Microscopy Techniques for Biomedical Education and Healthcare Practice: Principles in Light, Fluorescence, Super-Resolution and Digital Microscopy, and Medical Imaging (Biomedical Visualization, 2)

This edited book has a strong focus on advances in microscopy that straddles research, medical education and clinical practice. These advances include the shift in power from conventional to digital microscopy. The first section of this book covers imaging techniques and morphometric image analysis with its applications in biomedicine using different microscopy modes. Chapters highlight the rich development of fluorescence methods and technologies; particle tracking techniques with applications in biomedical research and nanomedicine; the way in which visualizations have revolutionized taxonomy from gross anatomy to genetics; and the psychology of perception and how it affects our understanding of cells and tissues. The book’s first section concludes by exploring the use of CT modalities to evaluate anterior deformities in craniosynostosis. In the second section of the book, chapters on anatomical and cell biology education explore the history of anatomical models and their use in educational settings. This includes examples in 3D printing and functional human anatomical models that can be created using easily available resources and the use of biomedical imaging in visuospatial teaching of anatomy; the novel use of ultrasound in medical education and practice; and skill acquisition in histology education using a flowchart called a ‘decision tree’. This book will appeal to histologists, microscopists, cell biologists, clinicians and those involved in anatomical education and biomedical visualization, as well as students in those respective fields. Preface Acknowledgement Contents Editors and Contributors Part I: Advances in Microscopy for Visualization, Education and Healthcare Practice 1: Visualizing the Invisible: Microscopy and How It Affects Our Understanding of Cells and Tissues 1.1 Introduction 1.2 Microscopy in Medical Research and Education 1.2.1 Old Textbook Knowledge Shapes our Understanding of Cellular Details 1.2.2 Finding Patterns in Biological Chaos: Histology as a Subject at Universities 1.3 Simple Microscopy and Advanced Variants 1.3.1 The Microscope-An Optical Assembly to Magnify Small Things 1.3.2 Sample Contrast Mechanisms 1.3.2.1 Brightfield, Labels, and Phase Contrast 1.3.2.2 Quantitative Phase Microscopy 1.3.2.3 Fluorescence Microscopy Autofluorescence in Pathology Applications of Fluorescence Microscopy in Medicine 1.3.3 Resolution and the Microscope ́s Blurring Function 1.3.4 Super-Resolution Microscopy 1.3.5 3D Microscopy 1.3.5.1 Optical Sectioning 1.3.5.2 Confocal 1.3.5.3 Light-Sheet Microscopy 1.4 Data Processing 1.4.1 Visualization 1.4.1.1 Grayscale and Color Images 1.4.1.2 Volumetric and Video Microscopy Images 1.4.2 Quantification 1.4.3 Machine Learning in Pathology 1.5 Synthesizing Microscopy, Visual Representation, and Learning 1.5.1 The Importance of Visualizations for Learning and Understanding 1.5.2 Seeing What we Want to See: Motivated Perception and the Downsides of Expertise References 2: Morphometric Image Analysis and its Applications in Biomedicine Using Different Microscopy Modes 2.1 Background 2.2 Microscopic Imaging, Morphometry, and Quantification of the Results 2.2.1 3D Confocal Cell Morphometry 2.2.2 Electron Microscopy Morphometry 2.3 Applications of Morphometrical Analysis in Biomedicine 2.3.1 Morphometric Image Analysis in Tumor Researches and Diagnostics 2.3.2 Morphometric Analysis in Brain Research 2.3.3 Morphometric Analysis in Immunohistochemical Investigations 2.4 Essential Requirements for Precise and Reproducible Morphometric Analysis of Microscopic Images 2.5 Future Perspectives References 3: The Shift in Power from Conventional to Digital and Virtual Microscopy 3.1 Conventional Optical Microscopy and its Shortfalls 3.2 The Use of Microscopes in Teaching