CUBIC-Cloud: An Integrative Computational Framework Towards Community-driven Whole-Mouse-Brain Mapping
CUBIC-Cloud: An Integrative Computational Framework Towards Community-driven Whole-Mouse-Brain Mapping
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DOI：
10.1101/2020.08.28.271031
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发表时间：
2020-08
期刊：
影响因子：
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通讯作者：
T. Mano;Ken Murata;K. Kon;Chika Shimizu;Hiroaki Ono;Shoi Shi;R. Yamada;Kazunari Miyamichi;E. Susaki;K. Touhara;H. Ueda
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文献类型：
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作者：
T. Mano;Ken Murata;K. Kon;Chika Shimizu;Hiroaki Ono;Shoi Shi;R. Yamada;Kazunari Miyamichi;E. Susaki;K. Touhara;H. Ueda
组织清理技术的最新进展为研究人员在细胞分辨率上探索整个小鼠大脑提供了无与伦比的机会。然而，随着这项实验技术的扩展，需要一种可扩展且易于使用的计算工具来有效地分析和整合全脑映射数据集。为此，我们提出了cbic - cloud，这是一个基于云的框架，用于量化、可视化和整合整个小鼠大脑数据。cbic - cloud是一个完全自动化的系统，用户可以上传他们的全脑数据，运行分析并发布结果。我们通过各种应用程序演示了cbic - cloud的通用性。首先，我们研究了PV、Sst、ChAT、Th和Iba1表达细胞的全脑分布。其次，定量测定AD模型小鼠脑内Aβ斑块沉积。第三，我们通过c-Fos免疫染色重建lps诱导炎症下的神经元活动谱。最后，我们展示了伪狂犬病毒的全脑连接映射。总之，cbic - cloud提供了一个集成平台，以推进可扩展和协作的全脑映射。
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.