Volume electron microscopy:
Saved in:
| Other Authors: | , , |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Cambridge, MA ; San Diego, CA ; Oxford ; London
Academic Press
2023
|
| Edition: | First edition |
| Series: | Methods in cell biology
volume 177 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | xviii, 399 Seiten Illustrationen, Diagramme |
| ISBN: | 9780323916073 |
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| 245 | 1 | 0 | |a Volume electron microscopy |c edited by Kedar Narayan (National Institutes of Health, Bethesda, MD, United States; Frederick National Laboratory for Cancer Research, Frederick, MD, United States), Lucy Collinson (The Francis Crick Institute, London, United Kingdom), Paul Verkade (University of Bristol, University Walk, Bristol, United Kingdom) |
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Contents Contributors. xi Preface. xvii Automated large volume sample preparation for vEM. 1 CHAPTER 1 Erin S. Stempinski, Lucas Pagano, Jessica L. Riesterer, Steven K. Adamou, Guillaume Thibault, Xubo Song, Young Hwan Chang, and Claudia S. López 1. Introduction. 2 2. Materials and methods. 5 3. Results. 17 4. Discussion. 24 Key resources table. 28 Acknowledgments. 30 References. 30 CHAPTER 2 Resin comparison for serial block face scanning volume electron microscopy. 33 Peter Borghgraef, Anna Kremer, Michiel De Bruyne, Christopher J. Guerin, and Saskia Lippens 1. Introduction. 34 2. Methods resin
comparison. 38 3. Results. 44 4. Discussion. 51 Acknowledgments.53 References. 53 CHAPTER 3 Nanogold based protein localization enables subcellular visualization of cell junction protein by SBF-SEM.55 Feng-Xia Liang, Joseph Sall, Chris Petzold, Chantal J.Μ. van Opbergen, Xiangxi Liang, and Mario Delmar 1. Introduction. 56 2. Before you begin. 59 V
vi Contents 3. Key resources table.59 4. Materials and equipment. 60 5. Step-by-step method details. 61 6. Critical: Antibody specificity is very important for the success of IEM experiment. 65 7. Critical·. Stable room temperature and fixed silver developing time is essential for the reproducibility of the experimental results. 67 8. Expected outcomes.74 9. Quantification and statisticalanalysis. 76 10. Advantages.76 11. Limitations.77 12. Safety Considerations andStandards. 78 Acknowledgments. 78 Author contribution.78 References. 78 CHAPTER 4 A conventional fixation volumeelectron microscopy protocol for plants. 83 Janithri S. Wickramanayake and Kirk
J. Czymmek 1. Introduction. 84 2. Rationale. 85 3. Methods. 86 4. Instrumentation and materials. 92 5. Discussion.94 Acknowledgments. 96 References.96 CHAPTER 5 Liver inter-organelie membrane contact sites revealed by serial section electrontomography. 101 Andrea Raimondi, Nicolò llacqua, and Luca Pellegrini 1. Introduction. 103 2. Methods. 107 3. Instrumentation and materials. 116 4. Discussion. 116 Acknowledgments. 119 References. 119
Contents CHAPTER 6 Neurons on tape: Automated Tape Collecting Ultramicrotomy-mediated volume EM for targeting neuropathology.125 Georg Kislinger, Cornelia Niemann, lucia Rodriguez, Hanyi Jiang, Maryam K. Fard, Nicolas Snaidero, Adrian-Minh Schumacher, Martin Kerschensteiner, Thomas Misgeld, and Martina Schifferer 1. Introduction. 127 2. Rationale. 129 3. Methods. 131 4. Key resources table. 158 5. Materials and Equipment. 159 6. Expected outcomes. 160 7. Limitations. 164 8. Advantages. 167 Acknowledgments.167 References. 168 CHAPTER 7 A practical guide to starting SEM array tomography—An accessible volume EM technique. 171 Ian J. White and Jemima J. Burden
