List of Contributors xi
Preface xiii
1 It's a Small, Small World: A Brief History of Biological Correlative Microscopy 1
Christopher J. Guerin, 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 Chichon, 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
