Implementation of LSIDs in the Open Microscopy Environment

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，记录在介质上，方便复制。然而，数字检测器在显微镜中的应用使生物显微镜变成了一种定量分析设备。数字成像显微镜的临床和研究应用是巨大的，但这些应用产生大量的数据/单个延时图像很容易达到500mb。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。图像数据管理的一个关键能力是理解所有数据的来源和历史。数据如何记录和图像采集系统规范的知识在生物成像中尤为重要，因为有大量不同的成像模式。我们已经为生物显微镜定义了一个通用的数据模型，该模型为存储和共享这些图像数据提供了框架。这种结构被称为OME数据模型，并被许多商业和独立实体用作生物图像数据标准。然而，OME数据模型可以捕获大量的信息，并且尽可能多地填写这些信息是至关重要的。不幸的是，填写复杂的数据表单非常耗时，因此不太可能被大多数用户采用，除非它是自动化和简化的。一个单独的项目指定了一个生命科学标识符（lsid）系统，作为生物数据和系统的唯一标识符。这项建议寻求资金，以支持将低岛屿发展中国家纳入显微镜的OME规范。最重要的是，我们将建立一个存储显微镜配置的用户工具，然后获得显微镜系统的LSID，该LSID可识别该系统，并可用于描述给定图像采集系统的大多数参数。一个复杂的仪器规格和配置可以通过一个单一的鼠标点击来指示。最重要的是，该规范是唯一标识的，与所有记录的映像一起存储，并且可以被任何OME服务器或其他符合lsid的系统访问（“可解析”）。

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. A critical capability in image data management is understanding the source and history of all data. Knowledge of how data was recorded and the specification of the image acquisition system is especially important in biological imaging, as there are a large range of different imaging modalities. We have defined a common data model for biological microscopy that provides the framework for storing and sharing this image data. This structure is referred to as the OME Data Model, and is being used by a number of commercial and independent entities as a biological image data standard. However, the OME Data Model can capture a large amount of information, and it is critical that as much of this information be filled out as possible. Unfortunately filling out complex data forms is time consuming and thus unlikely to be adopted by most users unless it is automated and simplified. A separate project has specified a system of Life Science Identifiers (LSIDs) as unique identifiers for biological data and systems. This proposal seeks funds to support the integration of LSIDs into the OME specification for microscopes. Most importantly, we will build a user tool that stores microscopes configurations and then obtains an LSID for a microscope system that identifiees that system and can be used to describe most of the parameters for a given image acquisition system. A complex instrument specification and configuration can then be indicated by a single mmouse-click. Most importantly, this specification is uniquely identified, stored with all recorded images, and accessible ('resolvable'') by any OME server or other LSID-compliant system.