Front cover -- Title page -- Copyright page -- About the Author -- Table of contents -- Preface -- Acknowledgments -- Color Plates -- Section I -- 1 The Basics (math, waves, etc.) for the Nonphysical Scientist -- 1.1 General Properties of Waves and Coordinates -- 1.2 Trigonometry -- 1.3 Imaginary Numbers -- 1.4 The Exponential e -- 1.5 Infinite Series -- 1.6 Differentiation -- 1.7 Integration -- 1.8 Differential Equations -- 1.9 Vectors and Scalars -- 1.10 Unit Vector -- 1.11 Scalar and Vector Fields -- 1.12 Matrices and Linear Algebra -- 1.13 Waves -- 1.14 Combining Waves of Two Wavelengths -- 1.15 Fourier Series and Integrals -- 1.15.1 Fourier Series -- 1.15.2 Fourier Integral -- 1.16 Dirac Delta Function -- 1.17 Miscellaneous Basic Physics -- References -- Appendix 1-1 -- 2 Light and Electromagnetic Waves -- 2.1 General -- 2.2 Electromagnetic Spectrum -- 2.3 Vector Calculus -- 2.3.1 Divergence -- 2.3.2 Curl -- 2.3.3 Gradient -- 2.4 Maxwell's Equations -- 2.4.1 Faraday's Law -- 2.4.2 Gauss's Law for Electrical Fields -- 2.4.3 Gauss's Law for a Magnetic Field -- 2.4.4 Ampere's Law -- 2.5 Polarization -- 2.6 Reflection -- 2.7 Refraction -- 2.8 Optical Components -- 2.9 Lens -- 2.10 Grin Lens -- 2.11 Optical Fiber -- 2.12 Energy Propagation -- 2.13 Doppler Shifts -- References -- Appendix 2-1 -- 3 Light in Matter -- 3.1 Oscillating Dipole Moment -- 3.2 Dispersion -- 3.3 Absorption -- 3.4 Scattering -- 3.5 Summary -- References -- 4 Interference, Coherence, Diffraction, and Transfer Functions -- 4.1 Coherence and Interference -- 4.1.1 Coherence -- 4.1.2 Interferometry and the Michelson Interferometer -- 4.1.3 Partial Coherence Using a Source with Continuous Frequencies -- 4.2 Diffraction -- 4.2.1 Huygens and Huygens-Fresnel Principle -- 4.2.2 Fraunhofer and Fresnel Diffraction -- 4.2.3 Diffraction Limited -- 4.3 Convolution and Transfer Functions.

4.3.1 Transfer Function -- References -- Appendix 4-1 -- Section II -- 5 Optical Coherence Tomography Theory -- 5.1 General -- 5.2 Time Domain OCT (TD-OCT) -- 5.2.1 Interferometry with a Monochromatic Source -- 5.2.2 Low Coherence Interferometry with OCT -- 5.2.3 Determination of Axial Resolution -- 5.2.4 Transfer Function -- 5.3 Dispersion -- 5.4 Lateral Resolution -- 5.4.1 Light Beam -- 5.4.2 Paraxial Wave Equation -- 5.4.3 Relationship between the Paraboloidal and Gaussian Wave -- 5.4.4 The Gaussian Wave -- 5.4.5 Properties of a Gaussian Wave -- 5.4.6 Important Points of a Gaussian Beam Relevant to OCT -- 5.4.7 Speckle -- 5.5 Spectral Radar or Fourier Domain OCT (FD-OCT) -- 5.6 Swept Source (SS-OCT) -- 5.6.1 The Resolution -- References -- Bibliography -- Appendix 5-1 -- 6 Optoelectronics and Optical Components -- 6.1 General -- 6.2 Sources -- 6.2.1 Semiconductor Sources -- 6.2.2 Femtosecond Lasers -- 6.2.3 Doped Fiber Amplifiers -- 6.2.4 Wavelength Scanning -- 6.3 Interferometers -- 6.4 Delay Lines -- 6.4.1 Galvonometer Retroreflector -- 6.4.2 Piezoelectric Fiber Stretcher -- 6.4.3 Grating Based Delay Lines -- 6.4.4 Rotating Elements -- 6.5 Detectors -- 6.6 Detection Electronics -- 6.6.1 TD-OCT -- 6.6.2 FD-OCT -- 6.6.3 A-D Conversion/Frame Grabbers -- 6.7 Light Delivery Devices -- 6.7.1 Rotational Catheters/Guidewires -- 6.7.2 Translational Devices -- 6.7.3 Forward Imaging -- 6.7.4 MEMS -- References -- Appendix 6-1 -- 7 Noise and System Performance with TD-OCT and SD-OCT -- 7.1 Introduction -- 7.2 Definitions -- 7.3 Noise -- 7.3.1 Overview -- 7.4 Noise in CCD versus Photodiode -- 7.5 A-D Conversion in SD-OCT and TD-OCT -- 7.6 Embodiment and Theory -- 7.6.1 TD-OCT -- 7.6.2 SD-OCT -- 7.6.3 Detector Array Signal Integration -- 7.6.4 SS-OCT -- 7.7 Conclusion -- References -- 8 Polarization and Polarization Sensitive OCT -- 8.1 General.

