Introduction to optical microscopy

Contents
Preface to Second Edition
Preface to First Edition
1 Introduction
	1.1 Complex Fields
	1.2 Intensity and Radiance
	1.3 Ray Optics
	1.4 Basic Transfer Properties of a Lens
		1.4.1 Fourier Transform with a Lens
		1.4.2 Imaging with a Lens
		1.4.3 Thick Lens
	1.5 Problems
	References
2 Monochromatic Wave Propagation
	2.1 Time-Dependent Wave Equation
	2.2 Time-Independent Wave Equation
		2.2.1 Propagating Versus Evanescent Waves
	2.3 Rayleigh–Sommerfeld Diffraction
		2.3.1 Primary Versus Secondary Sources
		2.3.2 Propagator Properties
	2.4 Approximations
		2.4.1 Fresnel Diffraction
		2.4.2 Fraunhofer Diffraction
	2.5 Problems
	References
3 Monochromatic Field Propagation Through a Lens
	3.1 Lens Transmission
	3.2 Fourier Transform with a Lens
		3.2.1 Gaussian Pupil
	3.3 Imaging with a Lens
		3.3.1 Arbitrary Pupil
		3.3.2 4f Imaging
		3.3.3 Amplitude Spread and Transfer Functions
		3.3.4 Spatial Bandwidth and Resolution
		3.3.5 Properties of Amplitude Spread Functions
	3.4 Effect of Surrounding Media
	3.5 Problems
	References
4 Intensity Propagation
	4.1 Field Correlations
	4.2 Free Space Propagation
		4.2.1 Quasi-Homogeneous Beams
		4.2.2 Reciprocity Between Coherence and Intensity
		4.2.3 Incoherent Beam Propagation
	4.3 Propagation Through a 2f System
	4.4 Propagation Through a 4f System: Imaging
		4.4.1 Circular Pupil
	4.5 Problems
	References
5 3D Imaging
	5.1 Defocus
		5.1.1 Gaussian Beam
	5.2 3D Imaging Functions
		5.2.1 3D Coherent Transfer Function
		5.2.2 3D Amplitude Spread Function
		5.2.3 3D Point Spread Function
		5.2.4 3D Optical Transfer Function
	5.3 3D Imaging Examples
	5.4 Frequency Support
		5.4.1 Optical Sectioning
		5.4.2 Extended Depth of Field
		5.4.3 Radiant Mutual Intensity
	5.5 Problems
	References
6 Radiometry
	6.1 Energy Flux Density
		6.1.1 Transport of Intensity
	6.2 Radiance
		6.2.1 Relation Between Flux Density and Radiance
	6.3 Étendue
		6.3.1 Conservation of Étendue
		6.3.2 Multimode Beam Propagation
	6.4 Throughput
		6.4.1 Apparent Source Coherence
		6.4.2 Transmission of Power
	6.5 Microscope Layout
		6.5.1 Field and Aperture Stops
		6.5.2 Illumination Configurations
		6.5.3 Detection Configuration
	6.6 Problems
	References
7 Intensity Fluctuations
	7.1 Temporal Coherence
		7.1.1 Quasi-Stationary Beams
	7.2 Coherence Functions
		7.2.1 Interrupted Phase Model
		7.2.2 Gaussian Light
		7.2.3 Köhler Illumination
		7.2.4 Central Limit Theorem
	7.3 Filtered Fluctuations
		7.3.1 Temporal Filtering
		7.3.2 Spatial Integration
	7.4 Coherence Examples
	7.5 Problems
	References
8 Detection Noise
	8.1 Shot Noise
		8.1.1 Power Spectral Density
		8.1.2 Gaussian Light Example
		8.1.3 Unit Conversion
	8.2 Other Noise Sources
		8.2.1 Dark-Current Noise
		8.2.2 Avalanche Noise
		8.2.3 Johnson Noise
		8.2.4 Noise Equivalent Power
		8.2.5 Example: Split Detector
	8.3 Cameras
		8.3.1 Readout Noise
		8.3.2 Photoelectron Preamplification
	8.4 Electronic Gain Versus Optical Gain
	8.5 Problems
	References
9 Absorption and Scattering
	9.1 2D Formalism
		9.1.1 Thin Sample Approximation
		9.1.2 Plane-Wave Illumination
		9.1.3 Beam Propagation Method
	9.2 3D Formalism
		9.2.1 Born Approximation
		9.2.2 Rytov Approximation
	9.3 Cross-Sections
		9.3.1 Scattering Amplitude
		9.3.2 Optical Theorem
	9.4 Vector Dipole Scattering
	9.5 Problems
	References
10 Widefield Microscopy
	10.1 Transmission Microscopy
		10.1.1 Thin Samples
		10.1.2 Brightfield Microscopy
		10.1.3 Phase Imaging
		10.1.4 Volume Samples
	10.2 Reflection Microscopy
		10.2.1 Brightfield Microscopy
		10.2.2 Darkfield Microscopy
	10.3 Problems
	References
11 Interference Microscopy
	11.1 Principle
	11.2 Coherent Illumination
		11.2.1 Fresnel Holography
		11.2.2 Lensless Fourier Holography
		11.2.3 Fourier Holography with a Lens
		11.2.4 Imaging Holography
	11.3 Incoherent Illumination
	11.4 Frequency Support
		11.4.1 Origin of Reference Beam
