Histology Core

组织学核心

• 批准号: 10461995
• 负责人: Thomas Mrsic-Flogel
• 金额: $ 14.43万
• 依托单位: COLUMBIA UNIV NEW YORK MORNINGSIDE
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-08-15 至 2026-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10461995
• 关键词: Anatomy; Area; Atlases; Behavior; Behavioral; Brain; Brain region; Calcium; Cells; Collaborations; Collection; Communication; Communities; Computer software; Data; Data Analyses; Data Collection; Data Science Core; Data Set; Decision Making; Development; Electrophysiology (science); Fiber; Fiber Optics; Goals; Histologic; Histological Labelings; Histology; Image; Image Analysis; International; Label; Laboratories; Learning; Methodology; Methods; Modeling; Mus; Nervous system structure; Occupational activity of managing finances; Optics; Outcome; Output; Pathway interactions; Photometry; Population; Procedures; Process; Protocols documentation; Reproducibility; Research Personnel; Sampling; Scientist; Services; Site; Software Tools; Standardization; Task Performances; Techniques; Testing; Theoretical model; Tissues; Ultrasonography; Update; Work; brain tissue; cell type; computerized data processing; data acquisition; data handling; experimental study; histological image; image registration; neural circuit; open source; optogenetics; reconstruction; relating to nervous system; software development; theories; tool; two-photon; working group

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.

摘要/摘要，核心C：组织学 此U19应用程序的总体目标是确定全脑神经基础和行为后果 内部状态，如任务参与，因为小鼠执行标准化的决策任务。登记 将电生理学记录部位整合到共同的解剖学框架中代表了 将这些实验在不同的项目中进行比较，并将结果综合成一个理论模型， 准确和稳健的组织学和图像分析方法对于开发高质量， 可重复的数据集。 因此，组织学核心C旨在提供两个关键成果。首先，这个核心将集中和规范 实验项目1、2和4的组织学数据采集和参考图谱配准。通过 参与该提案的团体以前的工作，解剖重建和配准管道， 使用连续切片双光子成像的Neuropixels探针记录已经建立，优化， 并得到验证。这个核心将开发一个开源软件包，用于艾伦鼠标的样本注册 脑共同坐标框架，第3版（CCF）。该软件包将包括用于评估 注册质量，并将扩展到处理新的实验记录方法所需的 建议的实验，包括重建和登记的标记细胞与钙 成像，将功能超声成像数据配准到艾伦CCF上，以及 细胞、通路和光纤插入位点在光纤光度学和光遗传学刺激实验中。 第二，为了支持本申请中提出的额外实验目的，特别是光遗传学目的， 项目2中的干扰和项目4中的钙成像，该核心将开发透明化和组织学标记 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。中央集权 国际脑实验室联盟的组织学处理已经很好地建立，并且第一个版本的 这个开放源码软件正处于开发的最后阶段。一种全脑组织透明化和光片 成像方法已得到证实，其可靠的登记，共同的框架是根据 考核一系列可以化学标记大块组织的组织学程序是 可用，并将形成进一步组织学研究的基础。总之，组织学核心C将执行 处理小鼠大脑进行组织学重建的基本任务， 从这个组织与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。