8.2 Polarization Properties of Tissue -- 8.3 Collagen -- 8.4 Single Detector PS-OCT -- 8.4.1 SDPS-OCT Theoretical Model -- 8.4.2 Simulations with Layered Birefringent Phantoms -- 8.4.3 Varying Differential Group Index (Layer Birefringence) -- 8.4.4 Different Intra-Layer Medium -- 8.4.5 Varying Layer Concentration -- 8.4.6 Periodical Rotation of Polarization State in Reference Arm -- 8.4.7 Use of the Fast Fourier Transform -- 8.4.8 SDPS-OCT of Human Tissue -- 8.5 Dual Detector PS-OCT -- 8.5.1 Measurement of the Stokes Vector, Mueller Matrix, and Poincare's Sphere -- References -- Appendix 8-1 -- 9 Adjuvant Techniques: Absorption Spectroscopy, Contrast Probes, Phase Contrast, Elastography, and Entangled Photons -- 9.1 General -- 9.2 Absorption Spectroscopy -- 9.2.1 Absorption -- 9.2.2 Intrinsic Absorption -- 9.2.3 Dual Source -- 9.2.4 Single Source Same Frequency (Spectroscopic OCT) -- 9.2.5 Second Harmonic Generation -- 9.2.6 OCT Dyes/Probes -- 9.3 Elastography -- 9.3.1 Basic Concepts -- 9.3.2 Ultrasound Elastography -- 9.3.3 OCT Elastography -- 9.3.4 Limitations of the Elastography Techniques -- 9.4 Differential Phase Measurements -- 9.4.1 Embodiment -- 9.4.2 Limitations -- 9.5 Entangled Photons -- 9.5.1 General -- 9.5.2 Entangled States Generation -- 9.5.3 Interference Experiments -- 9.5.4 Ghost Imaging -- 9.5.5 Entanglement and OCT -- 9.6 Conclusion -- References -- 10 Doppler Optical Coherence Tomography -- 10.1 The Principle of Doppler OCT -- 10.1.1 Doppler Shift and Laser Doppler Velocimetry -- 10.1.2 Optical Signal Evolution in Doppler OCT -- 10.1.3 Interferogram Detection in Doppler OCT -- 10.2 Signal Processing in Doppler OCT -- 10.2.1 Signal Processing in Time Domain Doppler OCT -- 10.2.2 Signal Processing in Spectral Domain Doppler OCT -- 10.3 Applications of Doppler OCT -- References.

