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.

项目摘要： 使用高通量集成体积的整个老鼠脑连接中心 电子显微镜（Hive） 大脑功能结构基础的两个基本组成部分是细胞类型组成， 这些单元格之间的接线图。在过去的十年中，范式转移了 了解大脑的细胞类型组成。现在是时候系统地发现大脑的布线了 图并将其放入单元类型的上下文中。关于秀丽隐杆线虫中完整连接的知识 果蝇和果蝇对这些系统中细胞类型和电路功能的理解彻底改变了。 透射电子显微镜（TEM）一直领导该革命的进展，并具有潜力 在某些区域的技术改进中扩展到整个鼠标大脑。在IARPA微米中 项目，Hive团队的成员建立了完整的管道，以进行部分和图像MM3并创建数据 处理，重建和分析基础架构，使细胞和连接可分析。结果就是 在任何系统中具有最大EM级重建的数据集，神经元包含多于 14,000个输入和15,000个输出。我们通过运用严格的结构化科学过程来实现这一目标 是艾伦学院（Allen Institute）团队科学方法的标志。 在这个项目中，我们旨在改善管道，开发关键技术以应对的挑战 扩展到整个小鼠大脑并链接到细胞类型。我们的建议将准备并部分 半球，以120 nm的分辨率对其进行图像，并在皮质内的突触分辨率最高10 mm3 基底神经节丘脑循环，为该电路内的电路机制提供了关键的见解。完成 这，我们需要改善管道的所有各个方面，同时保持一致的集成测试 这确保了碎片一起工作。我们将标准化整个鼠标脑染色方案和 将串行切片的自动化促进整个小鼠大脑的串行温度部分的收集。 串行部分倾斜TEM层析成像的发展将使EM成像扩展到整个小鼠大脑 多个尺度，利用串行部分TEM的重新成像能力。我们将开发开源数据 处理工具以降低细分成本，同时提高准确性并与 实时全球访问和分析平台。最后，我们将将数据与完整的数据集成 与基因表达相关的形态重建，使我们能够创建一个细胞类型的集成地图集 和连通性。我们的传播策略将通过使两者的访问民主化进一步扩大我们的影响 科学和教育社区。