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Petascale neural circuit reconstruction: automated methods

View ORCID ProfileThomas Macrina, Kisuk Lee, Ran Lu, View ORCID ProfileNicholas L. Turner, View ORCID ProfileJingpeng Wu, Sergiy Popovych, View ORCID ProfileWilliam Silversmith, View ORCID ProfileNico Kemnitz, View ORCID ProfileJ. Alexander Bae, Manuel A. Castro, View ORCID ProfileSven Dorkenwald, Akhilesh Halageri, Zhen Jia, Chris Jordan, Kai Li, Eric Mitchell, Shanka Subhra Mondal, Shang Mu, Barak Nehoran, William Wong, Szi-chieh Yu, Agnes L. Bodor, Derrick Brittain, JoAnn Buchanan, Daniel J. Bumbarger, Erick Cobos, Forrest Collman, Leila Elabbady, View ORCID ProfilePaul G. Fahey, Emmanouil Froudarakis, Daniel Kapner, Sam Kinn, Gayathri Mahalingam, View ORCID ProfileStelios Papadopoulos, Saumil Patel, View ORCID ProfileCasey M. Schneider-Mizell, Fabian H. Sinz, Marc Takeno, Russel Torres, Wenjing Yin, Xaq Pitkow, Jacob Reimer, Andreas S. Tolias, R. Clay Reid, View ORCID ProfileNuno Maçarico da Costa, View ORCID ProfileH. Sebastian Seung
doi: https://doi.org/10.1101/2021.08.04.455162
Thomas Macrina
1Princeton Neuroscience Institute, Princeton University
2Computer Science Department, Princeton University
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Kisuk Lee
1Princeton Neuroscience Institute, Princeton University
8Brain & Cognitive Sciences Department, Massachusetts Institute of Technology
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Ran Lu
1Princeton Neuroscience Institute, Princeton University
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Nicholas L. Turner
1Princeton Neuroscience Institute, Princeton University
2Computer Science Department, Princeton University
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Jingpeng Wu
1Princeton Neuroscience Institute, Princeton University
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Sergiy Popovych
1Princeton Neuroscience Institute, Princeton University
2Computer Science Department, Princeton University
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William Silversmith
1Princeton Neuroscience Institute, Princeton University
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Nico Kemnitz
1Princeton Neuroscience Institute, Princeton University
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J. Alexander Bae
1Princeton Neuroscience Institute, Princeton University
3Electrical and Computer Engineering Department, Princeton University
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Manuel A. Castro
1Princeton Neuroscience Institute, Princeton University
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Sven Dorkenwald
1Princeton Neuroscience Institute, Princeton University
2Computer Science Department, Princeton University
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Akhilesh Halageri
1Princeton Neuroscience Institute, Princeton University
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Zhen Jia
1Princeton Neuroscience Institute, Princeton University
2Computer Science Department, Princeton University
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Chris Jordan
1Princeton Neuroscience Institute, Princeton University
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Kai Li
2Computer Science Department, Princeton University
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Eric Mitchell
1Princeton Neuroscience Institute, Princeton University
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Shanka Subhra Mondal
1Princeton Neuroscience Institute, Princeton University
3Electrical and Computer Engineering Department, Princeton University
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Shang Mu
1Princeton Neuroscience Institute, Princeton University
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Barak Nehoran
1Princeton Neuroscience Institute, Princeton University
2Computer Science Department, Princeton University
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William Wong
1Princeton Neuroscience Institute, Princeton University
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Szi-chieh Yu
1Princeton Neuroscience Institute, Princeton University
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Agnes L. Bodor
4Allen Institute for Brain Science
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Derrick Brittain
4Allen Institute for Brain Science
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JoAnn Buchanan
4Allen Institute for Brain Science
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Daniel J. Bumbarger
4Allen Institute for Brain Science
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Erick Cobos
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
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Forrest Collman
4Allen Institute for Brain Science
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Leila Elabbady
4Allen Institute for Brain Science
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Paul G. Fahey
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
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Emmanouil Froudarakis
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
11Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
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Daniel Kapner
4Allen Institute for Brain Science
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Sam Kinn
4Allen Institute for Brain Science
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Gayathri Mahalingam
4Allen Institute for Brain Science
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Stelios Papadopoulos
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
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Saumil Patel
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
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Casey M. Schneider-Mizell
4Allen Institute for Brain Science
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Fabian H. Sinz
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
9Institute for Bioinformatics and Medical Informatics, University Tübingen
10Institute for Computer Science, University Göttingen
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Marc Takeno
4Allen Institute for Brain Science
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Russel Torres
4Allen Institute for Brain Science
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Wenjing Yin
4Allen Institute for Brain Science
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Xaq Pitkow
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
7Department of Electrical and Computer Engineering, Rice University
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Jacob Reimer
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
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Andreas S. Tolias
5Department of Neuroscience, Baylor College of Medicine
6Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine
7Department of Electrical and Computer Engineering, Rice University
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R. Clay Reid
4Allen Institute for Brain Science
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Nuno Maçarico da Costa
4Allen Institute for Brain Science
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H. Sebastian Seung
1Princeton Neuroscience Institute, Princeton University
2Computer Science Department, Princeton University
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  • For correspondence: sseung@princeton.edu
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Abstract

