An automated pipeline for macromolecular structure discovery in cellular electron cryo-tomography

细胞电子冷冻断层扫描中大分子结构发现的自动化流程

• 批准号: 9769773
• 负责人: NIELS VOLKMANN
• 金额: $ 92.84万
• 依托单位: SANFORD BURNHAM PREBYS MEDICAL DISCOVERY INSTITUTE
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-01 至 2020-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9769773
• 关键词: Address; Algorithms; Artificial Intelligence; Big Data; Biological; Biology; Cancer Diagnostics; Cell physiology; Cells; Classification; Collection; Complex; Computing Methodologies; Cryo-electron tomography; Cryoelectron Microscopy; Data; Data Analyses; Data Collection; Data Set; Detection; Development; Disease; Electron Microscopy; Electrons; Environment; Floods; Goals; Health; Heart; Human; Image; Imaging Device; Individual; Knowledge; Laboratories; Methodology; Methods; Molecular; Molecular Structure; Morphology; Pattern; Pharmaceutical Preparations; Phase; Preparation; Process; Production; Real-Time Systems; Research Personnel; Resolution; Sampling; Scientist; Stimulus; Structure; System; Techniques; Technology; Tomogram; Validation; Variant; Visualization software; base; computer framework; convolutional neural network; deep learning; electron tomography; experience; imaging detection; improved; insight; knowledge base; learning strategy; nanomachine; novel diagnostics; particle; programs; reconstruction; response; software development; statistics; tomography; tool; virtual

SUMMARY – OVERALL Cellular cryo-tomography has emerged as a critical tool for the visualization and structural study of the molecular nanomachines at the heart of cellular function. Although the basic electron cryo-tomography technique has been used for several decades, the technology is being revolutionized by recent advances in sample preparation, electron cryo-microscopy hardware, improved capabilities for automatic data collection, direct electron detection imaging devices, and phase plate technologies. Combined, these advances led to the ability to generate extraordinarily large numbers of cellular cryo-tomograms of exquisite quality. In principle, such large data sets offer insights into cellular variation in disease states as well as better insights into basic cellular function, opening new possibilities for studying the underpinnings of health and disease at the finest possible level, potentially leading to completely new diagnostics for cancer and other cell-altering diseases. However, collection of cellular data is now at a far faster rate than can currently be analyzed with existing methods, producing a serious barrier to progress: to match the data production rates of a single laboratory, at least 50 experienced scientists would need to handle the data analysis. The primary goal of this Program Project is to establish quantitative and highly automated tools for the reconstruction and interpretation of highly complex cellular tomographic data. We have assembled a highly synergistic team of PIs with complimentary expertise in cutting-edge computational and experimental electron microscopy techniques to achieve this goal through collaborative efforts. Project 1 (Hanein & Penczek) focuses on development and implementation of tomogram quality assessment and validation techniques and on experimentally guided optimization of data collection strategies. Project 2 focuses on automatic tomographic reconstruction technology, extraction of various features from the tomograms, and the analysis of distribution patterns derived from the extracted features. Project 3 focuses on development of quantitative tools for tomogram annotation through deep learning and sub-tomogram alignment as well as interactive visualization tools. The set of highly automated tools developed in this Program Project will permit us to interpret 5–10x as much data as is possible using existing methods, greatly expanding the types of cellular variations we can effectively study.

摘要-总体 细胞冷冻断层扫描已成为一种重要的工具，可视化和结构研究的， 分子纳米机器是细胞功能的核心虽然基本的电子冷冻断层扫描 技术已经使用了几十年，该技术正在革命性的最新进展， 样品制备，电子冷冻显微镜硬件，改进的自动数据收集能力， 直接电子检测成像装置和相位板技术。综合起来，这些进步导致了 能够生成大量高质量的细胞冷冻断层图像。在原则上， 这样的大数据集提供了对疾病状态中细胞变异的深入了解， 细胞功能，为研究健康和疾病的基础提供了新的可能性 可能的水平，可能导致癌症和其他细胞改变疾病的全新诊断。 然而，蜂窝数据的收集现在以比当前可以利用现有的无线通信系统分析的速率快得多的速率进行。 方法，产生了严重的进步障碍：为了匹配单个实验室的数据生产率， 至少需要50名有经验的科学家来处理数据分析。 该计划项目的主要目标是建立定量和高度自动化的工具， 高度复杂的细胞断层扫描数据的重建和解释。我们已经召集了一个 在尖端计算和实验电子领域拥有互补专业知识PI的协同团队 显微镜技术，以实现这一目标，通过合作努力。项目1（Hanein & Penczek）的重点是 X线断层成像质量评估和验证技术的开发和实施， 实验指导的数据收集策略优化。项目2侧重于自动断层扫描 重建技术，从断层图像中提取各种特征，并分析分布 从所提取的特征导出的图案。项目3侧重于开发定量工具， 通过深度学习和子断层图像对齐以及交互式可视化进行断层图像注释 工具.在这个程序项目中开发的一套高度自动化的工具将允许我们将5- 10倍解释为 使用现有的方法尽可能多的数据，大大扩展了我们可以使用的细胞变异类型。 有效学习。