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Accelerating data sharing and reuse in volume electron microscopy

Nature Cell Biology volume 26, pages 498–503 (2024)Cite this article

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Volume electron microscopy (vEM) generates large 3D volumes of cells or tissues at nanoscale resolutions, enabling analyses of organelles in their cellular environment. Here, we provide examples of vEM in cell biology and discuss community efforts to develop standards in sample preparation and image acquisition for enhanced reproducibility and data reuse.

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Fig. 1: Examples illustrating the power of vEM.
Fig. 2: Comparison of vEM platforms.
Fig. 3: Examples of structures for volumetric analysis.
Fig. 4: Map of core facilities offering vEM services.

Data availability

vEM datasets and segmentation models have been deposited in EMPIAR: U2-OS cell (EMPIAR-11746; https://doi.org/10.6019/EMPIAR-11746), N. tabacum leaf mesophyll cell (EMPIAR-11831; https://doi.org/10.6019/EMPIAR-11831) and GM130 labelling on Huh-7 cell (EMPIAR-11849; https://doi.org/10.6019/EMPIAR-11849). Sample preparation for heavy contrasting is described in detail in Zenodo (https://doi.org/10.5281/zenodo.10024014) and later in the EMPIAR Sample Preparation Widget. Extended animations of Fig. 1e–h, Fig. 3a–c and Supplementary Video 1 have been uploaded to Zenodo (https://doi.org/10.5281/zenodo.10024014). Workflows for image segmentation of a U2-OS cell have been uploaded to Zenodo (https://doi.org/10.5281/zenodo.10043460).

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Acknowledgements

K.J.C. at the Danforth Center Advanced Bioimaging Laboratory (RRID:SCR_018951) was supported by the Chan Zuckerberg Initiative no. DAF2023-321243 and the US Department of Energy BER DE-SC0020348. The work of L.C. was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (CC1076), the UK Medical Research Council (CC1076) and the Wellcome Trust (CC1076). E.J. was supported by the Research Council of Finland (1331998) and Electron Microscopy Unit of the Institute of Biotechnology. E.J. and I.B. were supported by Biocenter Finland and Helsinki Institute of Life Science.

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Authors and Affiliations

  1. Advanced Bioimaging Laboratory, Donald Danforth Plant Science Center, Saint Louis, MO, USA

    Kirk James Czymmek

  2. Electron Microscopy Unit, Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland

    Ilya Belevich & Eija Jokitalo

  3. Euro-BioImaging ERIC Bio-Hub, European Molecular Biology Laboratory (EMBL) Heidelberg, Heidelberg, Germany

    Johanna Bischof & Aastha Mathur

  4. Electron Microscopy Science Technology Platform, Francis Crick Institute, London, UK

    Lucy Collinson

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  1. Kirk James Czymmek
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  4. Aastha Mathur
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  5. Lucy Collinson
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  6. Eija Jokitalo
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Corresponding author

Correspondence to Eija Jokitalo.

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The authors declare no competing interests.

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Nature Cell Biology thanks Feng-Xia Liang and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Extended data

Supplementary information

Reporting Summary

Supplementary Video

An animation of human bone osteosarcoma epithelial cell (U2-OS) starting with volume rendering of FIB-SEM dataset and showing models of mitochondria (green), nuclear envelope (light blue), peroxisomes (light yellow), lysosomes (purple), lipid droplets (red), endoplasmic reticulum (yellow) and Golgi complex (dark blue). The extended version showing an additional sequence of block-face images can be viewed from Zenodo

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Czymmek, K.J., Belevich, I., Bischof, J. et al. Accelerating data sharing and reuse in volume electron microscopy. Nat Cell Biol 26, 498–503 (2024). https://doi.org/10.1038/s41556-024-01381-3

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