Volume Electron Microscopy
- 1st Edition, Volume 177 - June 23, 2023
- Editors: Kedar Narayan, Lucy Collinson, Paul Verkade
- Language: English
- Hardback ISBN:9 7 8 - 0 - 3 2 3 - 9 1 6 0 7 - 3
- eBook ISBN:9 7 8 - 0 - 3 2 3 - 9 1 6 0 8 - 0
Volume Electron Microscopy (vEM), Volume 177 is a collective term for a set of three-dimensional high-resolution ultrastructural imaging techniques that have delivered new insig… Read more
Purchase options
Institutional subscription on ScienceDirect
Request a sales quoteVolume Electron Microscopy (vEM), Volume 177 is a collective term for a set of three-dimensional high-resolution ultrastructural imaging techniques that have delivered new insights into biological systems in recent years, garnering substantial interest in the life and clinical sciences. In this book, users will find a variety of vEM workflows and technologies, highlighting application areas with biologically relevant examples. Topics covered include Automated large volume sample preparation for vEM, Resin comparison for Serial Block Face Scanning Volume Electron Microscopy, Immunolabelling for SBF-SEM, Electron Microscopy in Plants, Serial section electron tomography, Automated Tape Collecting Ultramicrotomy (ATUM) for targeting neuropathology, Array tomography, and much more.
Other sections focus on Mitochondria morphometry in 3d datasets of mouse brain obtained with serial block-face Scanning Electron Microscopy, Serial Block-face Scanning Electron Microscopy of Schmidtea mediterranea, Correlative multiscale microCT-SBF-SEM imaging of resin-embedded tissue, Methods of enhanced FIB-SEM sample preparation and image acquisition, Functional characterization of endo-lysosomal compartments by correlative live-cell and volume electron microscopy, and much more.
- Includes chapters written by key leaders and developers in the field
- Provides detailed protocols, allowing for the application of workflows in one’s own laboratory setting
- Presents real tips and tricks you won't get from standard research papers
PhD students, post-doctoral researchers, and imaging facility staff working in the life science research area with an interest in microscopy technologies and applying or aiming to apply 3D ultrastructural techniques to their research
- Cover image
- Title page
- Table of Contents
- Series Page
- Copyright
- Contributors
- Preface
- References
- Chapter 1: Automated large volume sample preparation for vEM
- Abstract
- 1: Introduction
- 2: Materials and methods
- 3: Results
- 4: Discussion
- Key resources table
- Acknowledgments
- References
- Chapter 2: Resin comparison for serial block face scanning volume electron microscopy
- Abstract
- 1: Introduction
- 2: Methods resin comparison
- 3: Results
- 4: Discussion
- Acknowledgments
- References
- Chapter 3: Nanogold based protein localization enables subcellular visualization of cell junction protein by SBF-SEM
- Abstract
- 1: Introduction
- 2: Before you begin
- 3: Key resources table
- 4: Materials and equipment
- 5: Step-by-step method details
- 6: Critical: Antibody specificity is very important for the success of IEM experiment
- 7: Critical: Stable room temperature and fixed silver developing time is essential for the reproducibility of the experimental results
- 8: Expected outcomes
- 9: Quantification and statistical analysis
- 10: Advantages
- 11: Limitations
- 12: Safety Considerations and Standards
- References
- Chapter 4: A conventional fixation volume electron microscopy protocol for plants
- Abstract
- 1: Introduction
- 2: Rationale
- 3: Methods
- 4: Instrumentation and materials
- 5: Discussion
- Acknowledgments
- References
- Chapter 5: Liver inter-organelle membrane contact sites revealed by serial section electron tomography
- Abstract
- 1: Introduction
- 2: Methods
- 3: Instrumentation and materials
- 4: Discussion
- Acknowledgments
- References
- Chapter 6: Neurons on tape: Automated Tape Collecting Ultramicrotomy-mediated volume EM for targeting neuropathology
- Abstract
- 1: Introduction
- 2: Rationale
- 3: Methods
- 4: Key resources table
- 5: Materials and Equipment
- 6: Expected outcomes
- 7: Limitations
- 8: Advantages
- Acknowledgments
- References
- Chapter 7: A practical guide to starting SEM array tomography—An accessible volume EM technique
- Abstract
- 1: Introduction
- 2: Rationale
- 3: Key resources table
- 4: Materials and equipment
- 5: Before you begin
- 6: Step-by-step method details
- 7: Discussion and advances
- 8: Prospects and future challenges
- Acknowledgments
- References
- Chapter 8: Mitochondria morphometry in 3D datasets obtained from mouse brains with serial block-face scanning electron microscopy
- Abstract
- 1: Introduction
- 2: Materials and equipment
- 3: Methods
- References
- Chapter 9: Serial block-face scanning electron microscopy of Schmidtea mediterranea
- Abstract
- 1: Introduction
- 2: Rationale
- 3: Methods
- 4: Summary
- Acknowledgments
- References
- Chapter 10: Correlative multiscale microCT-SBF-SEM imaging of resin-embedded tissue
- Abstract
- 1: Introduction
- 2: Methodology
- 3: Examples
- 4: Materials
- 5: Summary
- Acknowledgments
- References
- Chapter 11: Methods of enhanced FIB-SEM sample preparation and image acquisition
- Abstract
- 1: Introduction
- 2: Materials and instrumentation
- 3: Methods
- Acknowledgments
- References
- Chapter 12: Functional characterization of endo-lysosomal compartments by correlative live-cell and volume electron microscopy
- Abstract
- 1: Introduction
- 2: Materials and equipment
- 3: Step-by-step method details
- 4: Results
- 5: Quantification and statistical analysis
- 6: Advantages
- 7: Limitations
- Acknowledgments
- References
- Chapter 13: A protocol for cryogenic volumetric imaging using serial plasma FIB/SEM
- Abstract
- 1: Introduction
- 2: Overview of process
- 3: Methods
- 4: Conclusion
- Acknowledgments
- Funding
- Author contributions
- Conflict of interest
- References
- Chapter 14: Toward scalable reuse of vEM data: OME-Zarr to the rescue
- Abstract
- 1: Data challenges in the vEM community
- 2: OME-Zarr, a next-generation file format
- 3: How OME-Zarr meets the needs of vEM at scale
- 4: What does an OME-Zarr look like in more depth?
