Correlative Imaging: Focusing on the Future(RMS - Royal Microscopical Society)

Brings a fresh point of view to the current state of correlative imaging and the future of the field This book provides contributions from international experts on correlative imaging, describing their vision of future developments in the field based on where it is today. Starting with a brief historical overview of how the field evolved, it presents the latest developments in microscopy that facilitate the correlative workflow. It also discusses the need for an ideal correlative probe, applications in proteomic and elemental analysis, interpretation methods, and how correlative imaging can incorporate force microscopy, soft x-ray tomography, and volume electron microscopy techniques. Work on placing individual molecules within cells is also featured. Correlative Imaging: Focusing on the Future offers in-depth chapters on: correlative imaging from an LM perspective; the importance of sample processing for correlative imaging; correlative light and volume EM; correlation with scanning probe microscopies; and integrated microscopy. It looks at: cryo-correlative microscopy; correlative cryo soft X-ray imaging; and array tomography. Hydrated-state correlative imaging in vacuo, correlating data from different imaging modalities, and big data in correlative imaging are also considered. Brings a fresh view to one of the hottest topics within the imaging community: the correlative imaging field Discusses current research and offers expert thoughts on the field’s future developments Presented by internationally-recognized editors and contributors with extensive experience in research and applications Of interest to scientists working in the fields of imaging, structural biology, cell biology, developmental biology, neurobiology, cancer biology, infection and immunity, biomaterials and biomedicine Part of the Wiley–Royal Microscopical Society series Correlative Imaging: Focusing on the Future will appeal to those working in the expanding field of the biosciences, correlative microscopy and related microscopic areas. It will also benefit graduate students working in microscopy, as well as anyone working in the microscopy imaging field in biomedical research.

Table of Contents:
List of Contributors xi Preface xiii 1 It’s a Small, Small World: A Brief History of Biological Correlative Microscopy 1 Christopher J. Guérin, Nalan Liv, and Judith Klumperman 1.1 It All Began with Photons 1 1.2 The Electron Takes Its Place 2 1.3 Putting It Together, 1960s to 1980s 3 1.4 CLEM Matures as a Scientific Tool 1990 to 2017 4 Acknowledgments 13 References 13 2 Challenges for CLEM from a Light Microscopy Perspective 23 Kurt Anderson, Tommy Nilsson, and Julia Fernandez‐Rodriguez 2.1 Introduction 23 2.1.1 Electron and Light Microscopy 23 2.1.2 Correlative Microscopy: Two Cultures Collide 25 2.2 Microscopy Multiculturalism 26 2.2.1 When Fluorescence Light Microscopy Resolution is Not Enough 26 2.2.2 The Fluorescence Microscopy (FM), Needle/Haystack Localization 27 2.2.3 Electron Microscopy, Visualizing the Ultrastructure 27 2.2.4 Finding Coordinates 28 2.3 Bridging the Gap between Light and Electron Microscopy 29 2.3.1 Finding the Same Cell Structure in Light and Electron Microscopes 29 2.3.2 Making the Fluorescence Labels Visible in the Electron Microscope 29 2.3.3 Visualizing Membrane Trafficking Using CLEM 30 2.4 Future CLEM Applications and Modifications 31 2.4.1 Correlative Reflection Contrast Microscopy and Electron Microscopy in Tissue Sections 31 2.4.2 Dynamic and Functional Probes for CLEM 32 References 34 3 The