IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-45042-3.html
   My bibliography  Save this article

DeepFocus: fast focus and astigmatism correction for electron microscopy

Author

Listed:
  • P. J. Schubert

    (Max Planck Institute for Biological Intelligence)

  • R. Saxena

    (Max Planck Institute for Biological Intelligence)

  • J. Kornfeld

    (Max Planck Institute for Biological Intelligence)

Abstract

High-throughput 2D and 3D scanning electron microscopy, which relies on automation and dependable control algorithms, requires high image quality with minimal human intervention. Classical focus and astigmatism correction algorithms attempt to explicitly model image formation and subsequently aberration correction. Such models often require parameter adjustments by experts when deployed to new microscopes, challenging samples, or imaging conditions to prevent unstable convergence, making them hard to use in practice or unreliable. Here, we introduce DeepFocus, a purely data-driven method for aberration correction in scanning electron microscopy. DeepFocus works under very low signal-to-noise ratio conditions, reduces processing times by more than an order of magnitude compared to the state-of-the-art method, rapidly converges within a large aberration range, and is easily recalibrated to different microscopes or challenging samples.

Suggested Citation

  • P. J. Schubert & R. Saxena & J. Kornfeld, 2024. "DeepFocus: fast focus and astigmatism correction for electron microscopy," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-45042-3
    DOI: 10.1038/s41467-024-45042-3
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-45042-3
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-024-45042-3?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. Steffen Klein & Mirko Cortese & Sophie L. Winter & Moritz Wachsmuth-Melm & Christopher J. Neufeldt & Berati Cerikan & Megan L. Stanifer & Steeve Boulant & Ralf Bartenschlager & Petr Chlanda, 2020. "SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    2. Yunfeng Hua & Philip Laserstein & Moritz Helmstaedter, 2015. "Large-volume en-bloc staining for electron microscopy-based connectomics," Nature Communications, Nature, vol. 6(1), pages 1-7, 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. Scotland E. Farley & Jennifer E. Kyle & Hans C. Leier & Lisa M. Bramer & Jules B. Weinstein & Timothy A. Bates & Joon-Yong Lee & Thomas O. Metz & Carsten Schultz & Fikadu G. Tafesse, 2022. "A global lipid map reveals host dependency factors conserved across SARS-CoV-2 variants," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    2. Katelyn C. Cook & Elene Tsopurashvili & Jason M. Needham & Sunnie R. Thompson & Ileana M. Cristea, 2022. "Restructured membrane contacts rewire organelles for human cytomegalovirus infection," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
    3. Carles Bosch & Tobias Ackels & Alexandra Pacureanu & Yuxin Zhang & Christopher J. Peddie & Manuel Berning & Norman Rzepka & Marie-Christine Zdora & Isabell Whiteley & Malte Storm & Anne Bonnin & Chris, 2022. "Functional and multiscale 3D structural investigation of brain tissue through correlative in vivo physiology, synchrotron microtomography and volume electron microscopy," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    4. Gregg Wildenberg & Hanyu Li & Vandana Sampathkumar & Anastasia Sorokina & Narayanan Kasthuri, 2023. "Isochronic development of cortical synapses in primates and mice," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    5. Liang Wang & Ziyun Yang & Fudo Satoshi & Xavier Prasanna & Ziyi Yan & Helena Vihinen & Yaxing Chen & Yue Zhao & Xiumei He & Qian Bu & Hongchun Li & Ying Zhao & Linhong Jiang & Feng Qin & Yanping Dai &, 2024. "Membrane remodeling by FAM92A1 during brain development regulates neuronal morphology, synaptic function, and cognition," Nature Communications, Nature, vol. 15(1), pages 1-30, December.
    6. Emilie Murigneux & Laurent Softic & Corentin Aubé & Carmen Grandi & Delphine Judith & Johanna Bruce & Morgane Le Gall & François Guillonneau & Alain Schmitt & Vincent Parissi & Clarisse Berlioz-Torren, 2024. "Proteomic analysis of SARS-CoV-2 particles unveils a key role of G3BP proteins in viral assembly," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    7. Liv Zimmermann & Xiaohan Zhao & Jana Makroczyova & Moritz Wachsmuth-Melm & Vibhu Prasad & Zach Hensel & Ralf Bartenschlager & Petr Chlanda, 2023. "SARS-CoV-2 nsp3 and nsp4 are minimal constituents of a pore spanning replication organelle," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    8. Keisuke Tabata & Vibhu Prasad & David Paul & Ji-Young Lee & Minh-Tu Pham & Woan-Ing Twu & Christopher J. Neufeldt & Mirko Cortese & Berati Cerikan & Yannick Stahl & Sebastian Joecks & Cong Si Tran & C, 2021. "Convergent use of phosphatidic acid for hepatitis C virus and SARS-CoV-2 replication organelle formation," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    9. Selma Dahmane & Adeline Kerviel & Dustin R. Morado & Kasturika Shankar & Björn Ahlman & Michael Lazarou & Nihal Altan-Bonnet & Lars-Anders Carlson, 2022. "Membrane-assisted assembly and selective secretory autophagy of enteroviruses," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    10. Andreia L. Pinto & Ranjit K. Rai & Jonathan C. Brown & Paul Griffin & James R. Edgar & Anand Shah & Aran Singanayagam & Claire Hogg & Wendy S. Barclay & Clare E. Futter & Thomas Burgoyne, 2022. "Ultrastructural insight into SARS-CoV-2 entry and budding in human airway epithelium," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    11. Francisco S. Mesquita & Laurence Abrami & Lucie Bracq & Nattawadee Panyain & Vincent Mercier & Béatrice Kunz & Audrey Chuat & Joana Carlevaro-Fita & Didier Trono & F. Gisou van der Goot, 2023. "SARS-CoV-2 hijacks a cell damage response, which induces transcription of a more efficient Spike S-acyltransferase," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    12. Leonid Andronov & Mengting Han & Yanyu Zhu & Ashwin Balaji & Anish R. Roy & Andrew E. S. Barentine & Puja Patel & Jaishree Garhyan & Lei S. Qi & W. E. Moerner, 2024. "Nanoscale cellular organization of viral RNA and proteins in SARS-CoV-2 replication organelles," Nature Communications, Nature, vol. 15(1), pages 1-17, 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:15:y:2024:i:1:d:10.1038_s41467-024-45042-3. 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.