Histology Core

摘要/摘要，核心C：组织学 该U19应用程序的总体目标是确定全脑神经基础和行为后果 当小鼠执行标准化的决策任务时，内部状态的变化，如任务投入。注册 将电生理记录部位整合到一个共同的解剖框架中是 比较不同项目的这些实验，并将结果合成到理论模型中，因此 准确和稳健的组织学和图像分析方法对于开发高质量、 可复制的数据集。 因此，组织学核心C的目标是实现两个关键成果。第一，这个核心将集中和规范 获取组织学数据并注册到实验项目1、2和4的参考图集。至 参与这项提案的团体之前的工作，解剖重建和注册管道 已经建立、优化了使用连续截面双光子成像的神经像素探头记录， 并得到了验证。这个核心将开发一个开放源码的软件包，用于向Allen鼠标注册样本 大脑共同坐标框架，版本3(CCF)。该方案将包括评估功能 注册质量，并将根据需要扩展到处理新的实验记录方法 拟议的实验，包括用钙研究的标记细胞的重建和注册 成像，功能超声成像数据在Allen CCF上的配准，以及 光纤光度学和光遗传刺激实验中的细胞、通路和光纤插入位置。 第二，支持在本申请中提出的额外实验目标，特别是光遗传学 项目2中的扰动和项目4中的钙成像，该核心将发展透明和组织学标记 询问神经系统结构的协议。 实现这些目标的许多技术障碍已经克服。的集中化 国际脑实验室联盟的组织学处理已经很好地建立了，并且第一个版本的 这款开源软件已进入开发的最后阶段。一种全脑组织清理和照明片 已经证明了成像方法，其可靠地登记在共同框架下。 评估。可以用免疫组织化学方法标记大块组织的一系列组织学程序包括 可供参考，并将成为进一步组织学审讯的基础。总而言之，组织学核心C将表现 为组织重建处理小鼠大脑的基本任务，生成结构数据集 与U19项目密切合作，并提供由此产生的协议、软件工具、 和数据集提供给更广泛的社区。

Summary/Abstract, Core C: Histology The overall goal of this U19 application is to determine the brainwide neural basis and behavioral consequences of internal states, such as task engagement, as mice perform a standardized decision-making task. Registration of electrophysiological recording sites into a common anatomical framework represents a critical step in comparing these experiments across projects and synthesizing the results into a theoretical model, so an accurate and robust histological and image analysis methodology is essential for the development of high-quality, reproducible datasets. Histology Core C therefore aims to deliver two key outcomes. First, this core will centralize and standardize histology data acquisition and registration to a reference atlas across experimental Projects 1, 2, and 4. Through previous work by groups participating in this proposal, the anatomical reconstruction and registration pipeline for recordings with Neuropixels probes using serial-section two-photon imaging has been established, optimized, and validated. This core will develop an open-source software package for sample registration to the Allen mouse brain common coordinate framework, version 3 (CCF). This package will include functions for assessing registration quality, and will be extended to handle new experimental recording methods as needed for the proposed experiments, including the reconstruction and registration of labeled cells investigated with calcium imaging, the registration of functional ultrasound imaging data onto the Allen CCF, and the reconstruction of cells, pathways, and optic fiber insertion sites in fiber photometry and optogenetic stimulation experiments. Second, to support the additional experimental aims proposed in this application, particularly optogenetic perturbations in Project 2 and calcium imaging in Project 4, this core will develop clearing and histological labeling protocols to interrogate nervous system structure. Many of the technical hurdles to delivering these aims have already been overcome. The centralizing of histological processing in the International Brain Laboratory consortium is well established, and a first version of this open-source software is in its final stages of development. A whole-brain tissue clearing and lightsheet imaging methodology has been demonstrated, and its reliable registration to the common framework is under assessment. A range of histological procedures that can immunohistochemically label large blocks of tissue are available, and will form the basis for further histological interrogation. In conclusion, Histology Core C will perform the essential tasks of processing mouse brains for histological reconstruction, generating structural datasets from this tissue in close collaboration with U19 projects, and supplying the resulting protocols, software tools, and datasets to the wider community.