Towards integrated 3D reconstruction of whole human brains at subcellular resolution

以亚细胞分辨率对整个人脑进行集成 3D 重建

• 批准号: 9768578
• 负责人: Kwanghun Chung
• 金额: $ 200.34万
• 依托单位: MASSACHUSETTS INSTITUTE OF TECHNOLOGY
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-08-22 至 2023-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9768578
• 关键词: 3-Dimensional; Algorithms; Anatomy; Antibodies; Architecture; Atlases; Axon; Brain; Brain Mapping; Brain Stem; Brain region; Cell Nucleus; Cells; Cerebral hemisphere; Chemical Engineering; Chemical Synapse; Communities; Complex; Custom; Cytoplasm; Data; Data Set; Databases; Detection; Development; Diffusion; Dimensions; Disease; Dyes; Fiber; Formalin; Functional disorder; Goals; Histologic; Human; Hybrids; Hydrogels; Image; Imaging technology; Individual; Knowledge; Label; Left; Libraries; Link; Location; MRI Scans; Magnetic Resonance; Magnetic Resonance Imaging; Maps; Methods; Microscope; Mining; Molecular; Molecular Profiling; Morphology; Mus; Optics; Pattern; Permeability; Phenotype; Process; Property; Proteins; Proteome; Research; Resolution; Sampling; Scanning; Slice; Stains; Structure; Synapses; Techniques; Technology; Thick; Tissues; Work; antibody libraries; base; brain cell; brain tissue; cell type; cost; cost effective; deep learning; high dimensionality; imaging biomarker; insight; lens; macromolecule; molecular phenotype; multidisciplinary; multimodality; new technology; novel; novel therapeutics; preservation; reconstruction; spectrograph; two-photon

Project Summary A detailed understanding of the anatomical and molecular architectures of brain cells and their brain-wide organization is essential for interrogating human brain function and dysfunction. Extensive efforts have been made toward mapping brain cells through various lenses, which have established invaluable databases yielding new insights. However, integrative extraction of the multimodal properties of various cell-types brain-wide within the same brain, crucial to elucidating complex intercellular relationships, remains nearly impossible. We have developed high-throughput, cost-effective technology platforms to create a fully integrated three-dimensional (3D) human brain cell atlas by simultaneously mapping high-dimensional features (e.g., spatial, molecular, morphological, and microenvironment information) of all cells acquired from the same whole brain. The proposed work will establish the most comprehensive 3D human brain map to date, with unprecedented resolution and completeness. We envision that this atlas will facilitate the integration of a broad range of studies and allow the research community to interrogate human brain structure and function at multiple levels. In Aim 1, we will apply a novel technology to transform whole human brain tissue into indestructible hydrogel–tissue hybrids that allow highly multiplexed molecular labeling and subcellular-resolution volume imaging. In Aim 2, we will apply scalable labeling and imaging technologies to map the brain-wide 3D distribution of various cell-type and structural markers at subcellular resolution within the same brain. Our chemical engineering–based approach to this aim will enable cost-effective, lossless 3D labeling of the entire human brain at lower cost as traditional subsampling approaches. True volume labeling and subcellular-resolution imaging will allow us to extract fine morphological and connectivity information from labeled cells and reconstruct the microenvironment of all cells. In Aim 3, we will use a host of rapid and highly automated algorithms to perform unbiased, integrative high- dimensional phenotyping of all cells based on their spatial location, molecular expression, morphology, and microenvironment. In Aim 4, we will perform super-resolution phenotyping of cells in a selected brain region from the same sample used in Aim 3 to map inter-areal axonal connectivity at single-fiber resolution and to characterize chemical synapses. This integrative approach will likely unveil unique cell-types and brain regions, a crucial step toward a better understanding of brain function. The complete 3D dataset will be linked to magnetic resonance and diffusion spectrum images and existing reference atlases to facilitate the integration of a wide breadth of study at multiple levels and to make the data publicly accessible for mining and analysis.

项目摘要 详细了解脑细胞及其全脑的解剖学和分子结构 组织对于询问人脑的功能和功能障碍是必不可少的。已经做出了广泛的努力 旨在通过各种透镜绘制脑细胞图，这已经建立了无价的数据库 产生了新的见解。然而，不同类型细胞的多峰特性的综合提取 在同一个大脑中，对阐明复杂的细胞间关系至关重要的全脑范围内，几乎 不可能。我们开发了高吞吐量、高性价比的技术平台，创造了一个全面的 一种同时绘制高维脑细胞图谱的一体化三维人脑细胞图谱 获得的所有细胞的特征(例如，空间、分子、形态和微环境信息) 来自相同的整个大脑。这项拟议的工作将建立最全面的3D人脑图谱 迄今为止，以前所未有的决心和完整性。我们预计这本地图集将有助于 整合了广泛的研究，并允许研究界审问人脑 多层次的结构和功能。 在目标1中，我们将应用一种新技术将整个人脑组织转化为坚不可摧的 水凝胶-组织杂交物，允许高度复合的分子标记和亚细胞分辨率体积 成像。在目标2中，我们将应用可扩展的标记和成像技术来绘制全脑范围的3D 亚细胞分辨率的各种细胞类型和结构标记在同一大脑中的分布。我们的 实现这一目标的基于化学工程的方法将实现经济高效、无损的3D标签 随着传统的亚采样方法的临近，以更低的成本获得整个人脑。真正的卷标记和 亚细胞分辨率成像将使我们能够提取精细的形态和连接信息 标记细胞并重建所有细胞的微环境。 在目标3中，我们将使用一系列快速和高度自动化的算法来执行无偏、综合的高 基于所有细胞的空间位置、分子表达、形态和 微环境。在目标4中，我们将对选定的大脑区域的细胞进行超分辨率表型分析 来自Aim 3中使用的相同样本，以单纤维分辨率绘制区域间轴突连接图，并 描述化学突触的特征。这种综合的方法可能会揭示独特的细胞类型和大脑 这是更好地了解大脑功能的关键一步。完整的3D数据集将为 链接到磁共振和扩散光谱图像和现有参考地图集，以便于 整合多个层面的广泛研究，并使数据公开可供挖掘 和分析。