3D electron microscopy (EM) has been successful at mapping invertebrate nervous systems, but the approach has been limited to small chunks of mammalian brains. To scale up to larger volumes, we have built a computational pipeline for processing petascale image datasets acquired by serial section EM, a popular form of 3D EM. The pipeline employs convolutional nets to compute the nonsmooth transformations required to align images of serial sections containing numerous cracks and folds, detect neuronal boundaries, label voxels as axon, dendrite, soma, and other semantic categories, and detect synapses and assign them to presynaptic and postsynaptic segments. The output of neuronal boundary detection is segmented by mean affinity agglomeration with semantic and size constraints. Pipeline operations are implemented by leveraging distributed and cloud computing. Intermediate results of the pipeline are held in cloud storage, and can be effortlessly viewed as images, which aids debugging. We applied the pipeline to create an automated reconstruction of an EM image volume spanning four visual cortical areas of a mouse brain. Code for the pipeline is publicly available, as is the reconstructed volume.

Competing Interest Statement

TM and HSS disclose financial interests in Zetta AI LLC. JR and AST disclose financial interests in Vathes LLC.

Footnotes

  • https://www.microns-explorer.org/cortical-mm3

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Petascale neural circuit reconstruction: automated methods
Thomas Macrina, Kisuk Lee, Ran Lu, Nicholas L. Turner, Jingpeng Wu, Sergiy Popovych, William Silversmith, Nico Kemnitz, J. Alexander Bae, Manuel A. Castro, Sven Dorkenwald, Akhilesh Halageri, Zhen Jia, Chris Jordan, Kai Li, Eric Mitchell, Shanka Subhra Mondal, Shang Mu, Barak Nehoran, William Wong, Szi-chieh Yu, Agnes L. Bodor, Derrick Brittain, JoAnn Buchanan, Daniel J. Bumbarger, Erick Cobos, Forrest Collman, Leila Elabbady, Paul G. Fahey, Emmanouil Froudarakis, Daniel Kapner, Sam Kinn, Gayathri Mahalingam, Stelios Papadopoulos, Saumil Patel, Casey M. Schneider-Mizell, Fabian H. Sinz, Marc Takeno, Russel Torres, Wenjing Yin, Xaq Pitkow, Jacob Reimer, Andreas S. Tolias, R. Clay Reid, Nuno Maçarico da Costa, H. Sebastian Seung
bioRxiv 2021.08.04.455162; doi: https://doi.org/10.1101/2021.08.04.455162
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Petascale neural circuit reconstruction: automated methods
Thomas Macrina, Kisuk Lee, Ran Lu, Nicholas L. Turner, Jingpeng Wu, Sergiy Popovych, William Silversmith, Nico Kemnitz, J. Alexander Bae, Manuel A. Castro, Sven Dorkenwald, Akhilesh Halageri, Zhen Jia, Chris Jordan, Kai Li, Eric Mitchell, Shanka Subhra Mondal, Shang Mu, Barak Nehoran, William Wong, Szi-chieh Yu, Agnes L. Bodor, Derrick Brittain, JoAnn Buchanan, Daniel J. Bumbarger, Erick Cobos, Forrest Collman, Leila Elabbady, Paul G. Fahey, Emmanouil Froudarakis, Daniel Kapner, Sam Kinn, Gayathri Mahalingam, Stelios Papadopoulos, Saumil Patel, Casey M. Schneider-Mizell, Fabian H. Sinz, Marc Takeno, Russel Torres, Wenjing Yin, Xaq Pitkow, Jacob Reimer, Andreas S. Tolias, R. Clay Reid, Nuno Maçarico da Costa, H. Sebastian Seung
bioRxiv 2021.08.04.455162; doi: https://doi.org/10.1101/2021.08.04.455162

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