PT  - JOURNAL ARTICLE
AU  - Tomoyuki Mano
AU  - Ken Murata
AU  - Kazuhiro Kon
AU  - Chika Shimizu
AU  - Hiroaki Ono
AU  - Shoi Shi
AU  - Rikuhiro G. Yamada
AU  - Kazunari Miyamichi
AU  - Etsuo A. Susaki
AU  - Kazushige Touhara
AU  - Hiroki R. Ueda
TI  - CUBIC-Cloud: An Integrative Computational Framework Towards Community-driven Whole-Mouse-Brain Mapping
AID  - 10.1101/2020.08.28.271031
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.08.28.271031
4099  - http://biorxiv.org/content/early/2020/08/31/2020.08.28.271031.short
4100  - http://biorxiv.org/content/early/2020/08/31/2020.08.28.271031.full
AB  - 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 StatementT.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.