Correlative Imaging

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.

• List of Contributors xiPreface xiii1 It’s a Small, Small World: A Brief History of Biological Correlative Microscopy 1Christopher J. Guérin, Nalan Liv, and Judith Klumperman1.1 It All Began with Photons 11.2 The Electron Takes Its Place 21.3 Putting It Together, 1960s to 1980s 31.4 CLEM Matures as a Scientific Tool 1990 to 2017 4Acknowledgments 13References 132 Challenges for CLEM from a Light Microscopy Perspective 23Kurt Anderson, Tommy Nilsson, and Julia Fernandez‐Rodriguez2.1 Introduction 232.1.1 Electron and Light Microscopy 232.1.2 Correlative Microscopy: Two Cultures Collide 252.2 Microscopy Multiculturalism 262.2.1 When Fluorescence Light Microscopy Resolution is Not Enough 262.2.2 The Fluorescence Microscopy (FM), Needle/Haystack Localization 272.2.3 Electron Microscopy, Visualizing the Ultrastructure 272.2.4 Finding Coordinates 282.3 Bridging the Gap between Light and Electron Microscopy 292.3.1 Finding the Same Cell Structure in Light and Electron Microscopes 292.3.2 Making the Fluorescence Labels Visible in the Electron Microscope 292.3.3 Visualizing Membrane Trafficking Using CLEM 302.4 Future CLEM Applications and Modifications 312.4.1 Correlative Reflection Contrast Microscopy and Electron Microscopy in Tissue Sections 312.4.2 Dynamic and Functional Probes for CLEM 32References 343 The Importance of Sample Processing for Correlative Imaging (or, Rubbish In, Rubbish Out) 37Christopher J. Peddie and Nicole L. Schieber3.1 Introduction 373.2 Searching for Correlative Electron Microscopy Utopia 403.3 Sample Processing for Correlative Imaging: A Primer for the First Steps 403.4 Making It Go Faster (We Want More Speed, More Speed…) 423.5 Embedding Resins 443.6 Keeping the Region of Interest in Sight 453.7 Correlation and Relocation with Dual Modality Probes 483.8 Integration of Imaging Modalities, and In‐Resin Fluorescence 493.9 Streamlining the Correlative Approaches of the Future: SmartCLEM 513.10 How Deep Does the Rabbit Hole Go? 523.11 Hold That Thought, Though − Is This All Completely Necessary? 533.12 Improving Accessibility to Correlative Workflows 543.13 Coming to the End 55References 554 3D CLEM: Correlating Volume Light and Electron Microscopy 67Saskia Lippens and Eija Jokitalo4.1 Introduction 674.2 Imaging in 3D 684.3 Comparative and Correlative LM and EM Imaging 694.4 CLEM is More than LM + EM 694.5 3D CLEM 704.6 Two Workflows for 3D CLEM 714.7 Where is CLEM Going in the Future? 74Acknowledgments 76References 775 Can Correlative Microscopy Ever Be Easy? An Array Tomography Viewpoint 81Irina Kolotuev and Kristina D. Micheva5.1 Introduction 815.2 Why Array Tomography? 815.3 Array Tomography of Abundant Subcellular Structures: Synapses 825.4 Array Tomography of Sparsely Distributed Structures: Cisternal Organelle 845.5 Array Tomography of Small Model Organisms: C. elegans 875.6 To Summarize: Finding the Right AT Approach 905.7 Areas of Improvement 915.7.1 Resin 915.7.2 Serial Ultrathin Sectioning 915.7.3 Antibodies 925.7.4 EM Compatible Fluorophores 925.7.5 Detectors and EM Resolution 925.7.6 Image Registration and Alignment Tools 935.7.7 Data Sharing 935.7.8 “Dream” Resource 935.7.9 Dream Experiments 94Acknowledgments 95References 956 Correlative Microscopy Using Scanning Probe Microscopes 99Georg Fantner and Frank Lafont6.1 Introduction 996.2 Principles of AFM 1006.3 AFM and Optical Microscopy Correlative Approaches 1036.4 Correlation with CLSM 1046.5 Correlation with Cell Mechanics 1046.5.1 Correlation with Super‐Resolution Light Microscopy (SRLM) 1056.5.2 Future Developments 1076.6 AFM and Correlation with Electron Microscopy 1096.6.1 Correlation Involving AFM, EM, and Chemical Surface Characterization 1106.6.2 Future Developments 1136.7 Future Developments Involving Correlation Microscopy Using HS‐AFM 1136.8 Concluding Remarks 114Acknowledgments 114References 1157 Integrated Light and Electron Microscopy 119R. I. Koning, A. Srinivasa Raja, R. I. Lane, A. J. Koster, and