Optical Polarimetric Modalities for Biomedical Research (Biological and Medical Physics, Biomedical Engineering)

Preface
Tribute to Assoc. Prof. Ekaterina Borisova
Contents
Part I Stokes Mueller Based Polarimetry
1 Polarization Imaging of Optical Anisotropy in Soft Tissues
	1 Introduction
	2 Polarization Fundamentals
		2.1 Optical Anisotropy
		2.2 Polarization
		2.3 Polarization Properties
			2.3.1 Linear Retardance
			2.3.2 Circular Retardance
			2.3.3 Linear Diattenuation
			2.3.4 Circular Diattenuation
		2.4 Mueller–Stokes Formalism
		2.5 Decomposition
	3 Instrumentation
		3.1 Polarimeter Architectures
	4 Applications
		4.1 Quantitative Polarized Light Microscopy
		4.2 Mueller Matrix Imaging
		4.3 Polarized Spatial Frequency Domain Imaging
		4.4 Optomechanical Testing
	5 Conclusion
	References
2 Polarization Techniques in Biological Microscopy
	1 Optical Properties of Biological Samples
	2 Polarized Microscopy
	3 Polarized Light Microscopy Approaches
		3.1 Wide-Field Polarized Microscopy
		3.2 Polarized Fluorescence Microscopy
		3.3 Polarized Total Internal Reflection Fluorescence Microscopy
		3.4 Confocal Scanning Laser Polarimetric Microscopy
		3.5 Polarization-Sensitive Second Harmonic Microscopy
	References
3 Stokes –Mueller Matrix Polarimetry: Effective Parameters of Anisotropic Turbid Media: Theory and Application
	1 Introduction
	2 Stokes Vector and Mueller Matrix Formalism
	3 Decomposition Mueller Matrix for Extracting Effective Optical Parameters
	4 Experimental Results and Discussion
		4.1 Optical Fibers and Free-Space Media
		4.2 Baked Polarizer (LB and LD Properties)
		4.3 Depolarizer (LDep and CDep Properties)
		4.4 Quarter-Wave Plate and Depolarizer (LB, LDep, and CDep Properties)
		4.5 Dissolved Glucose Aqueous Solution (CB, LDep, and CDep Properties)
		4.6 Healthy and Nonmelanoma-Induced Mouse Skin Tissue Sample
		4.7 Human Blood Plasma
		4.8 Collagen Solution
		4.9 Healthy and Cancerous Human Skin Tissue
		4.10 Combination of Effective Parameters and Artificial Intelligent Classification Models for Human Skin Detection
	5 Conclusion
	References
4 Mueller Matrix Imaging
	1 Introduction
	2 Polarimetric Optical Properties
		2.1 Physical Origin of Polarimetric Effects
		2.2 Quantitative Interpretation of Mueller Matrix Polarimetry Data
	3 Imaging MM Instrumentation
		3.1 System Based on Two Rotating Compensators
		3.2 Systems Based on Tunable Liquid Crystals Compensators
		3.3 Use of Polarization Cameras for MM Imaging
	4 Practical Considerations and Examples
	5 Summary and Outlook
	References
5 Biological Imaging Through Optical Mueller Matrix Scanning Microscopy
	1 Introduction
	2 Complete Mueller Matrix Measurements
		2.1 Back to the Mueller Matrix Formalism
		2.2 Interpreting the Mueller Matrix
		2.3 Optical Scanning Microscopy Architecture
		2.4 Calibration of the SLM Mueller Matrix
	3 Optical Scanning Imaging Architecture
		3.1 Temporal Domain
		3.2 Spectral Domain
		3.3 Pros/Cons of the Different Mueller Matrix Approaches
	4 Multimodal Mueller Matrix Imaging
		4.1 MM and Non-Linear SLM Modality
		4.2 With OCT Modality
	5 Applications
		5.1 Ophthalmology
		5.2 Tissue Imaging
	References
6 Mueller Polarimetry for Biomedical Applications
	1 Introduction
	2 Theory of Mueller Matrix Polarimetry
		2.1 *-6pt
		2.2 *-6pt
		2.3 The Poincare Sphere
	3 Mueller Matrix and Stokes–Mueller Formalism
		3.1 Methods for Extraction of Mueller Matrix Parameters
			3.1.1 Mueller Matrix Decomposition Methods
			3.1.2 Nondecomposition Methods
		3.2 Mueller Matrix Studies in Biomedical Applications
	4 Instrumentation and Analysis
		4.1 Mueller Polarimetry
		4.2 Mueller Microscopy
		4.3 Mueller Polarimetric Endoscopy
		4.4 Multimodal Polarimetry Systems
		4.5 Nonlinear Mueller Polarimetry
		4.6 Analysis
	5 Applications
		5.1 Understanding Tissue Behavior: Role of Simulations and In-Vitro Experiments
		5.2 Examination and Characterization of Excised Tissues
		5.3 In Situ and In Vivo Applications
		5.4 Assessment of Body Fluids
		5.5 Bacterial Detection and Discrimination
		5.6 *-6pt
	6 Conclusion and Future Outlook
	References
7 Scattering Phase Functions and Polarimetric Responses of Selected Bioparticles
	1 Introduction
	2 Materials and Methods
	3 Results and Discussions
	4 Conclusion
	References
Part II Nonlinear Polarization Microscopy
8 Polarization-Resolved Nonlinear Optical Microscopy
	1 Introduction
