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CUBIC-Cloud: An Integrative Computational Framework Towards Community-driven Whole-Mouse-Brain Mapping

View ORCID ProfileTomoyuki Mano, Ken Murata, Kazuhiro Kon, Chika Shimizu, Hiroaki Ono, View ORCID ProfileShoi Shi, Rikuhiro G. Yamada, View ORCID ProfileKazunari Miyamichi, View ORCID ProfileEtsuo A. Susaki, View ORCID ProfileKazushige Touhara, View ORCID ProfileHiroki R. Ueda
doi: https://doi.org/10.1101/2020.08.28.271031
Tomoyuki Mano
1Department of Information Physics and Computing, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo 113-0033, Japan
2Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka 565-5241, Japan
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  • ORCID record for Tomoyuki Mano
Ken Murata
3Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
4ERATO Touhara Chemosensory Signal Project, JST, The University of Tokyo, Tokyo 113-8657, Japan
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Kazuhiro Kon
5Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
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Chika Shimizu
2Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka 565-5241, Japan
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Hiroaki Ono
5Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
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Shoi Shi
2Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka 565-5241, Japan
5Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
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Rikuhiro G. Yamada
2Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka 565-5241, Japan
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Kazunari Miyamichi
3Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
4ERATO Touhara Chemosensory Signal Project, JST, The University of Tokyo, Tokyo 113-8657, Japan
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Etsuo A. Susaki
2Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka 565-5241, Japan
5Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
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Kazushige Touhara
3Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
4ERATO Touhara Chemosensory Signal Project, JST, The University of Tokyo, Tokyo 113-8657, Japan
6International Research Center for Neurointelligence (WPI-IRCN), UTIAS, The University of Tokyo, Tokyo 113-0033, Japan
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Hiroki R. Ueda
1Department of Information Physics and Computing, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo 113-0033, Japan
2Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka 565-5241, Japan
5Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
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  • For correspondence: uedah-tky@umin.ac.jp
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ABSTRACT

Recent advancements in tissue clearing technologies have offered unparalleled opportunities for researchers to explore the whole mouse brain at cellular resolution. With the expansion of this experimental technique, however, a scalable and easy-to-use computational tool is in demand to effectively analyze and integrate whole-brain mapping datasets. To that end, here we present CUBIC-Cloud, a cloud-based framework to quantify, visualize and integrate whole mouse brain data. CUBIC-Cloud is a fully automated system where users can upload their whole-brain data, run analysis and publish the results. We demonstrate the generality of CUBIC-Cloud by a variety of applications. First, we investigated brain-wide distribution of PV, Sst, ChAT, Th and Iba1 expressing cells. Second, Aβ plaque deposition in AD model mouse brains were quantified. Third, we reconstructed neuronal activity profile under LPS-induced inflammation by c-Fos immunostaining. Last, we show brain-wide connectivity mapping by pseudo-typed Rabies virus. Together, CUBIC-Cloud provides an integrative platform to advance scalable and collaborative whole-brain mapping.

Competing Interest Statement

T.M. and H.R.U. filed a patent application regarding the CUBIC-Cloud software. CUBIC-Cloud web service is provided and maintained by CUBICStars Inc.

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 August 31, 2020.
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CUBIC-Cloud: An Integrative Computational Framework Towards Community-driven Whole-Mouse-Brain Mapping
Tomoyuki Mano, Ken Murata, Kazuhiro Kon, Chika Shimizu, Hiroaki Ono, Shoi Shi, Rikuhiro G. Yamada, Kazunari Miyamichi, Etsuo A. Susaki, Kazushige Touhara, Hiroki R. Ueda
bioRxiv 2020.08.28.271031; doi: https://doi.org/10.1101/2020.08.28.271031
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CUBIC-Cloud: An Integrative Computational Framework Towards Community-driven Whole-Mouse-Brain Mapping
Tomoyuki Mano, Ken Murata, Kazuhiro Kon, Chika Shimizu, Hiroaki Ono, Shoi Shi, Rikuhiro G. Yamada, Kazunari Miyamichi, Etsuo A. Susaki, Kazushige Touhara, Hiroki R. Ueda
bioRxiv 2020.08.28.271031; doi: https://doi.org/10.1101/2020.08.28.271031

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