J. P. Hoogenboom7.1 Introduction 1197.2 Large‐Scale and High‐Throughput (Volume) Microscopy 1207.2.1 Advantages and Challenges for Large‐Scale EM 1207.2.2 Advantages of CLEM for Large‐Scale EM 1217.2.3 Prospects for Integrated Microscopy 1217.3 Super‐Resolution Fluorescence Microscopy 1237.3.1 Advantages and Challenges for CLEM with Super‐Resolution Fluorescence 1237.3.2 Implementation of SR‐FM with CLEM 1247.3.3 Prospects for Integrated SR‐CLEM 1247.4 Cryo‐Electron Microscopy 1257.4.1 Advantages of CryoEM 1257.4.2 Possibilities and Challenges for Correlative Cryo‐Microscopy 1267.4.2.1 Super‐Resolution Fluorescence Cryo‐Microscopy: Probes and Instruments 1267.4.2.2 Transfer of Cryo‐Samples between Microscopes 1277.4.2.3 Sample Thickness 1277.4.2.4 Data Collection Speed 1287.4.3 Integrated Systems for CryoCLEM 1297.4.4 Prospects for Integrated Cryo‐Microscopy 1297.5 Outlook 130Acknowledgments 131References 1318 Cryo‐Correlative Light and Electron Microscopy: Toward in situ Structural Biology 137Tanmay A.M. Bharat and Wanda Kukulski8.1 Introduction 1378.2 Cryo‐CLEM to Support Single Particle Analysis of Purified Macromolecules 1388.3 Capturing Structural Dynamics of in vitro Reconstituted Systems 1418.4 Identifying Macromolecules in Plunge‐Frozen Whole Cells 1428.5 Macromolecular Structures in Thinned Samples from Thick Cell Areas 1448.6 Enabling Structural Biology in Multicellular Organisms and Tissues by Cryo‐CLEM 1458.7 Conclusions 147Acknowledgments 147References 1479 Correlative Cryo Soft X‐ray Imaging 155Eva Pereiro, Francisco Javier Chichón, and Jose L. Carrascosa9.1 Introduction to Cryo Soft X‐ray Microscopy 1559.2 Cryo‐SXT Correlation with Visible Light Microscopy 1599.3 Cryo‐SXT Correlation with Cryo X‐ray Fluorescence 1609.4 Cryo‐SXT Correlation with TEM 1639.5 Multiple Correlation and Integration of Methods 165Acknowledgments 165References 16610 Correlative Light‐ and Liquid‐Phase Scanning Transmission Electron Microscopy for Studies of Protein Function in Whole Cells 171Niels de Jonge10.1 Introduction 17110.2 Limitations of State‐of‐the‐Art Methods 17210.3 Principle of Liquid STEM 17310.3.1 Example 1: Determination of ORAI Channel Subunit Stoichiometry by Visualizing Single Molecules Using STEM 17510.3.1.1 Conclusions 17910.3.2 Example 2: New Insights into the Role of HER2 17910.3.2.1 Conclusions 18210.4 Advantages of Liquid STEM 18210.5 Future Prospects 184Acknowledgments 185References 18511 Correlating Data from Imaging Modalities 191Perrine Paul‐Gilloteaux and Martin Schorb11.1 Introduction 19111.2 Registration during CLEM Stages 19411.2.1 Registration to Guide Sample Preparation 19411.2.2 Registration to Guide the Acquisition 19511.2.2.1 Software Packages 19511.2.2.2 Typical Features and Fields of View 19511.2.3 Post‐Acquisition Registration (Accurate Relocation) 19611.2.3.1 Software and Approaches for Post‐Acquisition Registration 19611.2.4 Trust in Alignment: Accuracy in Practice 19811.3 Registration Paradigm 19811.3.1 Image Features to Guide the Registration 19811.3.2 Distance Function 19911.3.3 Transformation Basis 19911.3.4 Optimization Strategy 20011.4 Envisioned Future Developments 20111.4.1 Integrative Microscopy versus Correlative Microscopy 20111.4.2 Incorporate a Priori Knowledge of the Specimen 20211.4.3 Toward the Use of Machine Learning 20211.5 Visualization of Correlation 20411.6 Conclusion 204Acknowledgments 205References 20512 Big Data in Correlative Imaging 211Ardan Patwardhan and Jason R. Swedlow12.1 Introduction 21112.2 The Protein Data Bank 21212.3 Resources for Cryo‐EM 21212.4 Light Microscopy Data Resources 21412.5 EMPIAR 21512.6 IDR: A Prototype Image Data Resource 21612.7 Public Resources for Correlative Imaging 21712.7.1 CLEM Data Formats 21712.8 Future Directions 21812.8.1 A BioImage Archive 21812.8.2 CLEM Data Submission Pipelines 21912.8.3 Scaling Data Volumes and Usage 21912.8.4 Community Adoption and International Engagement 220Acknowledgments 220References 22113 The Future of CLEM: Summary 223Lucy Collinson and Paul VerkadeIndex 227