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A petascale automated imaging pipeline for mapping neuronal circuits with high-throughput transmission electron microscopy

Author

Listed:
  • Wenjing Yin

    (Allen Institute)

  • Derrick Brittain

    (Allen Institute)

  • Jay Borseth

    (Allen Institute)

  • Marie E. Scott

    (Allen Institute)

  • Derric Williams

    (Allen Institute)

  • Jedediah Perkins

    (Allen Institute)

  • Christopher S. Own

    (Voxa)

  • Matthew Murfitt

    (Voxa)

  • Russel M. Torres

    (Allen Institute)

  • Daniel Kapner

    (Allen Institute)

  • Gayathri Mahalingam

    (Allen Institute)

  • Adam Bleckert

    (Allen Institute)

  • Daniel Castelli

    (Allen Institute)

  • David Reid

    (Allen Institute)

  • Wei-Chung Allen Lee

    (Harvard Medical School)

  • Brett J. Graham

    (Harvard Medical School)

  • Marc Takeno

    (Allen Institute)

  • Daniel J. Bumbarger

    (Allen Institute)

  • Colin Farrell

    (Allen Institute)

  • R. Clay Reid

    (Allen Institute)

  • Nuno Macarico da Costa

    (Allen Institute)

Abstract

Electron microscopy (EM) is widely used for studying cellular structure and network connectivity in the brain. We have built a parallel imaging pipeline using transmission electron microscopes that scales this technology, implements 24/7 continuous autonomous imaging, and enables the acquisition of petascale datasets. The suitability of this architecture for large-scale imaging was demonstrated by acquiring a volume of more than 1 mm3 of mouse neocortex, spanning four different visual areas at synaptic resolution, in less than 6 months. Over 26,500 ultrathin tissue sections from the same block were imaged, yielding a dataset of more than 2 petabytes. The combined burst acquisition rate of the pipeline is 3 Gpixel per sec and the net rate is 600 Mpixel per sec with six microscopes running in parallel. This work demonstrates the feasibility of acquiring EM datasets at the scale of cortical microcircuits in multiple brain regions and species.

Suggested Citation

  • Wenjing Yin & Derrick Brittain & Jay Borseth & Marie E. Scott & Derric Williams & Jedediah Perkins & Christopher S. Own & Matthew Murfitt & Russel M. Torres & Daniel Kapner & Gayathri Mahalingam & Ada, 2020. "A petascale automated imaging pipeline for mapping neuronal circuits with high-throughput transmission electron microscopy," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-18659-3
    DOI: 10.1038/s41467-020-18659-3
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    Cited by:

    1. Sergiy Popovych & Thomas Macrina & Nico Kemnitz & Manuel Castro & Barak Nehoran & Zhen Jia & J. Alexander Bae & Eric Mitchell & Shang Mu & Eric T. Trautman & Stephan Saalfeld & Kai Li & H. Sebastian S, 2024. "Petascale pipeline for precise alignment of images from serial section electron microscopy," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    2. Zhihao Zheng & Christopher S. Own & Adrian A. Wanner & Randal A. Koene & Eric W. Hammerschmith & William M. Silversmith & Nico Kemnitz & Ran Lu & David W. Tank & H. Sebastian Seung, 2024. "Fast imaging of millimeter-scale areas with beam deflection transmission electron microscopy," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    3. Siva Venkadesh & Anthony Santarelli & Tyler Boesen & Hong-Wei Dong & Giorgio A. Ascoli, 2023. "Combinatorial quantification of distinct neural projections from retrograde tracing," Nature Communications, Nature, vol. 14(1), pages 1-10, December.

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