Virtual reconstruction: a primer in computer-assisted paleontology and biomedicine

Abstract

Preface. Acknowledgments. Introduction. 1. Virtual Reconstruction. 1.1 A Virtual Reality Contest. 1.2 Virtual Reconstruction. 1.3 Computer-Assisted Paleontology. 1.3.1 Data Acquisition. 1.3.2 Data Segmentation and Three-Dimensional Reconstruction. 1.3.3 Virtual Fossil Reconstruction. 1.3.4 From Virtual Reality to Real Virtuality. 1.3.5 Databases and Morphometry. 1.3.6 Virtual Reconstruction in Space and Time. 1.4 Computer-Assisted Surgery. 1.5 Further Reading. 2. Data Representation. 2.1 World Food on a Chessboard. 2.2 Facts About Data to Get Data About Facts. 2.2.1 Analog and Digital Data. 2.2.2 Bits, Bytes, and Words. 2.2.3 Characters, Numbers, Pixels, and Voxels. 2.2.4 Representing Gray Tones and Colors. 2.2.5 Data Compression. 2.2.6 Some Common Image File Formats. 2.2.7 Implicit Versus Explicit Representation of Object Data. 2.2.8 Modeling Three-Dimensional Objects. 2.3 A Taxonomy of Biomedical Data. 2.3.1 Perspectives on Data. 2.3.2 Volume Data. 2.3.3 Surface Data. 2.3.4 Landmark Data. 2.3.5 Extent-Based Data. 2.3.6 Relational Data. 2.4 Further Reading. 3. Data Acquisition. 3.1 Data and the Physical World. 3.2 Vision and Photography as Data Acquisition: Performance Considerations. 3.3 Computed Tomography. 3.3.1 Frau RAntgena s Wedding Ring. 3.3.2 Radiographic Projections. 3.3.3 Reconstructing CT Images. 3.3.4 CT Scanning: Technical Considerations. 3.3.5 Limitations of CT Data Acquisition. 3.3.6 Slice-to-Slice, Helical, and Multislice CT. 3.3.7 Industrial and Micro Computed Tomography. 3.3.8 Three-Dimensional Data Acquisition with a Medical Scanner. 3.4 Magnetic Resonance Imaging. 3.5 Surface Scanners. 3.6 3D Digitizers. 3.7 Further Reading. 4. Image Data Processing. 4.1 Recovering Objects from Images. 4.2 Converting a CT Image into a Screen Image. 4.3 Filtering Images. 4.3.1 Coffee and Kernels. 4.3.2 Convolution and Fourier Analysis. 4.3.3 Statistical Filters. 4.3.4 Edge Detection Filters. 4.4 Extracting Isosurfaces. 4.4.1 Determining Boundaries in CT Images. 4.4.2 From Edges to Isocontours and Isosurfaces. 4.5 Interactive Segmentation. 4.6 Further Reading. 5. Visualization and Interaction. 5.1 Visualizing Data in Two and More Dimensions. 5.2 Interaction with Virtual Worlds. 5.3 The Graphics Rendering Pipeline. 5.4 Setting Up a Virtual Environment. 5.4.1 Object Materials, Lighting, and Shading. 5.4.2 Setting Up the Camera. 5.4.3 Object Manipulation and Interaction. 5.5 Volume Rendering. 5.6 Further Reading. 6. Virtual Fossil Reconstruction. 6.1 A Baroque Puzzle. 6.2 Principles of Reconstruction. 6.3 Physical and Virtual Reconstruction. 6.4 Preparing and Restoring Fossils on the Computer Screen. 6.5 Reconstructing Fossil Morphologies. 6.5.1 Recovering Implicit Anatomic Information. 6.5.2 Combining Computer Graphics and Anatomy: The Globe Paradigm. 6.5.3 Inferring Missing Information. 6.5.4 Interpolation and Extrapolation. 6.6 Correcting Fossil Deformation. 6.6.1 Taphonomic Scenarios. 6.6.2 Correcting Plastic Deformation. 6.7 Validating Virtual Reconstructions. 6.8 Paleodiagnostics and Paleoforensics. 6.9 Inferring Soft Tissue Structures. 6.9.1 Motivation. 6.9.2 Fossil Soft Tissue Reconstruction: Classic and Virtual Approaches. 6.9.3 What Shall Be Reconstructed? 6.9.4 Soft Tissue Reconstruction and Measurement. 6.10 Virtual Surgery: A Paleoanthropologista s Eye View. 6.10.1 Motivation. 6.10.2 Virtual Planning and Simulation of Surgical Interventions. 6.10.3 Custom Implant Design. 6.10.4 Soft Tissue Reconstruction. 6.11 Further Reading. 7. From Virtual Reality to Real Virtuality. 7.1 Reifying Virtual Objects. 7.2 Principles of Rapid Prototyping. 7.3 Combining Virtual Reality and Real Virtuality. 7.4 Further Reading. 8. Morphometric Analysis. 8.1 Morphometry as Reconstruction. 8.2 Morphometry and Geometry. 8.2.1 The Role of Geometry. 8.2.2 The Role of Size and Shape. 8.2.3 Multivariate Morphometry. 8.2.4 Principal Components Analysis and Dimension Reduction. 8.2.5 Classic Multivariate Morphometry: Geometry Lost. 8.2.6 Geometric Morphometrics: Geometry Recovered. 8.3 Shape Space Analysis. 8.3.1 From Da Arcy Thompson to Kendall. 8.3.2 The Workflow of Shape Space Analysis. 8.3.3 Determining a Reference Shape. 8.3.4 Analyzing Data in Shape Space. 8.3.5 Visualizing Patterns of Shape Difference and Shape Change. 8.3.5 Visualizing Patterns of Shape Difference and Shape Change. 8.4 Euclidean Distance Matrix Analysis. 8.4.1 In Search of the Golden Mean. 8.4.2 Exploring Form Variability with EDMA. 8.5 Outline Analysis. 8.6 A Comparison of Geometric Morphometric Methods. 8.6.1 Criteria for Comparison. 8.6.2 From Pattern to Process. 8.7 Exploring Morphometric Patterns. 8.8 Further Reading. Appendix A. Image Data Acquisition Systems: Performance Considerations. Appendix B. Parameters Influencing the Quality of CT Image Data. Appendix C. CT Scanning of Fossil Specimens and Recent Skeletal Specimens: How to Proceed? Appendix D. Object Manipulation in Virtual Space. Appendix E. A Parsimonious Approach to Correction of Taphonomic Deformation. Appendix F. Morphometry. References. Index.