Bioelectronic Systems Group, Interuniversity Microelectronics Centre (Imec) Leuven, Belgium.
Front Neuroinform. 2011 Nov 25;5:25. doi: 10.3389/fninf.2011.00025. eCollection 2011.
Image acquisition, processing, and quantification of objects (morphometry) require the integration of data inputs and outputs originating from heterogeneous sources. Management of the data exchange along this workflow in a systematic manner poses several challenges, notably the description of the heterogeneous meta-data and the interoperability between the software used. The use of integrated software solutions for morphometry and management of imaging data in combination with ontologies can reduce meta-data loss and greatly facilitate subsequent data analysis. This paper presents an integrated information system, called LabIS. The system has the objectives to automate (i) the process of storage, annotation, and querying of image measurements and (ii) to provide means for data sharing with third party applications consuming measurement data using open standard communication protocols. LabIS implements 3-tier architecture with a relational database back-end and an application logic middle tier realizing web-based user interface for reporting and annotation and a web-service communication layer. The image processing and morphometry functionality is backed by interoperability with ImageJ, a public domain image processing software, via integrated clients. Instrumental for the latter feat was the construction of a data ontology representing the common measurement data model. LabIS supports user profiling and can store arbitrary types of measurements, regions of interest, calibrations, and ImageJ settings. Interpretation of the stored measurements is facilitated by atlas mapping and ontology-based markup. The system can be used as an experimental workflow management tool allowing for description and reporting of the performed experiments. LabIS can be also used as a measurements repository that can be transparently accessed by computational environments, such as Matlab. Finally, the system can be used as a data sharing tool.
图像采集、处理和对象量化（形态计量学）需要整合来自异构源的数据输入和输出。以系统的方式管理沿此工作流程的数据交换带来了一些挑战，特别是异构元数据的描述和所使用软件之间的互操作性。使用集成的形态计量学和成像数据管理软件解决方案与本体相结合，可以减少元数据丢失，并极大地促进后续数据分析。本文提出了一个名为 LabIS 的集成信息系统。该系统的目标是自动化 (i) 图像测量的存储、注释和查询过程，以及 (ii) 提供使用开放标准通信协议的第三方应用程序共享测量数据的手段。LabIS 采用三层架构实现，后端是关系数据库，中间层是应用程序逻辑，实现了基于 Web 的报告和注释用户界面以及 Web 服务通信层。图像处理和形态计量功能通过与 ImageJ 的互操作性得到支持，ImageJ 是一个公共领域的图像处理软件，通过集成客户端实现。后者的关键是构建一个表示通用测量数据模型的数据本体。LabIS 支持用户配置文件，并可以存储任意类型的测量值、感兴趣区域、校准和 ImageJ 设置。通过图谱映射和基于本体的标记，有助于解释存储的测量值。该系统可用作实验工作流管理工具，允许描述和报告执行的实验。LabIS 还可用作测量值存储库，可以由计算环境（如 Matlab）透明访问。最后，该系统可用作数据共享工具。
