The Electron Microscopy Data Bank

低温电子显微镜是一种显微镜技术，其中电子在传统显微镜中扮演光的角色，是试图了解活细胞内部工作原理的核心技术。它使研究人员能够以极高的分辨率获得细胞和分子的图像，这些细胞和分子被瞬间冻结并嵌入极薄的非晶体冰层中，从而可以识别驱动它们的分子机器的内部工作原理。电子显微镜数据库（EMDB）是存储和分发使用先进电子显微镜技术与生物样品拍摄的三维图像的中央数据库。该数据库由位于剑桥的欧洲生物信息学研究所（EBI）大分子结构数据库组的负责人Kim Henrick博士于2002年发起，目前已经包含了500多个大分子物体的结构，随着显微镜和标本制备技术的进步，预计在未来几年将迅速增长。它为世界范围内的结构生物学家提供了这些图像的沉积、分布和分析资源，以促进他们的研究，并进一步了解生命的基本机制，其最终目标将有助于提高对植物、动物和人类健康和疾病机制的理解。该数据库是一个交互式网站，研究人员可以在该网站上提交他们的数据以供存档。为了保持数据的高质量，每一份提交都由一位经验丰富的管理员进行管理，他在质量和技术正确性方面支持研究，然后通过一个简单、用户友好的网站向公众提供。特别注意收集准确的元数据，即关于实验背景的信息，如所研究的蛋白质或细胞，其制备条件，有关成像过程的信息以及应用于图像信息以重建最终三维信息的计算机程序的记录。在与邓迪大学Jason Swedlow教授及其同事开发的开放显微镜环境的合作下，该界面将进一步开发，为用户提供增强的功能。开放显微镜环境是一套针对光学显微镜研究人员的软件工具，用于支持大型图像数据集的管理。EMDB和OME之间的合作首次将光学和电子显微镜领域的研究人员联系起来，为公共研究图像数据库创建改进的工具，并利用OME开发的技术来改善一般用户体验。这里的一个特定目标是扩展用户界面以接受“丰富的提交”，即包含各种信息的复杂三维图像集。这可能包括通过将已知的原子结构“拟合”到图像中而获得的蛋白质原子结构的具体细节，或者在较大结构中告知分子的假定位置的注释。电子显微镜中的新计算技术也产生了显示蛋白质在生化过程中所经历的结构变化的图像集，从而直接有助于理解驱动生命过程的分子机器。在此资源中开发的技术不仅将使使用该资源的生物学家受益，而且还将作为未来公共生物图像数据库的试验场。随着许多领域成像技术的发展，单个图像捕获研究人员所需的所有信息的情况越来越少，越来越多的情况下，研究人员之间必须使用和交流大量的图像集。图像数据库和生物图像信息学的新领域将在这方面发挥重要作用。

Cryo-Electron Microscopy, a microscopy technique in which electrons play the role of light in conventional microscopes, is a central technology in attempting to understand the inner workings of the living cell. It enables researchers to obtain images of cells and molecules, instantaenously frozen and embedded in an extremely thin layer of non-crystalline ice, at an extremely high resolution, at which the inner workings of the molecular machines that drive them can be discerned. The Electron Microscopy Data Bank (EMDB) is the central data bank for storing and distributing the three-dimensional images taken using advanced electron microscopy techniques with biological samples. Initiated in 2002 by Dr Kim Henrick, the head of the Macromolecular Structure Database group of the European Bioinformatics Institute (EBI) in Cambridge, it already contains over 500 structures of macromolecular objects, and is expected to rapidly grow over the coming years, as improvements in microscope and specimen-preparation technology take effect. It provides structural biologists world-wide with a resource for the deposition, distribution, and analysis of such images to facilitate their research and further the understanding of the basic mechanisms of life, which as an ultimate goal will contribute to an improved understanding of the mechanisms of health and disease in plants, animals, and humans. The data bank is operated as an interactive web site at which researchers submit their data for deposition. To maintain the high quality of the data, every submission is curated by an experienced curator, who supports the researches in matters of quality and technical correctness, and then made publicly available through a simple, user-friendly web site. Particular care is taken to collect accurate metadata, i.e. information about the experimental background, such as the protein or cell under investigation, the conditions of its preparation, information about the imaging process and a record of the computer programs applied to the image information to reconstruct the final three-dimensional information. In cooperation with the Open Microscopy Environment developed by Prof Jason Swedlow and colleagues at the University of Dundee, the interface will be further developed to provide enhanced capabilities to its users. The Open Microscopy Environment is a set of software tools aimed at researchers in light microscopy to support the managemant of large image data sets. The collaboration between EMDB and OME for the first time links researchers in light and in electron microscopy to create improved tools for public research image databases, and leverages the technologies developed in OME to improve the general user experience. A particular goal here is to extend the user interface to accept 'rich submissions', i.e. complex three-dimensional image sets that contain a variety of information. This might include in particular details of the atomic structure of proteins derived by 'fitting' known atomic structures into the images, or annotations informing on the putative locations of molecules in larger structures. New computational techniques in electron microscopy also produce image sets showing structural variations that proteins undergo when performing in biochemical processes, and thus directly contribute to understanding the molecular machines that drive the processes of life. The technology developed in this resource will not only benefit biologists who use the resource, but also serves as a testing ground for future public biological image databases. As imaging technology in many areas develops, it is less and less often the case that a single image captures all the information a researcher needs, and more and more often large sets of images have to be used and communicated between researchers. Image databases and the new field of bioimage informatics will play a major role in this.