Correlative Light and Electron Microscopy III

Correlative Light and Electron Microscopy III, Volume 140 , a new volume in the Methods in Cell Biology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. Topics discussed in this new release include Millisecond time-resolved CLEM, Super resolution LM und SEM of high-pressure frozen C. elegans, Preservation fluorescence, super res CLEM, APEX in Tissue, Corrsight mit IBIDI flowthrough chamber, Correlative Light Atomic Force Electronic Microscopy (CLAFEM), Atmospheric EM CLEM, and High-precision correlation, amongst other topics.

Chapters in this ongoing series deal with different approaches for analyzing the same specimen using more than one imaging technique. The strengths and application area of each is presented, with this volume exploring the aspects of sample preparation of diverse biological systems for different CLEM approaches.

Author Notes

Dr. Thomas M#65533;ller-Reichert is interested in how the microtubule cytoskeleton is modulated within cells to fulfill functions in meiosis, mitosis and abscission. The M#65533;ller-Reichert lab is mainly applying correlative light microscopy and electron tomography to study the 3D organization of microtubules in the early embryo of the nematode Caenorhabditis elegans and in tissue culture cells. He got his PhD degree from the Swiss Federal Institute of Technology (ETH) in Zurich and moved afterwards to the EMBL in Heidelberg (Germany) for a post-doc with Dr. Tony Hyman. He was a visiting scientist with Dr. Kent McDonald (UC Berkeley, USA) and set up the electron microscope facility at the newly founded Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG). Since 2010 he is head of the Core Facility Cellular Imaging (CFCI) of the Medical Faculty Carl Gustav Carus of the TU Dresden (Germany).

Together with Dr. Paul Verkade he has developed a rapid transfer system for high-pressure freezing used for Correlative Light and Electron Microcopy. He has organized a number microscopy conferences and taught in several (CL)EM courses. He edited an MCB volume on the Electron Microscopy of Model Systems.

Dr. Paul Verkade's research focuses on the sorting mechanisms in intracellular transport pathways. His main tools are microscopy techniques, with an emphasis on electron microscopy (EM) in which field he has published over 50 papers. He has studied and got his PhD degree at the University of Utrecht, the Netherlands. After his post-doc time at the EMBL, Heidelberg, Germany in the group of Kai Simons and setting up a new EM lab at the Max Planck Institute for Molecular Cell Biology in Dresden, Germany he moved to the University of Bristol, UK in 2006. Here he set up a new EM unit as part of the Wolfson Bioimaging Facility, a fully integrated light and electron microscopy centre.

To support his transport studies, part of his research is to develop techniques and tools for the use of Correlative Light Electron Microscopy (CLEM). Amongst other things he has developed the Rapid Transfer System for the EMPACT2 high-pressure freezer together with Leica Microsystems. This allows for the combination of time-resolved CLEM with optimal preservation of ultrastructure for EM.

Dr. Verkade is chair of the Electron Microscopy section of the Royal Microscopical Society (RMS) and of the Cryo Microscopy Group, affiliated to the RMS. He has organised and taught on a large number of courses and workshops on subjects such as high-pressure freezing, Correlative Light Electron Microscopy, and immuno EM. He is also the principle organiser of the EMBO practical course on CLEM.

Ludek Stepanek and Gaia PiginoSebastian M. Markert and Vivien Bauer and Thomas S. Muenz and Nicola G. Jones and Frederik Helmprobst and Sebastian Britz and Markus Sauer and Wolfgang Rössler and Markus Engstler and Christian StigloherErrin Johnson and Rainer KaufmannNicole L. Schieber and Pedro Machado and Sebastian M. Markert and Christian Stigloher and Yannick Schwab and Anna M. SteyerAndroniki Kolovou and Martin Schorb and Abul Tarafder and Carsten Sachse and Yannick Schwab and Rachel Santarella-MellwigNicholas Ariotti and Thomas E. Hall and Robert G. PartonMiriam S. Lucas and Maja Günthert and Anne Greet Bittermann and Alex de Marco and Roger WepfClaudia S. López and Cedric Bouchet-Marquis and Christopher P. Arthur and Jessica L. Riesterer and Gregor Heiss and Guillaume Thibault and Lee Pullan and Sunjong Kwon and Joe W. GraySébastien Janel and Elisabeth Werkmeister and Antonino Bongiovanni and Frank Lafont and Nicolas BaroisChikara Sato and Takaaki Kinoshita and Nassirhadjy Memtily and Mari Sato and Shoko Nishihara and Toshiko Yamazawa and Shinya SugimotoDelfine Cheng and Gerald Shami and Marco Morsch and Minh Huynh and Patrick Trimby and Filip BraetRobert M. Lees and Christopher J. Peddie and Lucy M. Collinson and Michael C. Ashby and Paul VerkadeMatthia A. Karreman and Bernhard Ruthensteiner and Luc Mercier and Nicole L. Schieber and Gergely Solecki and Frank Winkler and Jacky G. Goetz and Yannick SchwabNicholas R. Ader and Wanda KukulskiMartin Schorb and Frank SieckmannXavier Heiligenstein and Perrine Paul-Gilloteaux and Graça Raposo and Jean Salamero

