Open image informatics software for biological microscopy

生物显微镜一直需要成像能力：传统上，样品的图像是在纸上绘制的，或者随着光敏胶片的出现，记录在便于复制的介质上。然而，数字探测器在显微镜中的应用已经将生物显微镜转变为一种定量分析装置。数字成像显微镜的临床和研究应用是巨大的，但这些应用会产生大量数据/单个延时图像可以很容易地达到500兆字节。四年前，我们开始为数字生物显微镜开发数据管理工具。我们的项目，开放显微镜环境(OME；http://openmicroscopy.org))现在是生物显微镜开源图像管理软件的领先提供商。该提案寻求资金，以支持OME创建的图像数据存储技术与过去十年产生的基因组测序数据的整合。人类和现代生物医学研究中使用的许多生物的基因组序列现在是已知的，并可在网络(例如，http://www.fllybase.org).)上获得然而，有一组日益丰富的辅助图像显示了基因突变、基因表达等的影响，这些站点应该提供这些图像，但没有标准的数据格式可以与研究人员或研究人员之间传递或共享这些信息。因此，我们将把其他项目建立的实验数据模型整合到现有的描述成像实验结果的OME数据模型中，并开发工具来帮助科学家以单一、连贯、可共享的格式记录关于成像实验的实验数据(例如，各种细胞、基因突变)。最后，随着OME项目的发展，我们确实需要资源来生成面向用户的文档、常见问题等，以及管理用户和开发人员的问题。目前，我们的开发人员正在提供这些服务，但我们没有资源来管理或记录联系人，并确保提供一致的支持。这种支持将大大有助于确保OME工具的实用性和传播性。

Biological microscopy has always required an imaging capability: traditionally, an image of a sample was drawn on paper, or with the advent of light-sensitive film, recorded on media that conveniently allowed reproduction. However, the application of digital detectors to microscopy has converted the biological microscope into a quantitative assay device. The clinical and research applications for digital imaging microscopy are enormous, but these applications generate large amounts of data/a single time-lapse image can easily be 500 Mbytes. Four years ago, we began developing a data management tool for digital biological microscopy. Our project, the Open Microscopy Environment (OME; http://openmicroscopy.org) is now the leading provider of open source image management software for biological microscopy. This proposal seeks funds to support the integration of image data storage technology created by OME with genome sequencing data generated over the last ten years. The genome sequences of humans and many of the organisms used in modern biomedical research are now known and available on the Web (e.g., http://www.fllybase.org). However, there is an increasingly rich set of accessory images showing effects of genetic mutations, gene expression, etc. that should be served by these sites, but no standard data format is available to allow delivery or sharing of this information with or between researchers. We will therefore incorporate the experimental data models built by other projects into the existing OME Data Model that describes the results of an imaging experiment, and develop tools to help scientists record experimental data about an imaging experiment (e.g., kinds of cells, gene mutations) in a single, coherent, shareable format. Finally, as the OME project grows, we have real need for resources for generating user-targeted documentation, FAQ's, etc., as well as managing user and developer questions. Currently, our developers are providing these services, but we have no resources for managing or logging contacts, and ensuring coherent support is provided. This support will go a long way to ensuring the usefulness and dissemination of the OME tools.