Kuan Leonard, Li Yang, Lau Chris, Feng David, Bernard Amy, Sunkin Susan M, Zeng Hongkui, Dang Chinh, Hawrylycz Michael, Ng Lydia
The Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA.
Methods. 2015 Feb;73:4-17. doi: 10.1016/j.ymeth.2014.12.013. Epub 2014 Dec 20.
The Allen Mouse Brain Connectivity Atlas is a mesoscale whole brain axonal projection atlas of the C57Bl/6J mouse brain. Anatomical trajectories throughout the brain were mapped into a common 3D space using a standardized platform to generate a comprehensive and quantitative database of inter-areal and cell-type-specific projections. This connectivity atlas has several desirable features, including brain-wide coverage, validated and versatile experimental techniques, a single standardized data format, a quantifiable and integrated neuroinformatics resource, and an open-access public online database (http://connectivity.brain-map.org/). Meaningful informatics data quantification and comparison is key to effective use and interpretation of connectome data. This relies on successful definition of a high fidelity atlas template and framework, mapping precision of raw data sets into the 3D reference framework, accurate signal detection and quantitative connection strength algorithms, and effective presentation in an integrated online application. Here we describe key informatics pipeline steps in the creation of the Allen Mouse Brain Connectivity Atlas and include basic application use cases.
艾伦小鼠脑连接图谱是C57Bl/6J小鼠脑的中尺度全脑轴突投射图谱。利用标准化平台将贯穿整个大脑的解剖轨迹映射到一个共同的三维空间中，以生成一个全面且定量的区域间和细胞类型特异性投射数据库。该连接图谱具有几个理想的特征，包括全脑覆盖、经过验证且通用的实验技术、单一的标准化数据格式、可量化且集成的神经信息学资源以及开放获取的公共在线数据库（http://connectivity.brain-map.org/）。有意义的信息学数据量化和比较是有效使用和解释连接组数据的关键。这依赖于成功定义一个高保真图谱模板和框架、将原始数据集精确映射到三维参考框架、准确的信号检测和定量连接强度算法，以及在集成在线应用中的有效呈现。在这里，我们描述了创建艾伦小鼠脑连接图谱过程中的关键信息学流程步骤，并包括基本的应用案例。
