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Petabyte-Scale Multi-Morphometry of Single Neurons for Whole Brains

View ORCID ProfileShengdian Jiang, View ORCID ProfileYimin Wang, View ORCID ProfileLijuan Liu, Sujun Zhao, Mengya Chen, View ORCID ProfileXuan Zhao, Peng Xie, View ORCID ProfileLiya Ding, Zongcai Ruan, View ORCID ProfileHong-Wei Dong, View ORCID ProfileGiorgio A. Ascoli, View ORCID ProfileMichael Hawrylycz, View ORCID ProfileHongkui Zeng, View ORCID ProfileHanchuan Peng
doi: https://doi.org/10.1101/2021.01.09.426010
Shengdian Jiang
1SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu, China
2School of Computer Science and Engineering, Southeast University, Nanjing, Jiangsu, China
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Yimin Wang
1SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu, China
3School of Computer Engineering and Science, Shanghai University, Shanghai, China
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Lijuan Liu
1SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu, China
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Sujun Zhao
1SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu, China
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Mengya Chen
3School of Computer Engineering and Science, Shanghai University, Shanghai, China
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Xuan Zhao
1SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu, China
2School of Computer Science and Engineering, Southeast University, Nanjing, Jiangsu, China
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Peng Xie
1SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu, China
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Liya Ding
1SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu, China
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  • ORCID record for Liya Ding
Zongcai Ruan
1SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu, China
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Hong-Wei Dong
4Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
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Giorgio A. Ascoli
5Volgenau School of Engineering, George Mason University, Fairfax, VA 22030, USA
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Michael Hawrylycz
6Allen Institute for Brain Science, Seattle, WA 98109, USA
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Hongkui Zeng
6Allen Institute for Brain Science, Seattle, WA 98109, USA
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Hanchuan Peng
1SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu, China
6Allen Institute for Brain Science, Seattle, WA 98109, USA
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  • For correspondence: h@braintell.org
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Abstract

Recent advances in brain imaging allow producing large amounts of 3-D volumetric data from which morphometry data is reconstructed and measured. Fine detailed structural morphometry of individual neurons, including somata, dendrites, axons, and synaptic connectivity based on digitally reconstructed neurons, is essential for cataloging neuron types and their connectivity. To produce quality morphometry at large scale, it is highly desirable but extremely challenging to efficiently handle petabyte-scale high-resolution whole brain imaging database. Here, we developed a multi-level method to produce high quality somatic, dendritic, axonal, and potential synaptic morphometry, which was made possible by utilizing necessary petabyte hardware and software platform to optimize both the data and workflow management. Our method also boosts data sharing and remote collaborative validation. We highlight a petabyte application dataset involving 62 whole mouse brains, from which we identified 50,233 somata of individual neurons, profiled the dendrites of 11,322 neurons, reconstructed the full 3-D morphology of 1,050 neurons including their dendrites and full axons, and detected 1.9 million putative synaptic sites derived from axonal boutons. Analysis and simulation of these data indicate the promise of this approach for modern large-scale morphology applications.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/SD-Jiang/MorphoHub/releases/tag/v1.0

  • https://github.com/SD-Jiang/MorphoHub

Copyright 
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 January 10, 2021.
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Petabyte-Scale Multi-Morphometry of Single Neurons for Whole Brains
Shengdian Jiang, Yimin Wang, Lijuan Liu, Sujun Zhao, Mengya Chen, Xuan Zhao, Peng Xie, Liya Ding, Zongcai Ruan, Hong-Wei Dong, Giorgio A. Ascoli, Michael Hawrylycz, Hongkui Zeng, Hanchuan Peng
bioRxiv 2021.01.09.426010; doi: https://doi.org/10.1101/2021.01.09.426010
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Petabyte-Scale Multi-Morphometry of Single Neurons for Whole Brains
Shengdian Jiang, Yimin Wang, Lijuan Liu, Sujun Zhao, Mengya Chen, Xuan Zhao, Peng Xie, Liya Ding, Zongcai Ruan, Hong-Wei Dong, Giorgio A. Ascoli, Michael Hawrylycz, Hongkui Zeng, Hanchuan Peng
bioRxiv 2021.01.09.426010; doi: https://doi.org/10.1101/2021.01.09.426010

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