		11.4.2 Extraction of Complex Interference
	11.5 Resolution and Sampling
	11.6 Applications
	11.7 Problems
	References
12 Optical Coherence Tomography
	12.1 Coherence Gating
	12.2 Extraction of Complex Interference
		12.2.1 Static Sample
		12.2.2 Dynamic Sample
	12.3 OCT Implementations
		12.3.1 Time-Domain OCT
		12.3.2 Frequency-Domain OCT
		12.3.3 Comparison
	12.4 Widefield OCT
		12.4.1 Frequency Support
	12.5 Problems
	References
13 Fluorescence
	13.1 Rate Equations
		13.1.1 Two-Level Fluorescent Molecule
		13.1.2 Three-Level Molecule: Triplet State
		13.1.3 Photobleaching
	13.2 Förster Resonance Energy Transfer (FRET)
	13.3 Fluorescence Lifetime Imaging Microscopy (FLIM)
		13.3.1 Time Domain
		13.3.2 Frequency Domain
	13.4 Fluorescence Correlation Spectroscopy (FCS)
		13.4.1 Molecular Diffusion
		13.4.2 Example: Hard-Sphere Volume with Photobleaching
	13.5 Problems
	References
14 Confocal Microscopy
	14.1 Scanning Configurations
	14.2 Non-Fluorescence Confocal Microscopy
		14.2.1 Transmission Confocal
		14.2.2 Reflection Confocal
		14.2.3 Comparison with Widefield Microscopy
	14.3 Confocal Fluorescence Microscopy
		14.3.1 Optical Sectioning
		14.3.2 Confocal Probe Volume
		14.3.3 Frequency Support
		14.3.4 Finite-Size Pinhole
		14.3.5 Offset Illumination and Detection Pupils
	14.4 Problems
	References
15 Structured Illumination Microscopy
	15.1 Principles
	15.2 Structured Illumination with Fringes
		15.2.1 Optical Sectioning
		15.2.2 Coherent Versus Incoherent Illumination
	15.3 Structured Illumination with Speckle
		15.3.1 Decoding with Known Patterns
		15.3.2 Decoding with Unknown Patterns
	15.4 Hybrid Techniques
		15.4.1 Aperture Correlation Microscopy
		15.4.2 Programmable Array Microscopy
	15.5 Pupil Synthesis
	15.6 Problems
	References
16 Multiphoton Microscopy
	16.1 Two-Photon Excited Fluorescence (TPEF) Cross-section
	16.2 Pulsed Excitation
	16.3 Two-Photon Excitation Volume
		16.3.1 Gaussian–Lorentzian Volume
		16.3.2 3D-Gaussian Volume
	16.4 Two-Photon Scanning Microscopy
	16.5 Broadband Excitation
	16.6 Temporal Focusing
	16.7 Multiphoton Microscopy
		16.7.1 Advantages of Multiphoton Microscopy
	16.8 Problems
	References
17 Multiharmonic Microscopy
	17.1 Nonlinear Susceptibilities
		17.1.1 Coherent Interactions
		17.1.2 Radiation Patterns
	17.2 Second-Harmonic Generation (SHG) Microscopy
		17.2.1 Symmetry Properties
		17.2.2 3D-Gaussian Approximation
		17.2.3 Applications
	17.3 Third-Harmonic Generation (THG) Microscopy
	17.4 Problems
	References
18 Pump-Probe Microscopy
	18.1 Raman Microscopy
		18.1.1 Incoherent Raman Microscopy
		18.1.2 Coherent Raman Microscopy
	18.2 Brillouin Microscopy
	18.3 Photothermal Microscopy
	18.4 Photoacoustic Imaging
	18.5 Problems
	References
19 Superresolution
	19.1 Restricted Superresolution
		19.1.1 PSF Engineering
		19.1.2 Synthetic Aperture Holography
		19.1.3 Structured Illumination Microscopy
	19.2 Unrestricted Superresolution
		19.2.1 Nonlinear Structured Illumination Microscopy
		19.2.2 Stimulated Emission Depletion (STED) Microscopy
		19.2.3 Molecular Switching
	19.3 Resolution Versus Localization
	19.4 Problems
	References
20 Imaging in Scattering Media
	20.1 Radiative Transfer Equation
	20.2 Diffusive Limit
	20.3 Small Scattering Angles
		20.3.1 Scattering Filter Function
	20.4 Propagation of Intensity and Coherence
		20.4.1 Plane-Wave Beam
		20.4.2 Focused Beam
	20.5 Connection with Index of Refraction
	20.6 Adaptive Optics
		20.6.1 Focus Enhancement
		20.6.2 Deep Focusing
	20.7 Problems
	References
Appendix A Properties of Fourier Transforms
	A.1 Fourier Transform Properties
	A.2 Fourier Transform Theorems
	A.3 Cylindrical Coordinates
	A.4 Spherical Symmetry
Appendix B Miscellaneous Math
	B.1 Green Theorem
	B.2 A Useful Integral
	B.3 Symmetry Properties of Hermitian and Anti-Hermitian Functions
	B.4 Properties of Variances
	B.5 Property of Gaussian Random Variables
Appendix C Jones Matrix Description of Polarizers
Index