	2 Nonlinear Optical Modalities for Microscopy
	3 3D Nonlinear Stokes–Mueller Polarimetry
	4 Nonlinear 2D Polarimetric Microscopy Techniques
		4.1 Polarization-Sensitive SHG Microscopy Techniques
			4.1.1 2D Double Stokes–Mueller Polarimetric SHG Microscopy
			4.1.2 PIPO SHG Microscopy
			4.1.3 pSHG Microscopy
			4.1.4 SS-pSHG Microscopy
			4.1.5 SHGCD Microscopy
			4.1.6 Circular Anisotropy of Circular Dichroism Microscopy
		4.2 Polarimetric THG Microscopy
			4.2.1 2D Triple Stokes–Mueller Polarimetric THG Microscopy
			4.2.2 PIPO THG Microscopy
	5 Polarimetric Nonlinear Microscopy Parameters
	6 Experimental Setups for Polarimetric Nonlinear Microscopy
	7 Numerical Modeling in Polarimetric Nonlinear Microscopy
	8 Concluding Remarks
	References
9 Polarization-Resolved SHG Microscopy for Biomedical Applications
	1 Introduction
	2 Second Harmonic Generation Microscopy
		2.1 Introduction to SHG
		2.2 SHG: Basic Theory
		2.3 SHG Microscopy Instrumentation
			2.3.1 Polarization-In SHG Microscopy
			2.3.2 Faster Fitting Polarization-In SHG Microscopy
			2.3.3 Circular Dichroism Polarization-In SHG Microscopy
			2.3.4 Polarization-Out SHG Microscopy
			2.3.5 Double Stokes–Mueller Polarimetric SHG Microscopy
			2.3.6 Polarization-In, Polarization-Out SHG Microscopy
	3 Biomedical Applications of Polarization-Resolved SHG Microscopy
		3.1 Initial Polarization-Resolved SHG Studies for Biomedical Applications
		3.2 Collagenous Tissues
			3.2.1 Cancerous Collagenous Tissues
			3.2.2 Diseased Collagenous Tissues
			3.2.3 Collagen Hydrogels
			3.2.4 Cornea and Sclera
			3.2.5 Skin
			3.2.6 Tendon and Cartilage
			3.2.7 Collagen in Cardiac Tissue
		3.3 Muscle
		3.4 Microtubules
		3.5 Other Biological Structures
	4 Conclusions and Outlook
	References
10 Polarization-Resolved Second-Harmonic Generation for Tissue Imaging
	1 Introduction
	2 Correlation Between Second-Harmonic Generation (SHG) and Second-Order Nonlinear Susceptibility Tensor, (2)
	3 Quantitative Measurement of P-SHG
		3.1 Theory for Conventional (2) Tensor Analysis
		3.2 Theory for Polarization-In, Polarization-Out (PIPO) SHG Microscopy
		3.3 Theory for Stokes Vector-Based SHG Microscopy
	4 Structural Constraint and Tissue Sources for SHG
	5 Polarization-Resolved SHG (P-SHG) Microscopy: Techniques
	6 Polarization-Resolved SHG (P-SHG) Microscopy: Applications
	7 Conclusion and Future Perspectives
	References
Part III Applications of Polarization Techniques
11 An Introduction to Fundamentals of Cancer Biology
	1 Introduction
	2 Difference Between Cancer Cells and Normal Cells
	3 Types of Cancer
	4 Cancer Development
	5 Causes of Cancer
	6 Properties of Cancer Cells
	7 Hallmarks of Cancer
		7.1 Uncontrolled and Sustained Proliferation
		7.2 Evading Growth Suppressor
		7.3 Resistance Against Cell Death
		7.4 Induction of Angiogenesis
		7.5 Metabolic Reprogramming
		7.6 Metastasis and Invasion Activation
		7.7 Replication Immortality Activation
		7.8 Evading Immune Destruction
	8 Methods of Cancer Detection
	9 Treatment
	References
12 Polarization-Enabled Optical Spectroscopy and Microscopic Techniques for Cancer Diagnosis
	1 Introduction
		1.1 Skin Structure and Optical Properties
	2 Experimental Setup
	3 Applications
		3.1 Spectroscopy Techniques
			3.1.1 Fluorescence Spectroscopy
		3.2 NIR Spectroscopy
			3.2.1 Hyperspectral Spectroscopy
			3.2.2 Raman Spectroscopy
		3.3 Microscopy Techniques
			3.3.1 Fluorescence Microscopy
			3.3.2 Confocal Microscopy
			3.3.3 Two-Photon Fluorescence Microscopy
			3.3.4 Second-Harmonic Generation Microscopy
			3.3.5 Third-Harmonic Generation Microscopy
			3.3.6 Coherent Anti-Stokes Raman Scattering
			3.3.7 Stimulated Raman Scattered Microscopy
			3.3.8 Surface-Enhanced Raman Scattering
			3.3.9 Optical Coherence Tomography
	4 Conclusion
	References
13 Polarization Microscopy in Biomedical Applications
	1 Introduction
	2 Imaging Techniques
		2.1 Traditional Polarization Microscope (PolScope)
		2.2 Optical Coherence Tomography
		2.3 Fluorescence-Based Microscopy
		2.4 Mueller Polarimetry
		2.5 Second-Harmonic Generation (SHG)
	3 Conclusion
	References
14 Machine Learning in Tissue Polarimetry
	1 Introduction
	2 Use of Stokes Parameters for Tissue Diagnosis
	3 Use of Mueller Matrix Data for Tissue Diagnosis
	4 Basics of ML Techniques Used in Polarimetry
	5 Applications of Machine Learning in Polarimetry
	6 Conclusion
	References
Index