Biophotonics: Concepts to Applications (Graduate Texts in Physics)

Preface
Acknowledgments
Contents
About the Author
Abbreviations
1 Overview of Biophotonics
	Abstract
	1.1 What Is Biophotonics?
	1.2 Diverse Applications
	1.3 Biophotonic Spectral Windows
	1.4 Light Absorption
	1.5 Decibel Notation for Signal Attenuation
	1.6 Structures of Biological Cells and Tissues
		1.6.1 Macromolecules
		1.6.2 Biological Cells
		1.6.3 Mitochondria
		1.6.4 Biological Tissues and Organs
	1.7 Summary
	References
2 Basic Principles of Light
	Abstract
	2.1 Lightwave Characteristics
		2.1.1 Monochromatic Waves
		2.1.2 Pulsed Plane Waves
	2.2 Polarization
		2.2.1 Linear Polarization
		2.2.2 Elliptical and Circular Polarization
	2.3 Quantized Photon Energy and Momentum
	2.4 Reflection and Refraction
		2.4.1 Snells’ Law
		2.4.2 The Fresnel Equations
		2.4.3 Diffuse Reflection
	2.5 Interference
	2.6 Optical Coherence
	2.7 Lightwave-Molecular Dipole Interaction
	2.8 Summary
	References
3 Optical Fibers for Biophotonic Applications
	Abstract
	3.1 Light Guiding Principles in Conventional Optical Fibers
		3.1.1 Ray Optics Concepts
		3.1.2 Modal Concepts
		3.1.3 Mode Field Diameter
		3.1.4 Effective Refractive Index
	3.2 Graded-Index Optical Fibers
		3.2.1 Core Index Structure
		3.2.2 Graded-Index Numerical Aperture
		3.2.3 Cutoff Condition in Graded-Index Fibers
	3.3 Performance Characteristics of Generic Optical Fibers
		3.3.1 Attenuation Versus Wavelength
		3.3.2 Mechanical Properties
		3.3.3 Optical Power-Handling Capability
		3.3.4 Biocompatibility of Fibers for Medical Use
	3.4 Conventional Solid-Core Fibers
	3.5 Specialty Solid-Core Fibers
		3.5.1 Photosensitive Optical Fiber
		3.5.2 Fibers Resistant to UV-Induced Darkening
		3.5.3 Bend Insensitive Fiber
		3.5.4 Polarization-Maintaining Fiber
	3.6 Double-Clad Fibers
	3.7 Hard-Clad Silica Fibers
	3.8 Coated Hollow-Core Fibers
	3.9 Photonic Crystal Fibers
	3.10 Plastic Fibers
	3.11 Side-Emitting or Glowing Fibers
	3.12 Middle-Infrared Fibers
	3.13 Tapered Optical Fibers
	3.14 Optical Fiber Bundles
	3.15 Summary
	References
4 Fundamentals of Light Sources
	Abstract
	4.1 Radiometry
		4.1.1 Radiant Energy
		4.1.2 Radiant Optical Flux and Power
		4.1.3 Irradiance or Exposure Rate
		4.1.4 Radiant Intensity
		4.1.5 Radiant Exposure or Radiant Fluence
		4.1.6 Radiance
	4.2 Arc Lamps
	4.3 Light-Emitting Diodes (LEDs)
		4.3.1 LED Operation and Structures
		4.3.2 LED Wavelengths and Device Uses
		4.3.3 Modulation of an LED
	4.4 Lasers for Biophotonics
		4.4.1 Basic Laser Actions
		4.4.2 Laser Diodes
		4.4.3 External Modulation of Semiconductor Lasers
		4.4.4 Solid-State Lasers
		4.4.5 Gas Lasers
		4.4.6 Optical Fiber Lasers
	4.5 Supercontinuum Light Sources
	4.6 Summary
	References
5 Fundamentals of Optical Detectors
	Abstract
	5.1 The pin Photodetector
	5.2 Avalanche Photodiodes
	5.3 Photodiode Noises
		5.3.1 Signal-to-Noise Ratio
		5.3.2 Sources of Photodetector Noise
		5.3.3 Signal-to-Noise Ratio Limits
		5.3.4 Noise-Equivalent Power and Detectivity
		5.3.5 Photodiode Linear Response
		5.3.6 Comparisons of Photodiodes
	5.4 Multichannel Detectors
		5.4.1 CCD Array Technology
		5.4.2 CMOS Array Technology
		5.4.3 Scientific CMOS
	5.5 High-Performance Detectors
		5.5.1 Photomultiplier Tubes (PMT)
		5.5.2 Silicon Photomultipliers (SiPM)
	5.6 Scientific Cameras
		5.6.1 Frontside Versus Backside Illumination
		5.6.2 Dynamic Range
		5.6.3 Resolution
		5.6.4 Response Speed
	5.7 Optical Filters
	5.8 Optical Couplers and Optical Circulators
	5.9 Summary
	References
6 Light-Tissue Interactions
