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细胞可视化和结构研究的重要工具。 分子纳米机器是细胞功能的核心，虽然是基本的电子冷冻断层扫描。 该技术已经使用了几十年，该技术正在因最新的进展而发生革命性的变化 样品制备、电子冷冻显微镜硬件、改进的自动数据收集功能、 直接电子检测成像设备和相位板技术相结合，这些进步导致了 原则上，能够生成大量高质量的细胞冷冻断层图。 如此大的数据集提供了对疾病状态下细胞变异的洞察，以及对基本数据的更好洞察。 细胞功能，为研究健康和疾病的基础提供新的可能性 可能的水平，有可能导致癌症和其他细胞改变疾病的全新诊断方法。 然而，现在蜂窝数据的收集速度远远快于现有现有技术的分析速度。 方法，对进展产生严重障碍：匹配单个实验室的数据生产率，在 至少需要 50 名经验丰富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组装了高度复杂的细胞断层扫描数据。 由 PI 组成的协同团队，在尖端计算和实验电子领域拥有互补的专业知识 项目 1（Hanein 和 Penczek）重点关注显微镜技术以实现这一目标。 关于断层图像质量评估和验证技术的开发和实施以及 数据收集策略的实验引导优化项目 2 重点关注自动断层扫描。 重建技术，从断层图像中提取各种特征，并进行分布分析 项目 3 侧重于开发定量工具，以提取特征。 通过深度学习和子断层图对齐以及交互式可视化进行断层图注释 该计划项目中开发的一套高度自动化的工具将使我们能够将 5-10x 解释为 使用现有方法获得尽可能多的数据，极大地扩展了我们可以研究的细胞变异类型 有效地学习。