CRCNS data sharing: Whole Mouse Brain Neuronal Morphology and Neurovasculature Browser

CRCNS 数据共享：全小鼠大脑神经元形态和神经血管浏览器

• 批准号: 0905041
• 负责人: Yoonsuck Choe
• 金额: $ 11.4万
• 依托单位: Texas A&M Engineering Experiment Station
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-15 至 2011-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0905041&HistoricalAwards=false
• 关键词: CRCNS; data; sharing; Whole; Mouse

This award supports the preparation and sharing of high-resolution, high-quality, whole mouse brain neuronal and vascular data obtained from the Knife-Edge Scanning Microscope (KESM). KESM is capable of slicing and imaging whole small animal organs (such as the mouse brain) at less than 1 um resolution within 100 hours, with a resulting data size exceeding 2 TB per specimen. The amount and complexity of the KESM data necessitates innovative approaches in data organization, storage/retrieval, and dissemination. The research team will develop an informatics framework for 3D volume data dissemination and visualization.The KESM, developed and housed in the PI's laboratory, has been used to dissect and image two whole mouse brains so far, one stained in Golgi to reveal the neuronal morphology, and the other in India ink to show the microvascular network in fine detail. The two data sets are unique in their detail and extent compared to other currently available data sets (orders of magnitude higher resolution along one or more of the x-, y-, and z-axis, and/or higher extent in the imaged volume). Such data enable researchers to conduct a full quantitative analysis of various morphological statistics and their variability across different brain regions and nuclei, estimate morphological parameters for computational simulation, and eventually help link structure to function.A hybrid approach will be employed that integrates a web-based light-weight data browser and a local data viewer/analyzer, under a multi-scale data scheme. The specific objectives of this project are as follows: (1) Standardized data sets for improved access and interoperability with other data sources, (2) Light-weight web-based volume browser with an open Application Programming Interface (API) for enhanced freedom of access and annotation, and (3) Unit volume viewer for the visualization and analysis of small unit volumes downloaded through the web-based interface.The data and software tools, including documentation, will be released in the public domain, to build a user/developer community that will help continued use and evolution of the framework.

该奖项支持高分辨率，高质量，整个小鼠脑神经元和血管数据的制备和共享，这些数据是从边缘扫描显微镜（KESM）获得的。KESM能够在100小时内以小于1 um的分辨率对整个小动物器官（如小鼠大脑）进行切片和成像，每个标本的数据量超过2 TB。科学、环境和安全管理数据的数量和复杂性要求在数据组织、储存/检索和传播方面采取创新办法。该研究团队将开发一个用于3D体积数据传播和可视化的信息学框架。该KESM由PI实验室开发和安装，迄今已用于解剖和成像两个完整的小鼠大脑，一个在高尔基体染色以显示神经元形态，另一个在印度墨水中显示微血管网络的细节。与其他当前可用的数据集相比，这两个数据集在其细节和范围上是独特的（沿着x轴、y轴和z轴中的一个或多个的数量级更高分辨率，和/或成像体积中的更高范围）。这些数据使研究人员能够对不同脑区和核团的各种形态学统计及其变异性进行全面的定量分析，估计用于计算模拟的形态学参数，并最终帮助将结构与功能联系起来。该项目的具体目标如下：（1）标准化数据集，以改进与其他数据源的访问和互操作性，（2）具有开放式应用程序编程接口（API）的轻量级网络卷浏览器，以增强访问和注释的自由度，以及（3）单位体积查看器，用于可视化和分析通过基于网络的界面下载的小单位体积。数据和软件工具，包括文档在内的所有文件将在公共领域发布，以建立一个用户/开发人员社区，帮助继续使用和发展该框架。