Intuitive Large-scale Image Processing for Biologists

现代细胞和发育生物学以及现已建立的系统生物学领域使用定量成像方法来测量固定和活细胞中分子的位置，动力学和相互作用，并且具有越来越高的空间和时间分辨率。定量成像依赖于复杂的图像处理和分析算法的开发、交付和使用。这些数据分析工具的可用性通常被认为是科学发现的主要瓶颈。以前，缺乏通用接口和定义的数据结构标准阻碍了新分析方法的共享和对图像数据集的开放共享访问。此外，在大型数据集上运行复杂算法的纯粹计算成本需要访问计算设施，而这些计算设施虽然存在，但对于大多数实验室生物学家来说，无法通过标准化的直观工具访问。该项目结合了由J Swedlow教授领导的开放显微镜联盟开发的OMERO应用程序和在英国国家电子科学中心的J I货车Hemert博士实验室开发的快速portlet开发工具的开发。生成的资源将是一个具有直观用户界面的服务，使实验室生物学家能够访问高性能计算资源，以处理和分析细胞和组织的多维图像。我们不建议在这个项目下开发一个单一的独立资源，而是为长凳生物学家提供一个重要的服务，基于在英国进行的世界领先的工作，使用通用的，标准化的界面和可用性的既定原则，为长凳生物学家提供尖端的图像分析方法。该资源将作为开源OMERO软件套件的一个组成部分发布，该软件套件目前正在英国的大多数成像站点和全球1200多个站点进行测试或日常使用。Rapid的稳定版本将在同一许可证下捆绑在这些版本中。我们将在爱丁堡计算数据设施和国家网格服务的基础上建立这项服务，以提供底层的电子基础设施。

Modern cell and developmental biology and the now-established domain of systems biology use quantitative imaging methods to measure the location, dynamics and interaction of molecules in fixed and living cells, and at increasingly high spatial and temporal resolution. Quantitative imaging depends on the development, delivery, and use of sophisticated image processing and analysis algorithms. The availability of these data analysis tools is commonly cited as a major bottleneck in scientific discovery. Previously, the absence of common interfaces and defined standards for data structures hindered the sharing of new analysis methods and the open, shared access to image datasets. Moreover the sheer computational cost of running complex algorithms on large datasets demands access to compute facilities that, while existing, are not accessible via standardised, intuitive tools for most bench biologists. This project combines developments in the OMERO application developed by the Open Microscopy Consortium led by Prof J Swedlow and the Rapid portlet development tool developed in Dr J I van Hemert's laboratory at the UK's National e-Science Centre. The resource generated will be a service with an intuitive user interface that enables bench biologists to access high performance computing resources for processing and analysing their multi-dimensional images of cells and tissues. We do not propose to develop a single stand-alone resource under this project but to provide a vital service for bench biologists, based on world-leading work performed in the UK that uses common, standardised interfaces and established principles in usability to provide access to cutting-edge image analysis methods for bench biologists. The resource will be released as a component of the open-source OMERO software suite that is currently either in testing or in daily use at most imaging sites in the UK and over 1200 sites worldwide. A stable version of Rapid will be bundled in these releases under the same license. We will build this service on top of the Edinburgh Compute Data Facility and the National Grid Service to provide the underlying e-Infrastructure.