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FLUORESCENCE MICROSCOPY

ELSEVIER

SUPER-RESOLUTION· AND OTHER NOVEL TECHNIQUES

Edited by

ANDA CoRNEA AND P. MrcHAEL CoNN

AMSTERDAM • BOSTON • HEIDELBERG • LONDON

NEW YORK • OXFORD • PARIS • SAN DIEGO

SAN FRANCISCO • SINGAPORE • SYDNEY • TOKYO

Academic Press is an Imprint of Elsevier

Contents

Preface vii List of Contributors lX

~ · ~~, . -.. .. . ' ..... :...,. ·: ... \. l. Evanescent Excitation and Emission ·. : .. ~ · :·.

DANIEL AXELROD

Introduction Evanescence in General 2 Evanescence in Excitation: TIR 2 Evanescence in Emission: The Fluorophore Near Field 7

Evanescence from a Point Source: NSOM 13

2. Adaptive Optics for Fluorescence Microscopy MARTIN J. BOOTH AND BRIAN R. PATTON

Introduction 15 Aberrations in Microscopy 15

Principles of Adaptive Optics 20

Adaptive Aberration Correction in Fluorescence Microscopes 22 Wavefront Sensing 26

Schemes for Modal Sensorless Adaptive Optics 28 Conclusion 32

3. Rapid Measurements of Orientation and Rotation in Ex Vivo Muscle Made Possible by Studying

Small Number of Cross-Bridges

Introduction 35

Kinetics 38

JULIAN BOREJDO

Distribution of Cross-Bridge Orientations 43 Conclusions 46

4. High Spatiotemporal Bioimaging Techniques to Study the Plasma Membrane N anoscale

Organization MARJOLEIN B.M. MEDDENS, SANDRA DE KEI]ZER, AND

ALESSANDRA CAMBI

Introduction 49

Spatial Resolution 50

Temporal Resolution 54 Conclusions and Outlook 59

v

S. High-Resolution 30 Imaging of Intact Transparent Organs by 3DISCO

ALl ERTORK

Introduction 65

Current Technologies for Imaging the Intact Brain 65

3DISCO 73

6. Using RNA Mimics of GFP to Image RNA Dynamics in Mammalian Cells RITA L. STRACK AND SAM IE R. jAFFREY

Introduction 83

Studying Trinucleotide-Repeat-Containing RNA 85 Optimizing Imaging of CGG Repeat-Containing RNA 86

Time-Lapse Imaging of CGG-Repeat•Containing RNAs 86

Monitoring CGG Repeat Foci During Cell Division 87

Examining the Stability of CGG6o RNA 88

Imaging the Effects of Small-Molecule Drugs on CGG Foci 88

Imaging Other RNAs Using Spinach2 89

Troubleshooting Imaging with Spinach2-Tagged Constructs 89 Imaging Rare RNAs 90

Future Directions 90

7. Surface Enhanced Raman Scattering (SERS) Image Cytometry for High-Content Screening

ER LIU AND JOHN P. NOLAN

High-Content Screening: Status and Needs 93

Labels and Probes for HCS: Fluorescence and SERS 93

Spectral Imaging for Fluorescence and SERS 95 SERS Imaging in Cell-Based Assays 101

Status and Prospects 105 Appendix 107

8. Light Sheet Fluorescence Microscopy Applications for Multicellular Systems

JULIEN COLOMBELU AND CORINNE LORENZO

Introduction 109

LSFM Implementations: A Universal Concept with Many Acronyms 111

LSFM at the Macroscopic Scale 111 3D Cancer Imaging Model: MCTS 113

Calcium Imaging, Fast Volumetric Calcium Imaging 116

Conclusions 118

Vl CONTENTS

9. Correlative Light Electron Microscopy as a Navigating Tool for Cryo-Electron Tomography

Analysis MELANIE BOKSTAD AND OHAD MEDAL!A

Introduction 121

Electron Microscopy in Cellular and Structural Biology 121

Sample Preparation for Electron Microscopy 122

Cryo-Electron Tomography 123 Correlative Light and Electron Microscopy (CLEM) 125

Correlated Light and Electron Microscopy Direct Observation • in Cryogenic Temperatures 127

CLEM Prospects 130

10. Cellular and Molecular Applications of Super-resolution Microscopy

EUGENIO F. FORNASIERO AND FELIPE OPAZO

Introduction 133

uper-res lution Microscopy Techniques 134 Troublcsh ting Sample Preparation 137

Thick, Li ving, Multicolor JD amplcs: Friends and Foes of uper-resolution Microscopy l40

Biological Applications 142 Conclusions 150

11. Use of Engineered Nanoparticle-Based Fluorescence Methods for Live-Cell Phenomena

CHAN-G! PACK, MIN-KYO JUNG, Ml-ROUNG SONG, )UN-SUNG KIM, SUNG-SJK HAN, AND YASUSH! SAKO

Introduction 153

Materials and Methods 154

Results and Discussion 157

Conclusions 165 Perspectives 166

12. High-Resolution Estimation of Multiple Cell Populations in Tissue Using Confocal Stereology

DANIEL A. PETERSON

Introduction 171 Design-Based Stereology as a Quantitative Tool 172

Sampling Requirements to Achieve a Population Estimate with High Resolution 176

Practical Requirements for Performing Stereology 179

Separation of Image Acquisition and Probe Analysis 180

Implementation of Systematic Random Sampling on a Confocal Microscope 181

Virtual Tissue with Post-Acquire Sampling 183

Conclusions 183

Conflict of Interest Disclosure 183

13. Multiphoton Microscopy Applications in Biology

MIKO YAMADA, LYNLEE L. LIN, AND TARL W. PROW

Introduction 185 Multiphoton Microscopy Applications 188

14. Super-resolution Microscopy: A Comparison of Commercially Available Options

jENNIFER A. THORLEY, JEREMY PIKE, AND JOSHUA Z. RAPPOPORT

Introduction 199

Technical Considerations 201 Single-Molecule Localization Microscopy 203

Structured Illumination Microscopy 206

Stimulated Emission Depletion Microscopy 208

Summary 210

Future Directions and Emerging Techniques 210

15. Structured Illumination Microscopy LIN SHAO AND E. HESPER REGO

Introduction 213

Theory 213

Materials and Methods 216

Results 223

Discussion 224

16. The Role of Image Analysis Algorithms in Super-resolution Localization Microscopy

ALEX SMALL AND SHANE STAHLHEBER

Introduction 22 7 Localization Algorithms and the Problem of Noise 228

Guidelines for Selecting a Localization Algorithm 229 Dipoles and 3D Localization 230 Rejection Algorithms for Multi-Molecule Images 231

Rejection Issues in 3D 239

Speeding Up Performance with Multi-Molecule Analysis 239

Conclusions 240

Index 243