IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-60545-3.html
   My bibliography  Save this article

Reduction of SEM charging artefacts in native cryogenic biological samples

Author

Listed:
  • Abner Velazco

    (Harwell Science & Innovation Campus)

  • Thomas Glen

    (Harwell Science & Innovation Campus)

  • Sven Klumpe

    (Max Planck Institute of Biochemistry)

  • Avery Pennington

    (Harwell Science & Innovation Campus)

  • Jianguo Zhang

    (Harwell Science & Innovation Campus)

  • Jake L. R. Smith

    (Harwell Science & Innovation Campus
    University of Oxford)

  • Calina Glynn

    (Harwell Science & Innovation Campus)

  • William Bowles

    (Harwell Science & Innovation Campus
    University of Oxford
    Harwell Science & Innovation Campus)

  • Maryna Kobylynska

    (King’s College London)

  • Roland A. Fleck

    (King’s College London
    King’s College London)

  • James H. Naismith

    (Physical and Life Science Division)

  • Judy S. Kim

    (Harwell Science & Innovation Campus
    University of Oxford)

  • Michele C. Darrow

    (Harwell Science & Innovation Campus)

  • Michael Grange

    (Harwell Science & Innovation Campus
    University of Oxford)

  • Angus I. Kirkland

    (Harwell Science & Innovation Campus
    University of Oxford)

  • Maud Dumoux

    (Harwell Science & Innovation Campus)

Abstract

Scanning electron microscopy (SEM) of frozen-hydrated biological samples allows imaging of subcellular structures at the mesoscale in a representation of their native state. Combined with focused ion beam milling (FIB), serial FIB/SEM can be used to build a 3-dimensional model of cells and tissues. The correlation of specific regions of interest with cryo-electron microscopy (cryoEM) can additionally enable subsequent high-resolution analysis. However, the use of serial FIB/SEM imaging-based methods is often limited due to charging artefacts arising from insulating areas of cryogenically preserved samples. Here, we demonstrate the use of interleaved scanning to attenuate these artefacts, allowing the observation of biological features that otherwise would be masked or distorted. We apply our method to samples where inherent features were not visible using conventional scanning. These examples include membrane contact sites within mammalian cells, visualisation of the degradation compartment in the algae E. gracilis and observation of a network of membranes within different types of axons in an adult mouse cortex. The proposed alternative scanning method could also be applied to imaging other non-conductive specimens in SEM.

Suggested Citation

  • Abner Velazco & Thomas Glen & Sven Klumpe & Avery Pennington & Jianguo Zhang & Jake L. R. Smith & Calina Glynn & William Bowles & Maryna Kobylynska & Roland A. Fleck & James H. Naismith & Judy S. Kim , 2025. "Reduction of SEM charging artefacts in native cryogenic biological samples," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-60545-3
    DOI: 10.1038/s41467-025-60545-3
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-60545-3
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-025-60545-3?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Niamh B. McNamara & David A. D. Munro & Nadine Bestard-Cuche & Akiko Uyeda & Jeroen F. J. Bogie & Alana Hoffmann & Rebecca K. Holloway & Irene Molina-Gonzalez & Katharine E. Askew & Stephen Mitchell &, 2023. "Microglia regulate central nervous system myelin growth and integrity," Nature, Nature, vol. 613(7942), pages 120-129, January.
    2. Larissa Heinrich & Davis Bennett & David Ackerman & Woohyun Park & John Bogovic & Nils Eckstein & Alyson Petruncio & Jody Clements & Song Pang & C. Shan Xu & Jan Funke & Wyatt Korff & Harald F. Hess &, 2021. "Whole-cell organelle segmentation in volume electron microscopy," Nature, Nature, vol. 599(7883), pages 141-146, November.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Zhongxiao Fu & Mallikarjunarao Ganesana & Philip Hwang & Xiao Tan & Melissa Marie Kinkaid & Yu-Yo Sun & Emily Bian & Aden Weybright & Hong-Ru Chen & Katia Sol-Church & Ukpong B. Eyo & Clare Pridans & , 2025. "Microglia modulate the cerebrovascular reactivity through ectonucleotidase CD39," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    2. Leon D. Lotter & Amin Saberi & Justine Y. Hansen & Bratislav Misic & Casey Paquola & Gareth J. Barker & Arun L. W. Bokde & Sylvane Desrivières & Herta Flor & Antoine Grigis & Hugh Garavan & Penny Gowl, 2024. "Regional patterns of human cortex development correlate with underlying neurobiology," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    3. Xiaofeng Yan & Shudong Li & Weilin Huang & Hao Wang & Tianfang Zhao & Mingtao Huang & Niyun Zhou & Yuan Shen & Xueming Li, 2025. "MPicker: visualizing and picking membrane proteins for cryo-electron tomography," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
    4. 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.
    5. Isshin Shiiba & Naoki Ito & Hijiri Oshio & Yuto Ishikawa & Takahiro Nagao & Hiroki Shimura & Kyu-Wan Oh & Eiki Takasaki & Fuya Yamaguchi & Ryoan Konagaya & Hisae Kadowaki & Hideki Nishitoh & Takehito , 2025. "ER-mitochondria contacts mediate lipid radical transfer via RMDN3/PTPIP51 phosphorylation to reduce mitochondrial oxidative stress," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
    6. Jianping Wu & Georg Kislinger & Jerome Duschek & Ayşe Damla Durmaz & Benedikt Wefers & Ruoqing Feng & Karsten Nalbach & Wolfgang Wurst & Christian Behrends & Martina Schifferer & Mikael Simons, 2024. "Nonvesicular lipid transfer drives myelin growth in the central nervous system," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    7. Xia Li & Feng Qiao & Jiansheng Guo & Ting Jiang & Huifang Lou & Huixia Li & Gangcai Xie & Hangjun Wu & Weizhen Wang & Ruoyu Pei & Sha Liu & Mei Ye & Jin Li & Shiqin Huang & Mengya Zhang & Chaoye Ma & , 2025. "In situ architecture of the intercellular organelle reservoir between epididymal epithelial cells by volume electron microscopy," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    8. Weria Pezeshkian & John H. Ipsen, 2024. "Mesoscale simulation of biomembranes with FreeDTS," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    9. Karl Zhanghao & Meiqi Li & Xingye Chen & Wenhui Liu & Tianling Li & Yiming Wang & Fei Su & Zihan Wu & Chunyan Shan & Jiamin Wu & Yan Zhang & Jingyan Fu & Peng Xi & Dayong Jin, 2025. "Fast segmentation and multiplexing imaging of organelles in live cells," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
    10. Katerina Jerabkova-Roda & Marina Peralta & Kuang-Jing Huang & Antoine Mousson & Clara Bourgeat Maudru & Louis Bochler & Ignacio Busnelli & Rabia Karali & Hélène Justiniano & Lucian-Mihai Lisii & Phili, 2025. "Peripheral positioning of lysosomes supports melanoma aggressiveness," Nature Communications, Nature, vol. 16(1), pages 1-16, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-60545-3. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.