and Learning 3.3 Limitations of Microscopes in Teaching and Learning 3.4 Challenges in Teaching and Learning of Microscopy and Histology 3.5 Reflection on Teaching Histology 3.6 Virtual and Digital Microscopy 3.7 Teaching and Learning Using a Virtual Online Platform-Experience at our Laboratory Setting 3.8 Creation of Digitized Database 3.9 Remodelling of Laboratory and Lecture Venues to Accommodate Virtual Platform 3.10 Delivering Histology Practical Sessions 3.11 Assessments, Tutorials and Correspondence 3.12 Impact of COVID-19 on Histology Practical Teaching 3.13 Digital and Virtual Microscopy as a Research Tool 3.14 Conclusion 3.15 Limitations of Digital and Virtual Microscopy References 4: How Visualizations Have Revolutionized Taxonomy: From Macroscopic, to Microscopic, to Genetic 4.1 Introduction 4.2 The Macroscopic: What Is Visible with the Naked Eye 4.2.1 The Aristotelian System 4.2.2 The Linnaean System 4.2.2.1 Linnaeus and Binomial Nomenclature 4.2.2.2 How Linnean Classification Visualizes Organisms? 4.3 The Microscopic 4.3.1 How Many Species Are There? 4.3.2 The Invention of the Microscope 4.3.3 The Uses of Microscopy 4.3.3.1 Early Microscopy and Taxonomy 4.3.3.2 The Development of Microscopy 4.3.3.3 Modern Microscopy and Taxonomy 4.4 Genetics 4.4.1 A Brief Introduction to Genetics 4.4.2 Evolutionary Biology and Taxonomy 4.4.3 What Genetics Reveals about Taxonomy: Divergence and Convergence 4.4.4 How we Visualize Genetics? 4.5 Conclusions References 5: Bright New World: Principles of Fluorescence and Applications in Spectroscopy and Microscopy 5.1 Introduction 5.2 Historical Context 5.3 Characteristics of Fluorescence Excitation and Emission 5.3.1 Photophysical Processes 5.3.2 Characterizing Fluorophores 5.3.3 Fluorescence Quenching 5.3.4 Fluorescence Resonance Energy Transfer 5.3.5 The ``Dark Side ́ ́ of Fluorescence 5.4 Spectrofluorimetry 5.5 Fluorescence Microscopy 5.5.1 Widefield Microscopy 5.5.2 Confocal Microscopy 5.5.3 The Diffraction Limit and the Advent of Super-Resolution Microscopy 5.6 Fluorescent Reporters 5.7 Image Analysis 5.8 Conclusion References 6: An Introduction to Particle Tracking Techniques with Applications in Biomedical Research 6.1 Introduction 6.2 Conceptualizing a Particle in Biological and Virtual Realms 6.3 Principles of Particle Tracking 6.4 Methodological Considerations 6.5 Software Packages 6.6 Overview of the Data Derived from Particle Tracking 6.7 Some Interesting Applications of Particle Tracking in Biomedical Systems 6.7.1 Designing Mucopermeative NPs for Drug Delivery 6.7.2 Cellular Microrheology and Biomechanics 6.7.3 Understanding the Dynamics of Biomembranes 6.7.4 Mechanistic Investigations on Intracellular and Intercellular Transport 6.7.5 Mechanistic Investigations on Cellular Uptake 6.8 Future Perspectives References 7: An Exploration of the Practice of CT Modalities to Evaluate Anterior Cranial Deformities in Craniosynostosis 7.1 Introduction 7.2 Anatomy of the Infant Skull 7.2.1 Gross Anatomy 7.2.2 Embryogenesis 7.3 What Is Craniosynostosis? 7.3.1 Scaphocephaly 7.3.2 Trigonocephaly 7.3.3 Anterior Plagiocephaly 7.4 Imaging Modalities Used in the Evaluation of Craniosynostosis 7.4.1 Plain Skull Radiography and Bone Scintigraphy 7.4.2 Computed Tomography 7.4.3 Magnetic Resonance Imaging and Sonography 7.5 A Novel Approach to Analyze ACF Morphometry in Craniosynostosis 7.5.1 Patients 7.5.2 Inclusion and Exclusion Criteria 7.5.2.1 Inclusion Criteria 7.5.2.2 Exclusion Criteria 7.5.3 Sample Size 7.5.4 Ethical Considerations 7.5.5 Image Acquisition 7.5.6 Image Analysis 7.5.7 Current Approach to Analyzing ACF Morphometry in the Craniosynostoses 7.5.7.1 Scaphocephaly 7.5.7.2 Trigonocephaly 7.5.7.3 Anterior Plagiocephaly 7.5.8 Use of Novel Anatomical Landmarks to Analyze ACF Morphometry in the Craniosynostoses 7.5.8.1 ACF Length and Width in Scaphocephaly 7.5.8.2 ACF Length and Width in Trigonocephaly 7.5.8.3 ACF Length and Width in AP 7.5.9 Statistical Data