	Abstract
	6.1 Reflection and Refraction Applications
		6.1.1 Refraction in Ophthalmology
		6.1.2 Specular Reflection
		6.1.3 Diffuse Reflection
	6.2 Absorption
		6.2.1 Absorption Characteristics
		6.2.2 Absorption in Biological Tissues
	6.3 Scattering
		6.3.1 Elastic Scattering
		6.3.2 Rayleigh Scattering
		6.3.3 Anisotropy Factor
		6.3.4 Inelastic (Raman) Scattering
	6.4 Scattering with Absorption
	6.5 Light-Tissue Interaction Mechanisms
		6.5.1 Photobiomodulation
		6.5.2 Photochemical Interaction
		6.5.3 Thermal Interaction
		6.5.4 Photoablation
		6.5.5 Plasma-Induced Photoablation
		6.5.6 Photodisruption
	6.6 Formation of Speckles
	6.7 Fluorescence Basics
	6.8 Summary
	References
7 Optical Probes and Biosensors
	Abstract
	7.1 Overview of Biosensors and Probes
	7.2 Optical Fiber Probe Configurations
	7.3 Optical Fiber Tip Geometries
	7.4 Optical Sensors
		7.4.1 Biorecognition Optical Fiber Sensors
		7.4.2 ELISA
		7.4.3 Sensors Based on Optical Fiber Movements
		7.4.4 Microbending Fiber Sensors
	7.5 Interferometric Sensors
		7.5.1 Mach–Zehnder Interferometer
		7.5.2 Michelson Interferometer
		7.5.3 Sagnac Interferometer
	7.6 Photonic Crystal Fiber Biosensors
		7.6.1 Interferometry Sensing Methods
		7.6.2 Liquid Infiltration Sensor
	7.7 Fiber Bragg Grating Sensors
		7.7.1 Smart-Bed FBG System
		7.7.2 Distributed FBG-Based Catheter Sensor
	7.8 Surface Plasmon Resonance Biosensors
	7.9 Single Nanoparticle Detection
	7.10 Summary
	References
8 Microscopy
	Abstract
	8.1 Concepts and Principles of Microscopy
		8.1.1 Viewing and Illumination Techniques
		8.1.2 Observation Methods
		8.1.3 Numerical Aperture
		8.1.4 Field of View
		8.1.5 Depth of Field
	8.2 Resolution and Diffraction Limit
	8.3 Confocal Microscopy
	8.4 Fluorescence Microscopy
	8.5 Multiphoton Microscopy
	8.6 Raman Microscopy
	8.7 Light Sheet Fluorescence Microscopy
	8.8 Super-Resolution Fluorescence Microscopy
	8.9 Expansion Microscopy
	8.10 Summary
	References
9 Spectroscopic Methodologies
	Abstract
	9.1 Fluorescence Spectroscopy
	9.2 FRET/FLIM
		9.2.1 Förster Resonance Energy Transfer
		9.2.2 Fluorescence Lifetime Imaging Microscopy
	9.3 Fluorescence Correlation Spectroscopy
	9.4 Elastic Scattering Spectroscopy
	9.5 Diffuse Correlation Spectroscopy
	9.6 Raman Spectroscopy
	9.7 Surface Enhanced Raman Scattering Spectroscopy
	9.8 Coherent Anti-Stokes Raman Scattering Spectroscopy
	9.9 Stimulated Raman Scattering Spectroscopy
	9.10 Photon Correlation Spectroscopy
	9.11 Fourier Transform Infrared Spectroscopy
	9.12 Brillouin Light-Scattering Spectroscopy
	9.13 Summary
	References
10 Optical Imaging Procedures
	Abstract
	10.1 Optical Coherence Tomography
		10.1.1 Time Domain OCT
		10.1.2 Spectral Domain OCT
		10.1.3 Swept Source OCT
	10.2 Endoscopy
		10.2.1 Basic Endoscopy
		10.2.2 Minimally Invasive Surgery
		10.2.3 Tethered Capsule Endomicroscopy
		10.2.4 Microendoscopy
	10.3 Laser Speckle Imaging
	10.4 Optical Coherence Elastography
	10.5 Photoacoustic Tomography
	10.6 Hyperspectral Imaging
	10.7 Summary
	References
11 Applications of Biophotonic Technologies
	Abstract
	11.1 Optical Manipulation
	11.2 Miniaturized Analyses Tools
		11.2.1 Microfluidic Platforms Using LOC Technology
		11.2.2 Lab-on-Fiber Concept
	11.3 Photonics in Dentistry
		11.3.1 Detection of Dental Caries
		11.3.2 PDT Applications to Periodontal Diseases
	11.4 Time-Correlated Single Photon Counting
	11.5 Smartphone Spectrometers
	11.6 Wearable Biophotonic Body Sensors
	11.7 Optogenetics
	11.8 Doppler OCT
	11.9 Robotic Surgery
	11.10 Summary
	References
Index