Super-Resolution Microscopy E-Book

Udo J. Birk

• Herausgeber: Wiley-VCH Verlag GmbH & Co. KGaA
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 882

Veröffentlichungsjahr: 2017

Beschreibung

This unique book on super-resolution microscopy techniques presents comparative, in-depth analyses of the strengths and weaknesses of the individual approaches. It was written for non-experts who need to understand the principles of super-resolution or who wish to use recently commercialized instruments as well as for professionals who plan to realize novel microscopic devices. Explaining the practical requirements in terms of hardware, software and sample preparation, the book offers a wealth of hands-on tips and practical tricks to get a setup running, provides invaluable help and support for successful data acquisition and specific advice in the context of data analysis and visualization. Furthermore, it addresses a wide array of transdisciplinary fields of applications.
The author begins by outlining the joint efforts that have led to achieving super-resolution microscopy combining advances in single-molecule photo-physics, fluorophore design and fluorescent labeling, instrument design and software development. The following chapters depict and compare current main standard techniques such as structured illumination microscopy, single-molecule localization, stimulated emission depletion microscopy and multi-scale imaging including light-sheet and expansion microscopy. For each individual approach the experimental setups are introduced, the imaging protocols are provided and the various applications illustrated. The book concludes with a discussion of future challenges addressing issues of routine applications and further commercialization of the available methods.
Guiding users in how to make choices for the design of their own experiments from scratch to promising application, this one-stop resource is intended for researchers in the applied sciences, from chemistry to biology and medicine to physics and engineering.

Leseprobe

Table of Contents

Cover

Title

Copyright

Dedication

Preface

Abbreviations

1 Introduction

1.1 Classical Resolution Limit

1.2 Methods to Circumvent the Classical Resolution Barrier in Fluorescence Microscopy

1.3 Implementation of Super-Resolution Microscopy

1.4 Contrast

1.5 Applications to the Study of Nuclear DNA

1.6 Other Applications

References

2 Physicochemical Background

2.1 Motivation

2.2 Labeling

2.3 Fluorophore Transitions

2.4 Samples

References

3 Hardware and Software

3.1 Hardware Requirements

3.2 Software

3.3 Open Source and Best Practice

References

4 Structured Illumination and Image Scanning Microscopy

4.1 Axially Structured Illumination Microscopy

4.2 Laterally Structured Illumination Microscopy

4.3 Image Scanning Microscopy

4.4 Super-Resolution Using Rotating Coherent Scattering (ROCS) Microscopy

References

5 Localization Microscopy

5.1 Principles of LocalizationMicroscopy

5.2 PALM/STORM/fPALM/SPDM Approach

5.3 Implementation of SMLM

5.4 Principles of Three-Dimensional SMLM

5.5 Reduction of Out-of-Focus Light

5.6 How to Build a Three-Dimensional SMLM

5.7 High-Density Single-Emitter Microscopy Methods: SOFI, 3B, SHRImP, and Others

5.8 Approaches to Counting Molecules

5.9 Requirements and Sample Preparation

5.10 Data Acquisition

5.11 Data Analysis

5.12 Troubleshooting

5.13 Meta Analysis Tailored for SMLM

5.14 Example Applications

References

6 Stimulated Emission Depletion Microscopy

6.1 Principles of Stimulated Emission Depletion Microscopy

6.2 Implementation of STED

6.3 Fluorescent Probes

6.4 Dye Combinations for Dual-Color STED

6.5 Requirements and Sample Preparation

6.6 Data Acquisition

6.7 Data Analysis and Visualization

6.8 Example Applications

6.9 Conclusion

References

7 Multi-Scale Imaging

7.1 Light-Sheet Fluorescence Microscopy

7.2 Optical Projection Tomography

7.3 Expansion Microscopy and Sample Clearing

7.4 Alternative Approaches

References

8 Discussion

8.1 Future Challenges

8.2 Commercialization of Super-Resolution Microscopes

8.3 Concluding Remarks

References

Index

End User License Agreement

List of Tables

3 Hardware and Software

Table 3.1

Objective lens characteristics for different NAs

Table 3.2

Reproducibility of correction of chromatic aberrations.

Table 3.3

Comparison of the three super-resolution techniques. “+”, good; “0”, medium; “−”, problematic. Published in Scientific Reports under the Creative Commons Attribution License (CC-BY) [31] by Wegel

et al

. [77], © 2016.

5 Localization Microscopy

Table 5.1

Excitation wavelength, dichroic mirrors, and emission filters used for characterization and imaging for each spectral range were 488 nm, T495LP (Chroma) and ET535/50m (Chroma) for blue-absorbing dyes; 561 nm, Di01-R561 (Semrock) and FF01-617/73-25 (Semrock) for yellow-absorbing dyes; 647 nm, Z660DCXRU (Chroma) and ET700/75m (Chroma) for red-absorbing dyes; 752 nm, and Q770DCXR (Chroma) and HQ800/60m (Chroma) for NIR-absorbing dyes. Dye-switching properties are reported in the presence of GLOX and 10 mM MEA as well as GLOX and 140 mM βME. Missing numbers (“–”) indicate that quantum yield values were not available from the dye manufacturer or McNamara data tables. Reprinted with permission from Macmillan Publishers Ltd: Nature Methods [84], © 2011.

Table 5.2

This list is an extended form of the troubleshooting advice published by van de Linde

et al

. Reprinted with permission from Macmillan Publishers Ltd: Nature Protocols [85], © 2011.

Table 5.3

Assessment of multi-color SMLM imaging of DNA in combination with other labeled structures. Several fluorescent probes are found to perform well in combination with the DNA dyes investigated (number of “+” signs reflects the quality of performance). For dyes marked with an asterisk, it was found that very-low-intensity illumination at the second (blue-shifted) wavelength effectively increased the number of localized single molecules of fluorophores, possibly owing to backpumping from a radical state. More recently, DNA labeling using YOYO-1 in eukaryotic cell nuclei yielded even higher-quality images [20].

6 Stimulated Emission Depletion Microscopy

Table 6.1

Selection of dye combinations for use with a 592 nm STED depletion laser.

Table 6.2

Selection of dye combinations for use with a 660 nm STED depletion laser

Table 6.3

Selection of dye combinations for use with a variable STED depletion wavelength. Use the lowest possible STED depletion wavelength at which no anti-Stokes excitation by the STED beam is detected, as this generally enhances the STED efficiency.