Importance of Sample Processing for Correlative Imaging (or, Rubbish In, Rubbish Out) 37 Christopher J. Peddie and Nicole L. Schieber 3.1 Introduction 37 3.2 Searching for Correlative Electron Microscopy Utopia 40 3.3 Sample Processing for Correlative Imaging: A Primer for the First Steps 40 3.4 Making It Go Faster (We Want More Speed, More Speed…) 42 3.5 Embedding Resins 44 3.6 Keeping the Region of Interest in Sight 45 3.7 Correlation and Relocation with Dual Modality Probes 48 3.8 Integration of Imaging Modalities, and In‐Resin Fluorescence 49 3.9 Streamlining the Correlative Approaches of the Future: SmartCLEM 51 3.10 How Deep Does the Rabbit Hole Go? 52 3.11 Hold That Thought, Though − Is This All Completely Necessary? 53 3.12 Improving Accessibility to Correlative Workflows 54 3.13 Coming to the End 55 References 55 4 3D CLEM: Correlating Volume Light and Electron Microscopy 67 Saskia Lippens and Eija Jokitalo 4.1 Introduction 67 4.2 Imaging in 3D 68 4.3 Comparative and Correlative LM and EM Imaging 69 4.4 CLEM is More than LM + EM 69 4.5 3D CLEM 70 4.6 Two Workflows for 3D CLEM 71 4.7 Where is CLEM Going in the Future? 74 Acknowledgments 76 References 77 5 Can Correlative Microscopy Ever Be Easy? An Array Tomography Viewpoint 81 Irina Kolotuev and Kristina D. Micheva 5.1 Introduction 81 5.2 Why Array Tomography? 81 5.3 Array Tomography of Abundant Subcellular Structures: Synapses 82 5.4 Array Tomography of Sparsely Distributed Structures: Cisternal Organelle 84 5.5 Array Tomography of Small Model Organisms: C. elegans 87 5.6 To Summarize: Finding the Right AT Approach 90 5.7 Areas of Improvement 91 5.7.1 Resin 91 5.7.2 Serial Ultrathin Sectioning 91 5.7.3 Antibodies 92 5.7.4 EM Compatible Fluorophores 92 5.7.5 Detectors and EM Resolution 92 5.7.6 Image Registration and Alignment Tools 93 5.7.7 Data Sharing 93 5.7.8 “Dream” Resource 93 5.7.9 Dream Experiments 94 Acknowledgments 95 References 95 6 Correlative Microscopy Using Scanning Probe Microscopes 99 Georg Fantner and Frank Lafont 6.1 Introduction 99 6.2 Principles of AFM 100 6.3 AFM and Optical Microscopy Correlative Approaches 103 6.4 Correlation with CLSM 104 6.5 Correlation with Cell Mechanics 104 6.5.1 Correlation with Super‐Resolution Light Microscopy (SRLM) 105 6.5.2 Future Developments 107 6.6 AFM and Correlation with Electron Microscopy 109 6.6.1 Correlation Involving AFM, EM, and Chemical Surface Characterization 110 6.6.2 Future Developments 113 6.7 Future Developments Involving Correlation Microscopy Using HS‐AFM 113 6.8 Concluding Remarks 114 Acknowledgments 114 References 115 7 Integrated Light and Electron Microscopy 119 R. I. Koning, A. Srinivasa Raja, R. I. Lane, A. J. Koster, and J. P. Hoogenboom 7.1 Introduction 119 7.2 Large‐Scale and High‐Throughput (Volume) Microscopy 120 7.2.1 Advantages and Challenges for Large‐Scale EM 120 7.2.2 Advantages of CLEM for Large‐Scale EM 121 7.2.3 Prospects for Integrated Microscopy 121 7.3 Super‐Resolution Fluorescence Microscopy 123 7.3.1 Advantages and Challenges for CLEM with Super‐Resolution Fluorescence 123 7.3.2 Implementation of SR‐FM with CLEM 124 7.3.3 Prospects for Integrated SR‐CLEM 124 7.4 Cryo‐Electron Microscopy 125 7.4.1 Advantages of CryoEM 125 7.4.2 Possibilities and Challenges for Correlative Cryo‐Microscopy 126 7.4.2.1 Super‐Resolution Fluorescence Cryo‐Microscopy: Probes and Instruments 126 7.4.2.2 Transfer of Cryo‐Samples between Microscopes 127 7.4.2.3 Sample Thickness 127 7.4.2.4 Data Collection Speed 128 7.4.3 Integrated Systems for CryoCLEM 129 7.4.4 Prospects for Integrated Cryo‐Microscopy 129 7.5 Outlook 130 Acknowledgments 131 References 