Cell type atlasing of whole human brains using HOLiS: an optimized pipeline for staining, clearing, imaging, and analysis

使用 HOLiS 对整个人脑进行细胞类型图谱分析：用于染色、透明化、成像和分析的优化流程

• 批准号: 10377810
• 负责人: Elizabeth M. C. Hillman
• 金额: $ 912.19万
• 依托单位: COLUMBIA UNIVERSITY HEALTH SCIENCES
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-22 至 2024-09-21
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10377810
• 关键词: 3-Dimensional; Algorithms; Anatomy; Atlases; Autopsy; Base of the Brain; Behavior; Benchmarking; Big Data; Brain; Brain Mapping; Brain imaging; Cells; Chemicals; Cognition; Collection; Complement; Complex; Costs and Benefits; Data; Data Analyses; Data Set; Development; Emotions; Ensure; Equilibrium; Foundations; Future; Genetic; Goals; Heterogeneity; Histologic; Human; Image; Image Analysis; Imaging technology; Information Retrieval; Infrastructure; Investigation; Knowledge; Label; Light; Link; Logic; Magnetic Resonance Imaging; Methodology; Methods; Microscopy; Modernization; Molecular; Molecular Profiling; Monoclonal Antibodies; Morphology; Mus; Names; Neuroglia; Neurons; Noise; Output; Pattern; Population; Production; Protocols documentation; Refractive Indices; Resolution; Sampling; Scanning; Scientist; Signal Transduction; Slice; Speed; Stains; Stereotyping; Structure; System; Techniques; Technology; Testing; Thick; Time; Tissues; Validation; analysis pipeline; base; brain cell; brain research; cell type; cellular imaging; comparative; computer science; computerized data processing; computerized tools; data analysis pipeline; deep learning; exhaustion; innovation; magnetic field; method development; multimodality; multiplexed imaging; new technology; novel; organizational structure; preservation; protein profiling; prototype; reconstruction; scale up; synergism; targeted imaging; tissue preparation; tissue processing

Project Summary (Abstract) Gaining a comprehensive understanding of brain-wide cellular organization in the human brain has long been recognized as a critical foundation for understanding complex brain functions, including who we are as humans. In this project we propose to take on this challenge and establish a pipeline capable of imaging the entire human brain at cellular resolution. We believe that the convergence of our novel technologies for tissue processing and clearing, ultra-fast 3D microscopy and highly efficient analysis will make this problem tractable and scalable, marking a new paradigm in human brain research. As part of BICCN, the Osten and Wu labs, have already made significant progress towards deciphering the cell type and three-dimensional organizational logic of the mouse brain, using both genetic and molecular labeling in combination with whole mouse brain imaging. However, scaling efforts ~2,000x from mouse to human brain requires both technical and conceptual innovation to extract maximum information and ensure high efficiency. Our approach will center on a new Human brain Optimized Light-Sheet HOLiS microscopy platform developed by the Hillman lab, whose speed, efficiency and multiplexing capabilities are expected to enable cellular- resolution imaging across the entire human brain in only a few days. The HOLiS platform is complemented by a new optimized tissue preparation method for human brain developed by the Wu lab, named HuB.Clear, optimized for multiplexed staining and clearing of highly tractable 5 mm thick, full human brain slabs. Our computational data analysis pipelines developed by the Osten lab will leverage deep learning-based data analysis and permit every cell in the brain to be registered within the whole brain 7T MRI volume. Our new human brain common coordinate framework will include cellular diversity analysis based on multiplex protein profiling and precise spatial characterization. The following benchmarks will be achieved during the 3-year project: Our tissue preparation method will provide: 1) complete tissue clearing while preserving morphology to allow faithful data production and integration with MRI, and 2) reliable and quantitative whole mount immunolabeling with diverse targets to allow multiplex molecular profiling across the entire brain. Our imaging technology will provide: 1) sufficient resolution and multiplexing capacity, and 2) high-throughput speed to allow exhaustive analyses across multiple whole human brains. Our data analysis methods will provide: 1) infrastructure capable of processing whole human brain imaging data, and 2) algorithms optimized for HOLiS to extract and interpret rich molecular and cellular information with the latest advances in computer science. The resulting pipeline will be easily scalable and sharable with maximized benefit-cost ratio, opening the door to imaging 100's or even 1,000's of human brains in coming years. Our results will link cellular diversity and morphology with molecular signatures across the entire human brain at a sufficient cellular resolution and to facilitate further functional investigations and cross-species comparisons in synergy with other BICCN efforts.

项目概要（摘要） 长期以来，人们一直致力于全面了解人脑的全脑细胞组织。 被认为是理解复杂大脑功能的重要基础，包括我们作为人类的身份。 在这个项目中，我们建议接受这一挑战并建立一个能够对整个人类进行成像的管道 细胞分辨率下的大脑。我们相信，我们的组织处理新技术的融合 透明、超快 3D 显微镜和高效分析将使这个问题变得易于处理和扩展， 标志着人类大脑研究的新范式。 作为 BICCN 的一部分，Osten 和 Wu 实验室已经在破译细胞方面取得了重大进展 使用遗传和分子标记研究小鼠大脑的类型和三维组织逻辑 结合小鼠全脑成像。然而，从小鼠大脑到人脑的规模扩大了约 2,000 倍 需要技术和理念创新来提取最大信息并确保高效率。 我们的方法将集中于开发的新型人脑优化光片 HOLiS 显微镜平台 由 Hillman 实验室开发，其速度、效率和复用能力预计将使蜂窝- 只需几天的时间即可对整个人脑进行高分辨率成像。 HOLiS 平台还补充了 吴实验室开发的新型优化人脑组织制备方法，名为HuB.Clear， 针对高度易处理的 5 毫米厚、全人脑板的多重染色和透明化进行了优化。我们的 Osten 实验室开发的计算数据分析管道将利用基于深度学习的数据 分析并允许在全脑 7T MRI 体积内记录大脑中的每个细胞。我们的新人类 大脑共同坐标框架将包括基于多重蛋白质分析的细胞多样性分析 和精确的空间表征。在为期 3 年的项目期间将实现以下基准： 我们的组织制备方法将提供：1）完整的组织透明化，同时保留形态，以允许 忠实的数据生成和与 MRI 的集成，以及 2) 可靠且定量的整体免疫标记 具有不同的目标，可以在整个大脑中进行多重分子分析。我们的成像技术将 提供：1) 足够的分辨率和复用能力，以及 2) 高通量速度以允许详尽的 对多个整个人类大脑进行分析。我们的数据分析方法将提供：1）基础设施能力 处理全人脑成像数据，2) 针对 HOLiS 提取和解释优化的算法 丰富的分子和细胞信息以及计算机科学的最新进展。 由此产生的管道将易于扩展和共享，并实现效益成本比最大化，从而打开 未来几年对数百甚至数千人脑进行成像的大门。我们的结果将细胞多样性与 以足够的细胞分辨率对整个人脑的分子特征进行形态学分析 与 BICCN 的其他工作协同促进进一步的功能研究和跨物种比较。