Introduction.172 Rationale. 174 3. Key resources table. 177 4. Materials and equipment. 177 5. Before you begin. 178 6. Step-by-step method details. 180 7. Discussion and advances. 189 8. Prospects and future challenges. 192 Acknowledgments. 194 References. 194 1. 2. CHAPTER 8 Mitochondria morphometry in 3D datasets obtained from mouse brains with serial block-facescanning electron microscopy.197 Wei Jiao, Jean-Yves Chatton, and Christel Genoud 1. Introduction. 198 2. Materials and equipment.201 3. Methods. 202 References. 209 vii
viii Contents CHAPTER 9 Serial block-face scanning electron microscopy of Schmidtea mediterranea. 213 Melainia L. McClain and Stephanie H. Nowotarski 1. Introduction. 214 2. Rationale. 217 3. Methods. 217 4. Summary. 234 Acknowledgments. 237 References. 237 CHAPTER 10 Correlative muniscale microCT-SBF-SEM imaging of resin-embedded tissue. 241 Davis Laundon, Orestis L Katsamenis, Janies Thompson, Patricia Goggin, David S. Châtelet, Pascale Chavatte-Palmer, Neil J. Gostling, and Rohan Μ. Lewis 1. Introduction. 242 2. Methodology. 245 3. Examples. 259 4. Materials. 262 5. Summary. 265
Acknowledgments. 265 References. 265 CHAPTER 11 Methods of enhanced FIB-SEM sample preparation and imageacquisition. 269 Song Pang and C. Shan Xu 1. Introduction.270 2. Materials and instrumentation. 273 3. Methods. 273 Acknowledgments. 297 References. 298 CHAPTER 12 Functional characterization of endo-lysosomal compartments by correlative live-cell and volume electron microscopy. 301 Nalan Liv, Job Fermie, Corlinda В.М. ten Brink, Cecilia de Heus, and Judith Klumperman 1. Introduction. 303 2. Materials and equipment. 306
Contents 3. Step-by-step method details. 308 4. Results. 313 5. Quantification and statistical analysis. 320 6. Advantages. 321 7. Limitations. 321 Acknowledgments. 322 References. 322 CHAPTER 13 A protocol for cryogenic volumetric imaging using serial plasma FIB/SEM. 327 Maud Dumoux, Jake LR. Smith, Thomas Glen, Michael Grange, Michele C. Darrow, and James H. Naismith 1. Introduction. 328 2. Overview of process. 330 3. Methods. 332 4. Conclusion. 356 Acknowledgments. 356 Funding. 357 Author
contributions. 357 Conflict of interest. 357 References. 357 CHAPTER 14 Toward scalable reuse of vEM data: OME-Zarr to the rescue. 359 Norman Rzepka, John A. Bogovič, and Joshua A. Moore 1, Data challenges in thevEM community. 360 2. OME-Zarr, a next-generation file format. 365 3. How OME-Zarr meets the needs of vEM at scale. 366 4. What does an OME-Zarr look like in more depth?. 372 5. Image metadata and collections. 374 6. Are OME-Zarrs for you?. 375 7. Other practical considerations before you start. 377 8. How can I view my OME-Zarrs?. 380 9. How can I use OME-Zarrsin Python, MATLAB, .?. 381 10. How do I share a collection of OME-Zarrs. 382 Acknowledgments.383 References. 383 Glossary. 385 ix
x Contents CHAPTER 15 Public archiving of volume EM data. 389 Andrii ludin, Matthew Hartley, Gerard J. Kleywegt, and Ardan Patwardhan 1. Benefits of public archiving. 390 2. Archiving vEM data at EMBL-EBI. 390 3. Future plans. 396 Acknowledgments. 397 References. 397 |
| adam_txt |
Contents Contributors. xi Preface. xvii Automated large volume sample preparation for vEM. 1 CHAPTER 1 Erin S. Stempinski, Lucas Pagano, Jessica L. Riesterer, Steven K. Adamou, Guillaume Thibault, Xubo Song, Young Hwan Chang, and Claudia S. López 1. Introduction. 2 2. Materials and methods. 5 3. Results. 17 4. Discussion. 24 Key resources table. 28 Acknowledgments. 30 References. 30 CHAPTER 2 Resin comparison for serial block face scanning volume electron microscopy. 33 Peter Borghgraef, Anna Kremer, Michiel De Bruyne, Christopher J. Guerin, and Saskia Lippens 1. Introduction. 34 2. Methods resin
comparison. 38 3. Results. 44 4. Discussion. 51 Acknowledgments.53 References. 53 CHAPTER 3 Nanogold based protein localization enables subcellular visualization of cell junction protein by SBF-SEM.55 Feng-Xia Liang, Joseph Sall, Chris Petzold, Chantal J.Μ. van Opbergen, Xiangxi Liang, and Mario Delmar 1. Introduction. 56 2. Before you begin. 59 V
