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An open-access volume electron microscopy atlas of whole cells and tissues

Author

Listed:
  • C. Shan Xu

    (Howard Hughes Medical Institute)

  • Song Pang

    (Howard Hughes Medical Institute)

  • Gleb Shtengel

    (Howard Hughes Medical Institute)

  • Andreas Müller

    (University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden
    Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden
    German Center for Diabetes Research (DZD e.V.))

  • Alex T. Ritter

    (Genentech)

  • Huxley K. Hoffman

    (University of Denver
    University of Colorado Anschutz Medical Campus)

  • Shin-ya Takemura

    (Howard Hughes Medical Institute)

  • Zhiyuan Lu

    (Howard Hughes Medical Institute)

  • H. Amalia Pasolli

    (Howard Hughes Medical Institute
    The Rockefeller University)

  • Nirmala Iyer

    (Howard Hughes Medical Institute)

  • Jeeyun Chung

    (Harvard T.H. Chan School of Public Health
    Harvard Medical School)

  • Davis Bennett

    (Howard Hughes Medical Institute)

  • Aubrey V. Weigel

    (Howard Hughes Medical Institute)

  • Melanie Freeman

    (Howard Hughes Medical Institute
    University of California)

  • Schuyler B. Engelenburg

    (University of Denver)

  • Tobias C. Walther

    (Harvard T.H. Chan School of Public Health
    Harvard Medical School
    Howard Hughes Medical Institute
    Broad Institute of Harvard and MIT)

  • Robert V. Farese

    (Harvard T.H. Chan School of Public Health
    Harvard Medical School)

  • Jennifer Lippincott-Schwartz

    (Howard Hughes Medical Institute)

  • Ira Mellman

    (Genentech)

  • Michele Solimena

    (University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden
    Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden
    German Center for Diabetes Research (DZD e.V.)
    Max-Planck Institute of Molecular Cell Biology and Genetics)

  • Harald F. Hess

    (Howard Hughes Medical Institute)

Abstract

Understanding cellular architecture is essential for understanding biology. Electron microscopy (EM) uniquely visualizes cellular structures with nanometre resolution. However, traditional methods, such as thin-section EM or EM tomography, have limitations in that they visualize only a single slice or a relatively small volume of the cell, respectively. Focused ion beam-scanning electron microscopy (FIB-SEM) has demonstrated the ability to image small volumes of cellular samples with 4-nm isotropic voxels1. Owing to advances in the precision and stability of FIB milling, together with enhanced signal detection and faster SEM scanning, we have increased the volume that can be imaged with 4-nm voxels by two orders of magnitude. Here we present a volume EM atlas at such resolution comprising ten three-dimensional datasets for whole cells and tissues, including cancer cells, immune cells, mouse pancreatic islets and Drosophila neural tissues. These open access data (via OpenOrganelle2) represent the foundation of a field of high-resolution whole-cell volume EM and subsequent analyses, and we invite researchers to explore this atlas and pose questions.

Suggested Citation

  • C. Shan Xu & Song Pang & Gleb Shtengel & Andreas Müller & Alex T. Ritter & Huxley K. Hoffman & Shin-ya Takemura & Zhiyuan Lu & H. Amalia Pasolli & Nirmala Iyer & Jeeyun Chung & Davis Bennett & Aubrey , 2021. "An open-access volume electron microscopy atlas of whole cells and tissues," Nature, Nature, vol. 599(7883), pages 147-151, November.
  • Handle: RePEc:nat:nature:v:599:y:2021:i:7883:d:10.1038_s41586-021-03992-4
    DOI: 10.1038/s41586-021-03992-4
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    Citations

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    Cited by:

    1. Chixiang Lu & Kai Chen & Heng Qiu & Xiaojun Chen & Gu Chen & Xiaojuan Qi & Haibo Jiang, 2024. "Diffusion-based deep learning method for augmenting ultrastructural imaging and volume electron microscopy," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    2. Güneş Parlakgül & Song Pang & Leonardo L. Artico & Nina Min & Erika Cagampan & Reyna Villa & Renata L. S. Goncalves & Grace Yankun Lee & C. Shan Xu & Gökhan S. Hotamışlıgil & Ana Paula Arruda, 2024. "Spatial mapping of hepatic ER and mitochondria architecture reveals zonated remodeling in fasting and obesity," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    3. Andreas Müller & Nikolai Klena & Song Pang & Leticia Elizabeth Galicia Garcia & Oleksandra Topcheva & Solange Aurrecoechea Duran & Davud Sulaymankhil & Monika Seliskar & Hassan Mziaut & Eyke Schöniger, 2024. "Structure, interaction and nervous connectivity of beta cell primary cilia," Nature Communications, Nature, vol. 15(1), pages 1-18, December.

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