New Open File Formats for the Biological Imaging Community

生物显微镜一直涉及“成像”：图像最初是手绘的，随着感光胶片的出现，记录下来，然后在纸上复制。这些方法扭曲了它们记录的信号之间的关系（正式地说，它们是“非线性介质”），使其难以用于科学测量。然而，数字探测器在显微镜中的应用提供了适合科学使用的“线性”测量。这与自动化相结合，在基础和临床研究中使用数字成像的数量和多样性方面产生了巨大的增长。每个平台都会产生许多GARCH数据，通常采用封闭的专有文件格式。这些都是强大的系统，但它们的全部效用受到封闭数据的限制，并且在标准台式计算机上难以查看和共享大型数据集。开放显微镜环境（OME）构建了开放的软件工具，可以访问，分析，查看和共享这些数据。这些工具最初是为光学显微镜而设计的，现在我们已经成功地将其扩展到电子显微镜、高含量筛选（用于药物研究中的药物发现）和数字病理学。该提案旨在扩展OME支持的文件格式，并确保有满足最先进生物成像模式需求的规范和软件。OME的所有软件和资源都是开源的，任何人都可以在线获得，并由一个专门的团队管理文档和社区推广。

Biological microscopy has always involved "imaging": images were initially hand drawn and with the advent of light-sensitive film, recorded and then reproduced on paper. These methods distorted the relationships between the signals they recorded (formally, they are "non-linear media"), making it difficult to use them for scientific measurements. However, the application of digital detectors to microscopy delivered "linear" measurements suitable for scientific use. This, combined with automation, spawned massive growth in the number and diversity of uses for digital imaging in basic and clinical research. Each platform produces many GBytes of data, usually in a closed, proprietary file format. These are powerful systems, but their full utility is limited by closed data and the difficulty of viewing and sharing large datasets on standard desktop computers.The Open Microscopy Environment (OME) has built open software tools that enable access, analysis, viewing and sharing of this data. Initially built for light microscopy, we have successfully extended these tools to electron microscopy, high content screening (used for drug discovery in pharmaceutical research) and digital pathology. This proposal seeks to extend the file formats that OME supports and ensure there are specifications and software that meet the demands of the most advanced biological imaging modalities. All of OME's software and resources are open source, available on-line to anyone, and supported by a dedicated team that manages documentation and community outreach.