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A Petascale Automated Imaging Pipeline for Mapping Neuronal Circuits with High-throughput Transmission Electron Microscopy

View ORCID ProfileWenjing Yin, Derrick Brittain, Jay Borseth, Marie E. Scott, Derric Williams, Jed Perkins, Chris Own, Matt Murfitt, View ORCID ProfileRussel M. Torres, Daniel Kapner, View ORCID ProfileAdam Bleckert, Daniel Castelli, David Reid, View ORCID ProfileWei-Chung Allen Lee, Brett J. Graham, View ORCID ProfileMarc Takeno, Dan J. Bumbarger, Colin Farrell, View ORCID ProfileR. Clay Reid, View ORCID ProfileNuno Macarico da Costa
doi: https://doi.org/10.1101/791889
Wenjing Yin
Allen Institute, Seattle, WA, USA
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  • For correspondence: wenjingy@alleninstitute.org clayr@alleninstitute.org nunod@alleninstitute.org
Derrick Brittain
Allen Institute, Seattle, WA, USA
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Jay Borseth
Allen Institute, Seattle, WA, USA
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Marie E. Scott
Allen Institute, Seattle, WA, USA
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Derric Williams
Allen Institute, Seattle, WA, USA
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Jed Perkins
Allen Institute, Seattle, WA, USA
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Chris Own
Voxa Inc., Seattle, WA, USA
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Matt Murfitt
Voxa Inc., Seattle, WA, USA
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Russel M. Torres
Allen Institute, Seattle, WA, USA
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Daniel Kapner
Allen Institute, Seattle, WA, USA
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Adam Bleckert
Allen Institute, Seattle, WA, USA
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Daniel Castelli
Allen Institute, Seattle, WA, USA
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David Reid
Allen Institute, Seattle, WA, USA
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Wei-Chung Allen Lee
Harvard Medical School, Boston, MA, USA
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Brett J. Graham
Harvard Medical School, Boston, MA, USA
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Marc Takeno
Allen Institute, Seattle, WA, USA
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Dan J. Bumbarger
Allen Institute, Seattle, WA, USA
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Colin Farrell
Allen Institute, Seattle, WA, USA
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R. Clay Reid
Allen Institute, Seattle, WA, USA
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  • For correspondence: wenjingy@alleninstitute.org clayr@alleninstitute.org nunod@alleninstitute.org
Nuno Macarico da Costa
Allen Institute, Seattle, WA, USA
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  • For correspondence: wenjingy@alleninstitute.org clayr@alleninstitute.org nunod@alleninstitute.org
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ABSTRACT

Serial-section electron microscopy is the method of choice for studying cellular structure and network connectivity in the brain. We have built a pipeline of parallel imaging using transmission electron automated microscopes (piTEAM) that scales this technology and enables the acquisition of petascale datasets containing local cortical microcircuits. The distributed platform is composed of multiple transmission electron microscopes that image, in parallel, different sections from the same block of tissue, all under control of a custom acquisition software (pyTEM) that implements 24/7 continuous autonomous imaging. The suitability of this architecture for large scale electron microscopy imaging was demonstrated by acquiring a volume of more than 1 mm3 of mouse neocortex spanning four different visual areas. Over 26,500 ultrathin tissue sections were imaged, yielding a dataset of more than 2 petabytes. Our current burst imaging rate is 500 Mpixel/s (image capture only) per microscope and net imaging rate is 100 Mpixel/s (including stage movement, image capture, quality control, and post processing). This brings the combined burst acquisition rate of the pipeline to 3 Gpixel/s and the net rate to 600 Mpixel/s with six microscopes running acquisition in parallel, which allowed imaging a cubic millimeter of mouse visual cortex at synaptic resolution in less than 6 months.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted October 03, 2019.
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A Petascale Automated Imaging Pipeline for Mapping Neuronal Circuits with High-throughput Transmission Electron Microscopy
Wenjing Yin, Derrick Brittain, Jay Borseth, Marie E. Scott, Derric Williams, Jed Perkins, Chris Own, Matt Murfitt, Russel M. Torres, Daniel Kapner, Adam Bleckert, Daniel Castelli, David Reid, Wei-Chung Allen Lee, Brett J. Graham, Marc Takeno, Dan J. Bumbarger, Colin Farrell, R. Clay Reid, Nuno Macarico da Costa
bioRxiv 791889; doi: https://doi.org/10.1101/791889
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A Petascale Automated Imaging Pipeline for Mapping Neuronal Circuits with High-throughput Transmission Electron Microscopy
Wenjing Yin, Derrick Brittain, Jay Borseth, Marie E. Scott, Derric Williams, Jed Perkins, Chris Own, Matt Murfitt, Russel M. Torres, Daniel Kapner, Adam Bleckert, Daniel Castelli, David Reid, Wei-Chung Allen Lee, Brett J. Graham, Marc Takeno, Dan J. Bumbarger, Colin Farrell, R. Clay Reid, Nuno Macarico da Costa
bioRxiv 791889; doi: https://doi.org/10.1101/791889

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