vi Contents 3. Key resources table.59 4. Materials and equipment. 60 5. Step-by-step method details. 61 6. Critical: Antibody specificity is very important for the success of IEM experiment. 65 7. Critical·. Stable room temperature and fixed silver developing time is essential for the reproducibility of the experimental results. 67 8. Expected outcomes.74 9. Quantification and statisticalanalysis. 76 10. Advantages.76 11. Limitations.77 12. Safety Considerations andStandards. 78 Acknowledgments. 78 Author contribution.78 References. 78 CHAPTER 4 A conventional fixation volumeelectron microscopy protocol for plants. 83 Janithri S. Wickramanayake and Kirk
J. Czymmek 1. Introduction. 84 2. Rationale. 85 3. Methods. 86 4. Instrumentation and materials. 92 5. Discussion.94 Acknowledgments. 96 References.96 CHAPTER 5 Liver inter-organelie membrane contact sites revealed by serial section electrontomography. 101 Andrea Raimondi, Nicolò llacqua, and Luca Pellegrini 1. Introduction. 103 2. Methods. 107 3. Instrumentation and materials. 116 4. Discussion. 116 Acknowledgments. 119 References. 119
Contents CHAPTER 6 Neurons on tape: Automated Tape Collecting Ultramicrotomy-mediated volume EM for targeting neuropathology.125 Georg Kislinger, Cornelia Niemann, lucia Rodriguez, Hanyi Jiang, Maryam K. Fard, Nicolas Snaidero, Adrian-Minh Schumacher, Martin Kerschensteiner, Thomas Misgeld, and Martina Schifferer 1. Introduction. 127 2. Rationale. 129 3. Methods. 131 4. Key resources table. 158 5. Materials and Equipment. 159 6. Expected outcomes. 160 7. Limitations. 164 8. Advantages. 167 Acknowledgments.167 References. 168 CHAPTER 7 A practical guide to starting SEM array tomography—An accessible volume EM technique. 171 Ian J. White and Jemima J. Burden
Introduction.172 Rationale. 174 3. Key resources table. 177 4. Materials and equipment. 177 5. Before you begin. 178 6. Step-by-step method details. 180 7. Discussion and advances. 189 8. Prospects and future challenges. 192 Acknowledgments. 194 References. 194 1. 2. CHAPTER 8 Mitochondria morphometry in 3D datasets obtained from mouse brains with serial block-facescanning electron microscopy.197 Wei Jiao, Jean-Yves Chatton, and Christel Genoud 1. Introduction. 198 2. Materials and equipment.201 3. Methods. 202 References. 209 vii
viii Contents CHAPTER 9 Serial block-face scanning electron microscopy of Schmidtea mediterranea. 213 Melainia L. McClain and Stephanie H. Nowotarski 1. Introduction. 214 2. Rationale. 217 3. Methods. 217 4. Summary. 234 Acknowledgments. 237 References. 237 CHAPTER 10 Correlative muniscale microCT-SBF-SEM imaging of resin-embedded tissue. 241 Davis Laundon, Orestis L Katsamenis, Janies Thompson, Patricia Goggin, David S. Châtelet, Pascale Chavatte-Palmer, Neil J. Gostling, and Rohan Μ. Lewis 1. Introduction. 242 2. Methodology. 245 3. Examples. 259 4. Materials. 262 5. Summary. 265
Acknowledgments. 265 References. 265 CHAPTER 11 Methods of enhanced FIB-SEM sample preparation and imageacquisition. 269 Song Pang and C. Shan Xu 1. Introduction.270 2. Materials and instrumentation. 273 3. Methods. 273 Acknowledgments. 297 References. 298 CHAPTER 12 Functional characterization of endo-lysosomal compartments by correlative live-cell and volume electron microscopy. 301 Nalan Liv, Job Fermie, Corlinda В.М. ten Brink, Cecilia de Heus, and Judith Klumperman 1. Introduction. 303 2. Materials and equipment. 306
Contents 3. Step-by-step method details. 308 4. Results. 313 5. Quantification and statistical analysis. 320 6. Advantages. 321 7. Limitations. 321 Acknowledgments. 322 References. 322 CHAPTER 13 A protocol for cryogenic volumetric imaging using serial plasma FIB/SEM. 327 Maud Dumoux, Jake LR. Smith, Thomas Glen, Michael Grange, Michele C. Darrow, and James H. Naismith 1. Introduction. 328 2. Overview of process. 330 3. Methods. 332 4. Conclusion. 356 Acknowledgments. 356 Funding. 357 Author
