Volume scanning electron microscopy for imaging biological ultrastructure
Abstract
Electron microscopy (EM) has been a key imaging method to investigate biological ultrastructure for over six decades. In recent years, novel volume EM techniques have significantly advanced nanometre-scale imaging of cells and tissues in three dimensions. Previously, this had depended on the slow and error-prone manual tasks of cutting and handling large numbers of sections, and imaging them one-by-one with transmission EM. Now, automated volume imaging methods mostly based on scanning EM (SEM) allow faster and more reliable acquisition of serial images through tissue volumes and achieve higher z-resolution. Various software tools have been developed to manipulate the acquired image stacks and facilitate quantitative analysis. Here, we introduce three volume SEM methods: serial block-face electron microscopy (SBEM), focused ion beam SEM (FIB-SEM) and automated tape-collecting ultramicrotome SEM (ATUM-SEM). We discuss and compare their capabilities, provide an overview of the full volume SEM workflow for obtaining 3D datasets and showcase different applications for biological research.
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Focused Ion Beam Milling and Scanning Electron Microscopy (FIB-SEM) enables automated serial sectioning of large volumes of tissue, without any mechanical interaction with the sample.
“This technology was chosen because it enables automated serial sectioning of large volumes of tissue, without any mechanical interaction with the sample (e.g., see Knott et al., 2008; Merchán-Pérez et al., 2009; Titze and Genoud, 2016; Kubota et al., 2018; Rollenhagen et al., 2020).”
From Unambiguous identification of asymmetric and symmetric synapses using volume electron microscopy (2024) · cites this paper as Titze and Genoud, 2016
Cites
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“Notable among research efforts that pushed the limits of this technique was the reconstruction of the entire nervous system of the roundworm Caenorhabditis elegans (White et al., 1986).”
BackgroundSerial Block-Face Scanning Electron Microscopy to Reconstruct Three-Dimensional Tissue Nanostructure
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Enhanced FIB-SEM systems for large-volume 3D imaging
Xu, C. S., Hayworth, K. J., Lu, Z., Grob, P., Hassan, A. M., García-Cerdán, J. G., Niyogi, K. K., Nogales, E., Weinberg, R. J., & Hess, H. F. (2017) · eLife · doi:10.7554/elife.25916 · Cited by 411 · see citing works
Unambiguous identification of asymmetric and symmetric synapses using volume electron microscopy
Cano-Astorga, N., Plaza-Alonso, S., Turegano-Lopez, M., Rodrigo-Rodríguez, J., Merchan-Perez, A., & DeFelipe, J. (2024) · Frontiers in Neuroanatomy · doi:10.3389/fnana.2024.1348032 · Cited by 17 · see citing works
“This technology was chosen because it enables automated serial sectioning of large volumes of tissue, without any mechanical interaction with the sample (e.g., see Knott et al., 2008; Merchán-Pérez et al., 2009; Titze and Genoud, 2016; Kubota et al., 2018; Rollenhagen et al., 2020).”
Method
- Authors
- Titze, B., & Genoud, C.
- Affiliations
- Friedrich Miescher Institute (CH)
- Corresponding author
- Titze, Benjamin
- Venue
- Biology of the Cell
- Publisher
- Wiley
- Published
- 2016-08-12
- Volume
- 108
- Issue
- 11
- Pages
- 307-323
- ISSN
- 0248-4900 (ISSN-L)
- 1768-322X
- OpenAlex
- W2480732292
- Cited by
- 287
- References
- 6
- Citations by year
- 2026: 20 · 2025: 21 · 2024: 31 · 2023: 51 · 2022: 37 · 2021: 28 · 2020: 41 · 2019: 19 · 2018: 23 · 2017: 14 · 2016: 1 · 2015: 1
- FWCI
- 1.93
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Biology of the Cell (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
- Physical Sciences › Engineering › Biomedical Engineering › Advanced Materials Characterization Techniques
- Physical Sciences › Materials Science › Surfaces, Coatings and Films › Electron and X-Ray Spectroscopy Techniques
- Keywords
- volume electron microscopy, serial block-face electron microscopy, z-resolution
- MeSH terms
- Animals, Brain, Humans, Image Processing, Computer-Assisted, Microscopy, Electron, Scanning, Microtomy, Histocytological Preparation Techniques
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