Establishing Common Coordinate Framework for Quantitative Cell Census in Developing Mouse Brains

摘要 大脑发育的特征是一组不同的细胞类型，这些细胞类型出生并与快速生长有关 跨越时间的复杂的3D结构。细胞类型组成和分布的定量认识 不同的大脑区域提供有关大脑组成部分的基本知识，并充当 评估脑部疾病可能发生的变化的基本基线。这件事的重要性 信息反映在神经科学界的重大努力中，包括创建 Brain Initiative细胞普查网络，以提高我们对不同类型细胞组成的理解 成年小鼠大脑中的大脑区域。这些努力已经成为可能，并通过技术手段加速 高分辨率三维成像与可揭示细胞类型的计算分析方法相结合的进展 在大脑中以前所未有的细节安排。例如，我们开发了一种定量脑图 方法揭示成年小鼠脑内GABA能神经元亚型的空间分布。对于 成年小鼠大脑，艾伦共同坐标框架(CCF)目前作为标准图谱 用于映射和整合不同研究结果的资源。神经科学界，在 另一方面，对于发育中的小鼠大脑，没有类似的CCF。缺乏发展性合作伙伴关系 通过限制重复性，显著阻碍了发育中小鼠大脑细胞类型图谱的进展 以及整合来自不同研究的数据。为了解决这一不足，我们组装了一个高度协同的、 具有互补技能集的多机构团队，以创建具有关联本体的发展性CCF 和真正的3D解剖标签，同时还演示了我们的CCF的应用 发育中的小鼠脑内GABA能神经元的定位。为此，我们将首先利用核磁共振和 光片荧光显微镜(LSFM)在七种不同的条件下开发高分辨率发育CCF 发育时间点(E11.5、E13.5、E15.5、E18.5、P4、P14和P56)具有不同的细胞特征， 包括总细胞密度、髓鞘形成和神经血管形成。其次，我们将创建真正的3D解剖标签 基于细胞和基因表达信息的CCF，并构建一个全面的本体，将 允许解剖区域的变化在发育和成熟过程中联系起来。最后，我们将生成一个 应用组织清晰度和激光扫描共聚焦显微镜成像的GABA能神经元亚型细胞分辨率定量图 开发小鼠大脑，这将作为加速发育的大量数据来源 神经科学的发现。该项目的成功完成将使更广泛的科学家领域能够 更有效地利用现代脑成像技术研究发育中的小鼠大脑。

Abstract Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing complex 3D structures across time. Quantitative understanding of cell type composition and distribution in different brain regions provides fundamental knowledge about the building blocks of the brain and serves as an essential baseline with which to assess changes that may occur in brain disorders. The importance of this information is reflected by the significant effort among the neuroscience community, including the creation of the BRAIN Initiative Cell Census Network, to improve our understanding of cell type compositions across different brain regions in the adult mouse brain. These efforts have been made possible and accelerated by technological advances in high-resolution 3D imaging coupled with computational analysis methods that can reveal cell type arrangement in the brain with unprecedented detail. For example, we developed a quantitative brain mapping method to uncover the spatial arrangement of GABAergic neuron subtypes in the adult mouse brain. For the adult mouse brain, the Allen Common Coordinate Framework (CCF) currently serves as the standard atlas resource with which to map and integrate results from different studies. The neuroscience community, on the other hand, does not have similar CCFs for the developing mouse brain. The lack of developmental CCFs significantly hinders progress on cell type mapping of the developing mouse brain by limiting the reproducibility and integration of data from different studies. To address this deficiency, we have assembled a highly synergistic, multi-institutional team with complementary skill sets to create developmental CCFs with associated ontology and true 3D anatomical labels while also demonstrating the application of our CCFs by generating quantitative mappings of GABAergic neurons in the developing mouse brain. Toward this end, we will first utilize MRI and light sheet fluorescent microscopy (LSFM) to develop high-resolution developmental CCFs at seven different developmental time points (E11.5, E13.5, E15.5, E18.5, P4, P14, and P56) with different cellular features, including total cell density, myelination, and neurovasculature. Second, we will create true 3D anatomical labels for the CCFs based on cellular and gene expression information, and build a comprehensive ontology that will allow anatomical region changes to be linked across development and maturation. Lastly, we will generate a cellular-resolution quantitative map of GABAergic neuronal subtypes using tissue clearing and LSFM imaging in developing mouse brains, which will serve as a substantial data resource to accelerate developmental neuroscience discovery. The successful completion of this project will enable a broad field of scientists to leverage modern brain mapping technologies more effectively in studying the developing mouse brain.