11 Digital Image Processing Techniques for Speckle Reduction, Enhancement, and Segmentation of Optical Coherence Tomography (OCT) Images -- 11.1 Introduction -- 11.2 Speckle Reduction Techniques -- 11.2.1 Mean, Median, and Hybrid Median Filters -- 11.2.2 Adaptive Filtering -- 11.2.3 Other Techniques -- 11.3 Image Segmentation Techniques -- 11.3.1 Thresholding -- 11.3.2 Region Growing -- 11.3.3 Watershed Algorithm -- 11.3.4 Edge-Based Segmentation Techniques -- 11.3.5 Other Segmentation Techniques -- 11.4 Summary -- References -- Section III -- 12 Application of OCT to Clinical Imaging: Introduction -- 12.1 Introduction -- 12.2 Areas Where OCT Shows Promise as a Clinical Imaging Device -- 12.2.1 When Biopsy Cannot Be Performed -- 12.2.2 Where Sampling Errors with Conventional Biopsy Are Likely -- 12.2.3 Guiding Surgical and Microsurgical Procedures -- 12.2.4 Three-Dimensional Reconstruction of In Vitro Pathology -- 12.3 Factors That Influence Decisions on The Clinical Relevance of OCT -- 12.4 OCT Imaging of Human Tissue -- 12.5 Methods for Validating the Structure in OCT Images -- 12.5.1 General -- 12.5.2 Histopathology -- 12.5.3 Immunohistochemistry -- 12.5.4 Enzymatic Assay -- 12.5.5 High-Performance Liquid Chromatography -- 12.5.6 Scanning Electron Microscopy -- 12.6 Animal Models -- 12.6.1 Justification of Need for Animals -- 12.6.2 Justification for the Species -- 12.6.3 Justification of the Total Number of Animals -- 12.6.4 Drugs and Their Dosages Used for Anesthesia and Euthanasia -- 12.6.5 Will the Animal Experience Discomfort and Is a Survival Model Utilized? -- 12.6.6 Use of Experienced Personnel -- 12.6.7 Registration -- 12.6.8 Example Rat Protocol -- 12.7 Statistical Analysis -- 12.8 Role of Human Perception on Image Interpretation -- 12.9 Conclusion -- References -- 13 Other Technologies -- 13.1 General -- 13.2 Structural Imaging.

13.2.1 Confocal Microscopy -- 13.2.2 High Frequency Ultrasound -- 13.2.3 Magnetic Response Imaging -- 13.2.4 Computer Tomography -- 13.2.5 Light-Scattering Spectroscopy -- 13.3 Spectroscopic Techniques -- 13.3.1 Fluorescence -- 13.3.2 Two-Photon Laser Scanning Microscopy -- 13.3.3 Near Infrared Absorption Spectroscopy -- 13.3.4 Raman Scattering -- References -- 14 Introduction to Clinical Research Design and Analysis -- 14.1 Elements of Study Design -- 14.1.1 Choosing a Primary Research Question -- 14.1.2 Descriptive versus Analytical Studies -- 14.1.3 Threats to Validity -- 14.1.4 Random Variability -- 14.1.5 Bias -- 14.1.6 Confounding -- 14.1.7 Effect Modification -- 14.1.8 Evaluating Threats to Validity -- 14.2 Choice of Study Design -- 14.2.1 Randomized, Blinded, Controlled Clinical Trials -- 14.3 Other Study Designs -- 14.3.1 Longitudinal Studies -- 14.3.2 Cohort Studies -- 14.3.3 Cross-Sectional Studies -- 14.3.4 Case-Control Studies -- 14.3.5 Nested Case-Control Studies -- 14.3.6 Secondary Data -- 14.3.7 Diagnostic Test Evaluation -- 14.4 Elements of Data Analysis -- 14.4.1 Types of Numerical Data -- 14.4.2 Summarizing and Describing Data -- 14.4.3 Variability in Data -- 14.4.4 Making an Inference from Data -- 14.4.5 Common Statistical Tests for Comparing Two Groups -- 14.4.6 Power and Sample Size -- 14.4.7 Evaluating Relationships among Continuous Measurements -- 14.4.8 Multivariate Models -- References -- Appendix 14-1 -- 15 OCT in Cardiovascular Medicine -- 15.1 General -- 15.2 Acute Coronary Syndromes -- 15.2.1 General -- 15.2.2 Epidemiology -- 15.2.3 Coronary Circulation -- 15.2.4 Classification of Plaque -- 15.2.5 Unstable Plaque Histopathology -- 15.2.6 Triggers of Plaque Rupture -- 15.2.7 Interventions -- 15.2.8 Imaging Modalities -- 15.2.9 OCT for Coronary Imaging -- 15.2.10 Limitations.

15.2.11 Current State of Intravascular OCT Imaging.