October 2015)

“Techniques for Virtual Palaeontology thus provides an excellent background for students who are likely to encounter virtual techniques as they embark on a palaeontological career. It also successfully informs more established palaeontologists who either plan to enter the field or, like me, dabble in 3D but would like more background information. It is a valuable addition to the palaeontological bookshelf.”  (Geological Journal, 1 May 2015)  

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