BRAIN CONNECTS: Center for a pipeline of high throughput integrated volumetric electron microscopy for whole mouse brain connectomics

大脑连接：用于全小鼠大脑连接组学的高通量集成体积电子显微镜管道中心

• 批准号: 10665386
• 负责人: Forrest Christie Collman
• 金额: $ 613.25万
• 依托单位: ALLEN INSTITUTE
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-01 至 2028-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10665386
• 关键词: Animals; Area; Atlases; Automation; BRAIN initiative; Basal Ganglia; Behavior; Biological Models; Brain; Caenorhabditis elegans; Calcium; Cell physiology; Cells; Collection; Community Health Education; Complement; Coupled; Data; Data Compression; Data Set; Detection; Development; Disease; Disease model; Dorsal; Drosophila genus; Education and Outreach; Electron Microscopy; Elements; Ensure; Environment; Expert Systems; Film; Gene Expression; Generations; Goals; Image; Individual; Infrastructure; Knowledge; Learning; Life Cycle Stages; Light; Link; Maps; Medial; Memory; Mental Health; Methods; Microscope; Microscopic; Modeling; Morphology; Movement; Mus; Nature; Neurons; Neurosciences; Output; Parkinson Disease; Phase; Preparation; Process; Protocols documentation; Psychological reinforcement; Research; Resolution; Rewards; Route; Sampling; Science; Scientist; Societies; Software Tools; Source; Stains; Standardization; Structure; Synapses; System; Technology; Testing; Thalamic Nuclei; Thalamic structure; Thick; Thinking; Time; Transmission Electron Microscopy; Ventral Tegmental Area; Work; X-Ray Computed Tomography; X-Ray Tomography; addiction; cell type; computerized data processing; connectome; cost; data acquisition; data integration; data management; data mining; deep learning; dissemination strategy; dopaminergic neuron; electron tomography; energy efficiency; feasibility testing; imaging modality; improved; innovative technologies; insight; knowledge integration; light microscopy; member; microscopic imaging; millimeter; multimodality; neural circuit; neural model; next generation; open data; open source; patch sequencing; programs; reconstruction; scaffold; scale up; software development; supervised learning; tomography; tool; transcriptomics

Project Summary: Center for whole mouse brain connectomics using high-throughput integrated volumetric electron microscopy (HIVE) Two fundamental components of the structural basis of brain function are cell type composition and the wiring diagram between those cells. Over the past decade there has been paradigm-shifting progress in understanding cell type composition of the brain. Now it’s time to systematically uncover the brain’s wiring diagram and place it into the context of cell types. Knowledge about the complete connectomes in C. elegans and Drosophila have revolutionized the understanding of cell types and circuit function in those systems. Transmission Electron Microscopy (TEM) has consistently led progress in that revolution and has the potential to scale up to the entire mouse brain with technical improvements in certain areas. During the IARPA MICrONS project, members of the HIVE team built a complete pipeline to section and image the mm3 and created the data processing, reconstruction and analysis infrastructure to make cells and connections analyzable. The result was a dataset with the largest EM level reconstructions of cells in any system, with neurons containing more than 14,000 inputs and 15,000 outputs. We accomplished this by applying a rigorous structured science process that is a hallmark of the Allen Institute’s team science approach. In this project we aim to improve our pipeline, developing critical technologies to tackle the challenges of scaling up to the whole mouse brain and linking to cell types. Our proposal will prepare and section an entire hemisphere, image it at 120 nm resolution, and image up to 10 mm3 at synaptic resolution within the Cortical Basal Ganglia Thalamic loop to provide key insights into circuit mechanisms within this circuit. To accomplish this, we will need to improve all individual aspects of the pipeline, while maintaining consistent integration tests that ensure that the pieces work together. We will standardize a whole mouse brain staining protocol and advance the automation of serial sectioning to collection of serial TEM sections across a whole mouse brain. Developments of serial section tilt TEM tomography will allow to scale EM imaging to a whole mouse brain at multiple scales, leveraging the re-imaging capacity of serial section TEM. We will develop open source data processing tools to bring down the cost of segmentation and while improving accuracy and integrating with a real-time globally accessible proofreading and analysis platform. Finally, we will integrate our data with full morphology reconstructions linked to gene expression, allowing us to create an integrated atlas of cell types and connectivity. Our dissemination strategy will further amplify our impact by democratizing access for both the scientific and educational community.

项目总结： 使用高通量集成体积的全小鼠脑连接中心 电子显微镜(HIVE) 大脑功能的结构基础的两个基本组成部分是细胞类型组成和 这些单元之间的接线图。在过去十年中，在以下方面取得了范式转变的进展 了解大脑的细胞类型组成。现在是系统地揭开大脑线路的时候了 图表并将其放入单元格类型的上下文中。关于线虫完整连接体的知识 和果蝇已经彻底改变了对这些系统中细胞类型和电路功能的理解。 在这场革命中，透射电子显微镜一直引领着进步，并具有潜力 通过在某些领域进行技术改进，扩大到整个小鼠的大脑。在IARPA微米 项目中，蜂巢团队的成员建立了一条完整的管道来对MM3进行分割和成像，并创建了数据 处理、重建和分析基础设施，使细胞和连接可分析。结果是 具有任何系统中最大的EM级别细胞重建的数据集，其神经元包含超过 14,000个投入和15,000个产出。我们通过应用严格的结构化科学过程实现了这一点 是艾伦研究所团队科学方法的标志。 在这个项目中，我们的目标是改进我们的管道，开发关键技术来应对 放大到整个小鼠的大脑，并与细胞类型相联系。我们的提案将准备和分割整个 半球，以120 nm分辨率成像，在大脑皮层内以突触分辨率成像高达10mm3 基底节丘脑环，以提供对此回路内回路机制的关键见解。要完成 因此，我们需要改进管道的各个方面，同时保持一致的集成测试 以确保这些部件协同工作。我们将标准化整个小鼠脑染色方案，并 将连续切片的自动化推进到收集整个小鼠大脑的连续透射电子显微镜切片。 连续切片倾斜电子显微镜断层扫描的发展将允许将电磁成像扩展到小鼠的整个大脑 多尺度，利用连续切片的再成像能力。我们将开发开源数据 处理工具，可降低分段成本，同时提高准确性并与 全球可访问的实时校对分析平台。最后，我们将把我们的数据与完整的 与基因表达相关联的形态重建，使我们能够创建一个完整的细胞类型图谱 和连通性。我们的传播战略将进一步扩大我们的影响，使两者的访问民主化 科学和教育界。