An anatomical cell type atlas of gene expression, morphology and connectivity

项目摘要（研究部分2） 大脑回路是一个由众多细胞类型组成的错综复杂的互联网络。为了理解 在大脑回路中的信息处理中，确定细胞类型的目录是至关重要的， 分布在整个大脑中，以及它们如何相互连接。一个细胞在细胞中的精确位置 大脑（它在哪里？），其特定的树突和轴突形态（它看起来像什么？），及其结构 与电路和网络中的其他细胞的连接（它连接到谁？）都是重要的解剖学因素 其有助于不同细胞类型的定义和计数。我们将提供全面 成年雄性和雌性小鼠大脑的解剖细胞普查数据， 参考和连接地图集，并采用三种主要的可扩展方法。我们将绘制空间地图 使用多路复用错误鲁棒性组织在研究部分1中鉴定的转录组细胞类型 荧光原位杂交（MERFISH）与单细胞中鉴定的组合标记基因集 RNA-seq实验此外，我们将使用MERFISH来确定微环境、组织 各种细胞类型的组成和比例。我们将生成代表性细胞的完整神经元形态 类型的主要大脑区域，使用两种不同的高通量和高分辨率全脑荧光 成像方法和半自动形态重建方法。这些系统收集的 数据将被用来发现由完整的树突和轴突定义的细胞类型的基本规则 形态学我们将使用优化的狂犬病追踪系统进行单突触，逆行跨突触 追踪以将全脑输入映射到全脑范围内的遗传识别的细胞群。通过将其与 艾伦研究所已经创建了顺行投影机，我们将能够生成第一个迭代的 中尺度，输入/输出电路接线图。这些不同类型的解剖数据将与 以各种方式，包括耦合， 狂犬病示踪，完整的神经元形态学，或体内功能成像与多重FISH，以获得一个完整的神经元， 综合细胞类型分类方案。

Project Summary (Research Segment 2) The brain circuit is an intricately interconnected network of numerous cell types. To understand the principles of information processing in the brain circuit, it is essential to determine a catalog of cell types, how they are distributed throughout the brain, and how they are connected to each other. A cell's precise location within the brain (where is it?), its specific dendritic and axonal morphology (what does it look like?), and its structural connectivity with other cells in circuits and networks (who does it connect to?) are all critical anatomical factors which contribute to the definition and accounting of different cell types. We will produce comprehensive anatomical cell census data from brains of adult male and female mice, leveraging our existing mouse brain reference and connectivity atlases, and employing three major scalable approaches. We will map the spatial organization of transcriptomic cell types identified in Research Segment 1 using multiplexed error-robust fluorescence in situ hybridization (MERFISH) with combinatorial marker gene sets identified in the single-cell RNA-seq experiments. Furthermore, we will use MERFISH to determine the microenvironment, tissue composition and ratio of various cell types. We will generate full neuronal morphologies of representative cell types in major brain regions, using two different high-throughput and high-resolution whole-brain fluorescent imaging approaches and semi-automated morphology reconstruction methods. These systematically collected data will be used to discover rules underlying cell types as defined by their full dendritic and axonal morphologies. We will use an optimized rabies tracing system to do monosynaptic, retrograde trans-synaptic tracing to map whole-brain inputs to genetically-identified cell populations brain-wide. By combining this with the Allen Institute's already created anterograde projectome, we will be able to generate a first iteration of the mesoscale, input/output circuit wiring diagram. These different types of anatomical data will be integrated with each other and with other cell type characterization data modalities in a variety of ways, including coupling rabies tracing, full neuronal morphology, or in vivo functional imaging with multiplexed FISH, to derive an integrated cell type classification scheme.