- 5: Image metadata and collections
- 6: Are OME-Zarrs for you?
- 7: Other practical considerations before you start
- 8: How can I view my OME-Zarrs?
- 9: How can I use OME-Zarrs in Python, MATLAB, …?
- 10: How do I share a collection of OME-Zarrs
- Acknowledgments
- References
- Chapter 15: Public archiving of volume EM data
- Abstract
- 1: Benefits of public archiving
- 2: Archiving vEM data at EMBL-EBI
- 3: Future plans
- Acknowledgments
- References
- No. of pages: 358
- Language: English
- Edition: 1
- Volume: 177
- Published: June 23, 2023
- Imprint: Academic Press
- Hardback ISBN: 9780323916073
- eBook ISBN: 9780323916080
KN
Kedar Narayan
Kedar Narayan is a senior scientist and group leader at the Center for Molecular Microscopy at Frederick National Laboratory and National Cancer Institute, USA. Kedar has a Ph.D. in immunology, with an emphasis on biophysics and imaging, and a background in chemistry, pathology and software engineering. His group has developed and applied FIB-SEM and other volume EM (vEM) technologies to questions in cancer and cell biology. Specific areas of Kedar’s research focus are correlative imaging, deep learning/AI and vEM tool development; he has co-authored more than forty papers and given invited talks around the world. His community work includes co-organizing symposia on volume EM and “large data”, leadership on data working groups, and creating common metadata standards for the field. As a leading member of the volume EM community, Kedar is committed to the growth and democratization of the field.
Affiliations and expertise
Frederick National Laboratory, NIH, Frederick, MD, USALC
Lucy Collinson
Dr. Lucy Collinson is an electron microscopist with a background in microbiology and cell biology. She has a degree and PhD in Medical Microbiology, and post-doctoral research investigating membrane trafficking pathways. She has run a series of biological EM facilities since 2004, at UCL and then at the Cancer Research UK London Research Institute, which became part of the Francis Crick Institute in 2015. With a team of 10 electron microscopists and 3 physicists, she oversees more than 100 research projects with more than 60 research groups within the Crick, imaging across scales from proteins to whole organisms. Her microscopy and technology development interests include volume EM, correlative imaging techniques, cryo-microscopy, X-ray microscopy, image analysis, citizen science, microscope design and prototyping. In 2019, she was one of four scientists who led the formation of a volume EM community initiative, and in 2023 will co-chair the first volume EM Gordon Research Conference.
Affiliations and expertise
The Francis Crick Institute, London, UKPV
Paul Verkade
Paul Verkade is a Professor of Bioimaging at the University of Bristol, UK where his research group works on the development and application of microscopy techniques to Biomedical questions. The main tools in the lab are Electron microscopy (EM) and Correlative Light Electron Microscopy (CLEM) in which fields he has published over 100 papers and edited 5 books on CLEM (including 4 Volumes of the Methods in Cell Biology series). PV obtained his PhD at the University of Utrecht, The Netherlands in 1996. Subsequently he did a post-doc at the EMBL, Heidelberg, Germany, after which he set up the electron microscopy unit at the newly formed Max Planck Institute for Molecular Cell Biology in Dresden, Germany from 2001. He moved to the UK in 2006 to set up another EM unit as part of an integrated LM and EM bioimaging facility, which facilitates CLEM workflows. He is actively involved in shaping the future microscopy landscape with roles in the Royal Microscopical Society and BioimagingUK and a current focus on putting volumeEM on the imaging map through community building and the organisation and co-chairing of the 1st Gordon Research Conference on vEM.
Affiliations and expertise
The University of Bristol, Bristol, UKRead Volume Electron Microscopy on ScienceDirect