Contributors	p. xi
Preface	p. xvii
Chapter 1 Millisecond Time Resolution Correlative Light and Electron Microscopy for Dynamic Cellular Processes	p. 1
Introduction	p. 2
1 Methods	p. 3
2 Instrumentation and Materials	p. 15
3 Discussion and Outlook	p. 17
Acknowledgments	p. 18
References	p. 18
Chapter 2 3D Subcellular Localization With Superresolution Array Tomography on Ultrathin Sections of Various Species	p. 21
Introduction and Rationale	p. 22
1 Methods-Core Protocol	p. 23
2 Methods-Model-Specific Adaptations and Considerations	p. 34
3 Instrumentation and Materials	p. 41
Conclusions	p. 43
Acknowledgments	p. 45
References	p. 45
Chapter 3 Preserving the Photoswitching Ability of Standard Fluorescent Proteins for Correlative In-Resin Super-resolution and Electron Microscopy	p. 49
Introduction	p. 50
1 Rationale	p. 52
2 Materials	p. 54
3 Methods	p. 55
4 Discussion	p. 63
Acknowledgments	p. 65
References	p. 65
Chapter 4 Minimal Resin Embedding of Multicellular Specimens for Targeted FIB-SEM Imaging	p. 69
Introduction	p. 70
1 Rationale	p. 71
2 Methods	p. 71
3 Results: FIB-SEM Targeting and Imaging	p. 75
4 Instrumentation and Materials	p. 77
5 Discussion	p. 79
Acknowledgments	p. 81
References	p. 81
Chapter 5 A New Method for Cryo-Sectioning Cell Monolayers Using a Correlative Workflow	p. 85
Introduction	p. 86
1 Rationale	p. 87
2 Methods	p. 88
3 Instrumentation, Materials, and Reagents	p. 98
4 Results and Discussion	p. 100
Acknowledgments	p. 101
References	p. 101
Chapter 6 Correlative Light and Electron Microscopic Detection of GFP-Labeled Proteins Using Modular APEX	p. 105
1 Vectors for Correlative Light and Electron Microscopy in Mammalian Cell Culture and Whole Zebrafish	p. 107
2 Correlative Light and Electron Microscopy in Cell Culture	p. 108
3 Subcellular Protein Distribution Analysis of Transgenic Zebrafish	p. 115
References	p. 121
Chapter 7 Correlation of Live-Cell Imaging With Volume Scanning Electron Microscopy	p. 123
Introduction	p. 124
1 Rationale	p. 126
2 Methods	p. 126
3 Materials	p. 139
4 Discussion	p. 140
Conclusions	p. 145
Acknowledgments	p. 146
References	p. 146
Chapter 8 A Fully Integrated, Three-Dimensional Fluorescence to Electron Microscopy Correlative Workflow	p. 149
Introduction	p. 150
1 Materials and Methods	p. 151
2 Discussion	p. 159
3 Summary	p. 161
Acknowledgments	p. 161
Supplementary data	p. 162
References	p. 162
Chapter 9 CLAFEM: Correlative Light Atomic Force Electron Microscopy	p. 165
Introduction	p. 166
1 Materials and Methods	p. 170
2 Results and Discussion	p. 173
Acknowledgments	p. 181
References	p. 181
Chapter 10 Correlative Light-Electron Microscopy in Liquid Using an Inverted SEM (ASEM)	p. 187
Introduction	p. 188
1 Instrument Design and Sample Geometry of the Atmospheric Scanning Electron Microscopy	p. 189
2 The Application of Correlative Light-Electron Microscopy Using Atmospheric Scanning Electron Microscopy	p. 193
3 Discussion	p. 208
Conclusion	p. 210
Acknowledgments	p. 211
References	p. 211
Chapter 11 Relocation is the Key to Successful Correlative Fluorescence and Scanning Electron Microscopy	p. 215
Introduction	p. 216
1 Rationale	p. 219
2 Methods	p. 220
3 Instrumentation and Materials	p. 228
4 Results	p. 230
5 Discussion	p. 235
Acknowledgments	p. 240
References	p. 240
Chapter 12 Correlative Two-Photon and Serial Block Face Scanning Electron Microscopy in Neuronal Tissue Using 3D Near-Infrared Branding Maps	p. 245
Introduction	p. 246
1 Rationale	p. 251
2 Methods	p. 251
Concluding Remarks	p. 273
Acknowledgments	p. 274
References	p. 274
Chapter 13 Find Your Way With X-Ray: Using microCT to Correlate In Vivo Imaging With 3D Electron Microscopy	p. 277
Introduction	p. 278
1 Methods	p. 280
2 Instrumentation and Materials	p. 297
3 Discussion	p. 298
Acknowledgments	p. 299
References	p. 299
Chapter 14 triCLEM: Combining High-Precision, Room Temperature CLEM With Cryo-Fluorescence Microscopy to Identify Very Rare Events	p. 303
Introduction	p. 304
1 Methods	p. 307
2 Instrumentation and Materials	p. 315
3 Discussion	p. 316
Acknowledgments	p. 317
References	p. 318
Chapter 15 Matrix MAPS-An Intuitive Software to Acquire, Analyze, and Annotate Light Microscopy Data for CLEM	p. 321
Introduction	p. 322
1 The Software	p. 323
2 Workflow	p. 325
3 Discussion/Outlook	p. 330
Acknowledgments	p. 331
References	p. 331
Chapter 16 eC-CLEM: a Multidimension, Multimodel Software to Correlate Intermodal Images With a Focus on Light and Electron Microscopy	p. 335
Introduction	p. 336
1 Material	p. 336
2 Image Preprocessing and Automatic Detection of the Melanosomes in Both Imaging Modalities	p. 338
3 Identify the Transformation Project	p. 343
4 Setting the Autofinder Parameters to Get Accurate Initial Registration	p. 346
5 Manual Registration Versus Autofinder	p. 350
6 3D Transformations	p. 351
References	p. 351

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