131 8 Cryo‐Correlative Light and Electron Microscopy: Toward in situ Structural Biology 137 Tanmay A.M. Bharat and Wanda Kukulski 8.1 Introduction 137 8.2 Cryo‐CLEM to Support Single Particle Analysis of Purified Macromolecules 138 8.3 Capturing Structural Dynamics of in vitro Reconstituted Systems 141 8.4 Identifying Macromolecules in Plunge‐Frozen Whole Cells 142 8.5 Macromolecular Structures in Thinned Samples from Thick Cell Areas 144 8.6 Enabling Structural Biology in Multicellular Organisms and Tissues by Cryo‐CLEM 145 8.7 Conclusions 147 Acknowledgments 147 References 147 9 Correlative Cryo Soft X‐ray Imaging 155 Eva Pereiro, Francisco Javier Chichón, and Jose L. Carrascosa 9.1 Introduction to Cryo Soft X‐ray Microscopy 155 9.2 Cryo‐SXT Correlation with Visible Light Microscopy 159 9.3 Cryo‐SXT Correlation with Cryo X‐ray Fluorescence 160 9.4 Cryo‐SXT Correlation with TEM 163 9.5 Multiple Correlation and Integration of Methods 165 Acknowledgments 165 References 166 10 Correlative Light‐ and Liquid‐Phase Scanning Transmission Electron Microscopy for Studies of Protein Function in Whole Cells 171 Niels de Jonge 10.1 Introduction 171 10.2 Limitations of State‐of‐the‐Art Methods 172 10.3 Principle of Liquid STEM 173 10.3.1 Example 1: Determination of ORAI Channel Subunit Stoichiometry by Visualizing Single Molecules Using STEM 175 10.3.1.1 Conclusions 179 10.3.2 Example 2: New Insights into the Role of HER2 179 10.3.2.1 Conclusions 182 10.4 Advantages of Liquid STEM 182 10.5 Future Prospects 184 Acknowledgments 185 References 185 11 Correlating Data from Imaging Modalities 191 Perrine Paul‐Gilloteaux and Martin Schorb 11.1 Introduction 191 11.2 Registration during CLEM Stages 194 11.2.1 Registration to Guide Sample Preparation 194 11.2.2 Registration to Guide the Acquisition 195 11.2.2.1 Software Packages 195 11.2.2.2 Typical Features and Fields of View 195 11.2.3 Post‐Acquisition Registration (Accurate Relocation) 196 11.2.3.1 Software and Approaches for Post‐Acquisition Registration 196 11.2.4 Trust in Alignment: Accuracy in Practice 198 11.3 Registration Paradigm 198 11.3.1 Image Features to Guide the Registration 198 11.3.2 Distance Function 199 11.3.3 Transformation Basis 199 11.3.4 Optimization Strategy 200 11.4 Envisioned Future Developments 201 11.4.1 Integrative Microscopy versus Correlative Microscopy 201 11.4.2 Incorporate a Priori Knowledge of the Specimen 202 11.4.3 Toward the Use of Machine Learning 202 11.5 Visualization of Correlation 204 11.6 Conclusion 204 Acknowledgments 205 References 205 12 Big Data in Correlative Imaging 211 Ardan Patwardhan and Jason R. Swedlow 12.1 Introduction 211 12.2 The Protein Data Bank 212 12.3 Resources for Cryo‐EM 212 12.4 Light Microscopy Data Resources 214 12.5 EMPIAR 215 12.6 IDR: A Prototype Image Data Resource 216 12.7 Public Resources for Correlative Imaging 217 12.7.1 CLEM Data Formats 217 12.8 Future Directions 218 12.8.1 A BioImage Archive 218 12.8.2 CLEM Data Submission Pipelines 219 12.8.3 Scaling Data Volumes and Usage 219 12.8.4 Community Adoption and International Engagement 220 Acknowledgments 220 References 221 13 The Future of CLEM: Summary 223 Lucy Collinson and Paul Verkade Index 227

About the Author :
PROFESSOR PAUL VERKADE, PHD, has been working in the field of Correlative Microscopy for over 15 years and is currently based at the School of Biochemistry at the University of Bristol, United Kingdom. DR LUCY COLLINSON, PHD, has been working in the field of Correlative Microscopy for the last 18 years and is currently Head of Electron Microscopy at the Francis Crick Institute, London, United Kingdom.