contributions. 357 Conflict of interest. 357 References. 357 CHAPTER 14 Toward scalable reuse of vEM data: OME-Zarr to the rescue. 359 Norman Rzepka, John A. Bogovič, and Joshua A. Moore 1, Data challenges in thevEM community. 360 2. OME-Zarr, a next-generation file format. 365 3. How OME-Zarr meets the needs of vEM at scale. 366 4. What does an OME-Zarr look like in more depth?. 372 5. Image metadata and collections. 374 6. Are OME-Zarrs for you?. 375 7. Other practical considerations before you start. 377 8. How can I view my OME-Zarrs?. 380 9. How can I use OME-Zarrsin Python, MATLAB, .?. 381 10. How do I share a collection of OME-Zarrs. 382 Acknowledgments.383 References. 383 Glossary. 385 ix
x Contents CHAPTER 15 Public archiving of volume EM data. 389 Andrii ludin, Matthew Hartley, Gerard J. Kleywegt, and Ardan Patwardhan 1. Benefits of public archiving. 390 2. Archiving vEM data at EMBL-EBI. 390 3. Future plans. 396 Acknowledgments. 397 References. 397 |
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| spelling | Volume electron microscopy edited by Kedar Narayan (National Institutes of Health, Bethesda, MD, United States; Frederick National Laboratory for Cancer Research, Frederick, MD, United States), Lucy Collinson (The Francis Crick Institute, London, United Kingdom), Paul Verkade (University of Bristol, University Walk, Bristol, United Kingdom) First edition Cambridge, MA ; San Diego, CA ; Oxford ; London Academic Press 2023 xviii, 399 Seiten Illustrationen, Diagramme txt rdacontent n rdamedia nc rdacarrier Methods in cell biology volume 177 Elektronenmikroskopie (DE-588)4014327-2 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Elektronenmikroskopie (DE-588)4014327-2 s DE-604 Narayan, Kedar edt Collinson, Lucy edt Verkade, Paul (DE-588)113549391X edt Methods in cell biology volume 177 (DE-604)BV002534878 177 Digitalisierung UB Regensburg - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=034632239&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
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| title | Volume electron microscopy |
| title_auth | Volume electron microscopy |
| title_exact_search | Volume electron microscopy |
| title_exact_search_txtP | Volume electron microscopy |
| title_full | Volume electron microscopy edited by Kedar Narayan (National Institutes of Health, Bethesda, MD, United States; Frederick National Laboratory for Cancer Research, Frederick, MD, United States), Lucy Collinson (The Francis Crick Institute, London, United Kingdom), Paul Verkade (University of Bristol, University Walk, Bristol, United Kingdom) |
| title_fullStr | Volume electron microscopy edited by Kedar Narayan (National Institutes of Health, Bethesda, MD, United States; Frederick National Laboratory for Cancer Research, Frederick, MD, United States), Lucy Collinson (The Francis Crick Institute, London, United Kingdom), Paul Verkade (University of Bristol, University Walk, Bristol, United Kingdom) |
| title_full_unstemmed | Volume electron microscopy edited by Kedar Narayan (National Institutes of Health, Bethesda, MD, United States; Frederick National Laboratory for Cancer Research, Frederick, MD, United States), Lucy Collinson (The Francis Crick Institute, London, United Kingdom), Paul Verkade (University of Bristol, University Walk, Bristol, United Kingdom) |
| title_short | Volume electron microscopy |
| title_sort | volume electron microscopy |
| topic | Elektronenmikroskopie (DE-588)4014327-2 gnd |
| topic_facet | Elektronenmikroskopie Aufsatzsammlung |
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