Imaging ATUM ultrathin section libraries with WaferMapper: a multi-scale approach to EM reconstruction of neural circuits
Open accessAbstract
The automated tape-collecting ultramicrotome (ATUM) makes it possible to collect large numbers of ultrathin sections quickly-the equivalent of a petabyte of high resolution images each day. However, even high throughput image acquisition strategies generate images far more slowly (at present ~1 terabyte per day). We therefore developed WaferMapper, a software package that takes a multi-resolution approach to mapping and imaging select regions within a library of ultrathin sections. This automated method selects and directs imaging of corresponding regions within each section of an ultrathin section library (UTSL) that may contain many thousands of sections. Using WaferMapper, it is possible to map thousands of tissue sections at low resolution and target multiple points of interest for high resolution imaging based on anatomical landmarks. The program can also be used to expand previously imaged regions, acquire data under different imaging conditions, or re-image after additional tissue treatments.
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The masking of membrane specializations is probably one of the reasons why many ultrastructural studies that used high concentrations of potassium ferrocyanide/ferricyanide (1.5-3.0%) provided no data on SS.
“This is probably one of the reasons why many ultrastructural studies that utilized high concentrations of potassium ferrocyanide/ferricyanide (1.5–3.0%) provided no data on SS (e.g., Harris and Stevens, 1989; Hayworth et al., 2014; Yakoubi et al., 2019a; Yin et al., 2020; Gour et al., 2021; Phelps et al., 2021; Peddie et al., 2022; Turner et al., 2022).”
From Unambiguous identification of asymmetric and symmetric synapses using volume electron microscopy (2024) · cites this paper as Hayworth et al., 2014
In Sample preparation > Tissue processing (page not provided), Hayworth et al. say they often use (R)OTO staining and that its thickening and darkening of membranes can make synapses harder to identify in single sections. Our copy does not specify 1.5–3.0% potassium ferrocyanide/ferricyanide or say that masking membrane specializations caused the absence of SS data. (LLM, conf=0.82)
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“The images were acquired using a Zeiss Field-Emission Scanning Electron Microscope using WaferMapper software 65 .”
Unambiguous identification of asymmetric and symmetric synapses using volume electron microscopy
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- Authors
- Hayworth, K. J., Morgan, J. L., Schalek, R., Berger, D. R., Hildebrand, D. G. C., & Lichtman, J. W.
- Affiliations
- Howard Hughes Medical Institute (US)
- Harvard University (US)
- Corresponding author
- Hayworth, Kenneth J.
- Morgan, Josh L.
- ORCID
- Venue
- Frontiers in Neural Circuits
- Publisher
- Frontiers Media SA
- Published
- 2014-06-27
- Volume
- 8
- Pages
- 68-68
- ISSN
- 1662-5110 (ISSN-L)
- PMC
- PMC4073626
- OpenAlex
- W2157151515
- Cited by
- 282
- References
- 2
- Citations by year
- 2026: 17 · 2025: 24 · 2024: 26 · 2023: 19 · 2022: 18 · 2021: 29 · 2020: 20 · 2019: 23 · 2018: 26 · 2017: 21 · 2016: 27 · 2015: 29 · 2014: 3
- FWCI
- 14.55
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Frontiers in Neural Circuits (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Institutes of Health
- National Heart, Lung, and Blood Institute (T32HL007901)
- National Institute of Mental Health (P50MH094271, 5T32MH20017, T32MH020017)
- National Institute of Neurological Disorders and Stroke (U01NS090449, R01NS076467, TR01 1R01NS076467-01)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Cell Image Analysis Techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Advanced Fluorescence Microscopy Techniques
- Keywords
- multiscale imaging, neural circuit reconstruction, high-throughput imaging
- MeSH terms
- Animals, Brain, Brain Mapping, Image Processing, Computer-Assisted, Microscopy, Electron, Microtomy, Software, Staining and Labeling, Tissue Embedding, Imaging, Three-Dimensional
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