Ultrastructurally smooth thick partitioning and volume stitching for large-scale connectomics
Open accessAbstract
Focused-ion-beam scanning electron microscopy (FIB-SEM) has become an essential tool for studying neural tissue at resolutions below 10 nm × 10 nm × 10 nm, producing data sets optimized for automatic connectome tracing. We present a technical advance, ultrathick sectioning, which reliably subdivides embedded tissue samples into chunks (20 μm thick) optimally sized and mounted for efficient, parallel FIB-SEM imaging. These chunks are imaged separately and then 'volume stitched' back together, producing a final three-dimensional data set suitable for connectome tracing.
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We used improved hot-knife sectioning to section the brain into 37 sagittal slabs of 20 μm thickness with estimated material loss between consecutive slabs of only ∼30 nm - sufficiently small to allow tracing of long-distance neurites.
“We used an improved version of our previously published ‘hot-knife’ ultrathick sectioning procedure (Hayworth et al., 2015) which uses a heated, oil-lubricated diamond knife, to section the Drosophila brain into 37 sagittal slabs of 20 μm thickness with an estimated material loss between consecutive slabs of only ∼30 nm – sufficiently small to allow tracing of long-distance neurites.”
From A connectome and analysis of the adult Drosophila central brain (2020) · cites this paper as Hayworth et al., 2015
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- Authors
- Hayworth, K. J., Xu, C. S., Lu, Z., Knott, G. W., Fetter, R. D., Tapia, J. C., Lichtman, J. W., & Hess, H. F.
- Affiliations
- Howard Hughes Medical Institute (US)
- Dalhousie University (CA)
- École Polytechnique Fédérale de Lausanne (CH)
- Columbia University Irving Medical Center (US)
- Harvard University (US)
- Corresponding author
- Hayworth, Kenneth J
- ORCID
- Venue
- Nature Methods
- Published
- 2015-02-16
- Volume
- 12
- Issue
- 4
- Pages
- 319-322
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC4382383
- OpenAlex
- W2083707522
- Cited by
- 144
- References
- 22
- Citations by year
- 2026: 9 · 2025: 11 · 2024: 12 · 2023: 15 · 2022: 9 · 2021: 10 · 2020: 12 · 2019: 17 · 2018: 16 · 2017: 12 · 2016: 9 · 2015: 11 · 2014: 1
- FWCI
- 7.89
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
- Funders
- Howard Hughes Medical Institute
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Cell Image Analysis Techniques
- Keywords
- FIB-SEM, connectomics, parallel imaging, 3D reconstruction
- MeSH terms
- Animals, Brain, Microscopy, Electron, Scanning, Imaging, Three-Dimensional, Connectome
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