Analysis 7.6 A New and Improved Approach to ACF Morphometry 7.6.1 ACF Morphometry in Scaphocephaly 7.6.2 ACF Morphometry in Trigonocephaly 7.6.3 ACF Morphometry in AP 7.7 Limitations 7.8 Recommendations 7.9 Conclusion References Part II: Anatomical and Cell Biology Education 8: The Use of Biomedical Imaging in Visuospatial Teaching of Anatomy 8.1 Introduction 8.2 History of Traditional Anatomical Teaching Techniques 8.3 Modernisation of Anatomical Teaching 8.4 The Benefits of Incorporating Biomedical Technology in Teaching Anatomy 8.5 Three-Dimensional Printing 8.5.1 Three-Dimensional Modelling Software 8.5.1.1 Incorporation of 3Dp in a Lecture Series 8.6 MacroView 8.6.1 Role of MacroView in Lecture Series 8.7 Ultrasound 8.7.1 Echogenicity 8.7.2 Transducers 8.7.2.1 Curvilinear Transducer 8.7.2.2 Linear Transducer 8.7.2.3 Phased Array Transducer 8.7.3 Frequency and Resolution 8.7.4 Knobology 8.7.4.1 Basic Ultrasound Modes 8.7.4.2 Incorporation of Ultrasound in Lecture Series 8.8 Anatomage Table 8 8.8.1 Gross Anatomy Folder 8.8.2 Assessments 8.8.2.1 Incorporation of Anatomage in Lecture Series 8.9 Pilot Study 8.9.1 Material and Methods 8.10 Results and Outcomes 8.11 Discussion 8.12 Conclusion References 9: Ultrasound Imaging for Musculoskeletal Research 9.1 Introduction 9.1.1 History of Musculoskeletal US 9.1.2 The Role of US in Musculoskeletal Applications 9.1.3 Advantages and Limitations of Using US for Diagnostic Purposes in Musculoskeletal Injuries 9.2 Types of Transducers for Musculoskeletal Imaging 9.3 US Imaging for Seated Anatomy 9.3.1 The Role of US in the Early Detection of Pressure Ulcers 9.3.1.1 US Imaging of the Ischial Tuberosity 9.4 Recent US Imaging Advances 9.5 Conclusion References 10: Skill Acquisition in Histology Education 10.1 Introduction 10.1.1 Traditional Histology Education 10.1.2 Action Research 10.1.3 Teaching in the Context of Medicine 10.1.4 Ensuring Quality and Rigour in AR 10.2 Aims for the Research Project 10.3 Project Overview 10.4 Methods 10.4.1 Ethics 10.4.2 Methods Overview 10.4.3 Creation of the Resources 10.4.4 Data Collection 10.4.4.1 Questionnaires 10.4.4.2 Field Notes 10.4.4.3 Quiz and Assessment Results 10.4.5 Control Groups 10.4.6 Ethical Considerations 10.5 Cycle Overview 10.5.1 Pre-Cycle 10.5.2 Cycle 1: Use of a Decision Tree in the Practical Setting 10.5.2.1 Cycle 1 Outline 10.5.2.2 Cycle 1 Logistics 10.5.2.3 Cycle 1 Field Notes 10.5.2.4 Cycle 1 Questionnaire Data 10.5.2.5 Cycle 1 Discussion 10.5.2.6 Cycle 1 Reflections for Implementation in Cycle 2 (Table 10.1) 10.5.3 Cycle 2: Use of the Decision Tree in a Digital Format 10.5.3.1 Cycle 2 Outline 10.5.3.2 Cycle 2 Logistics 10.5.3.3 Cycle 2 Field Notes 10.5.3.4 Cycle 2 Questionnaire Data 10.5.3.5 Quiz and Worked Example Results 10.5.3.6 Cycle 2 Discussion 10.5.3.7 Cycle 2 Reflections for Implementation in Cycle 2.5 (Table 10.2) 10.5.4 Cycle 2.5: Modification of the Digitally Available Resources 10.5.4.1 Cycle 2.5 Outline 10.5.4.2 Cycle 2.5 Logistics 10.5.4.3 Cycle 2.5 Field Notes 10.5.4.4 Cycle 2.5 Questionnaire Data 10.5.4.5 Quiz and Worked Example Results 10.5.4.6 Cycle 2.5 Discussion 10.5.5 Post-cycle 10.5.5.1 Quiz and Worked Example Results 10.5.5.2 Summative Practical Exam (OSSE) Results and Field Notes 10.5.5.3 Post-cycle Discussion 10.6 Was This Project Successful? 10.6.1 The Data Can Be Generalised 10.6.2 The Data Are Reliable 10.6.3 The Results and Conclusions Are Objective 10.6.4 The Results and Conclusions Are Valid 10.6.4.1 Generation of New Knowledge 10.6.4.2 Achievement of Action-Oriented Outcomes 10.6.4.3 Education of Researcher and Participants 10.6.4.4 Results Are Relevant to the Local Setting 10.6.4.5 Sound and Appropriate Research Methodology 10.6.5 The Project Was Ethically Conducted 10.6.6 The Results Are Repeatable 10.6.7 Summary: This Was a Successful Project 10.7 Overall Discussion and Conclusions 10.7.1 Skill Development 10.7.2 Formative Assessment and Feedback 10.8 Future Plans References