Development And Applications Of The Open Microscopy Environment (OME)

在过去的一年里，我们发布了一个公开的软件版本(2.6.1)，其中包含对基于Web的用户界面的重大改进，与我们在华盛顿大学麦迪逊分校的合作者Kevin Elicieri所做的BioFormats项目的互操作性，以及与通常用于用户身份识别和身份验证的LDAP的互操作性。 基于浏览器的用户界面的重要新功能之一是由Harry Hochheiser开发的分层表格查看器的开发。该表查看器用于显示沿着多个并发层次结构表征的图像，并在我们新的公共OME演示站点上使用：http://ome.grc.nia.nih.gov.可以使用的层次结构类型完全是通用的，并且可以由用户使用可编辑的HTML模板轻松指定。该方案非常灵活，可以用于Ko博士的干细胞鉴定项目，该项目涉及选定基因的过度表达或抑制，然后使用原位或抗体探针或活细胞进行成像。所有这些实验参数，包括被操纵的基因和用于检测的基因，都可以使用这个表格查看器同时显示。 今年，我们还继续改进了与OME的MatLab接口，并广泛使用它来计算我们成像项目的图像描述符。在20,000多幅图像上计算了1,000多个图像描述符。最后，整个WND-CHAME分类系统已在OME中实现，允许最终用户使用该系统，而无需在MatLab中编程。有关使用WND-CHAME的详细说明，请访问OME网站(http://openmicroscopy.org).

Over the past year, we've made a public software release (2.6.1) containing significant improvements to the web-based user interface, interoperability with the BioFormats project from our collaborator Kevin Elicieri at UW-Madison, and interoperability with LDAP - which is commonly used for user identification and authentication. One of the significant new features in the browser-based user interface is the development of a hierarchical table viewer developed by Harry Hochheiser. This table viewer is used to display images characterized along multiple concurrent hierarchies and is in use at our new public OME demonstration site: http://ome.grc.nia.nih.gov. The types of hierarchies that can be used are completely general, and can be easily specified by users using editable HTML templates. The scheme is flexible enough to use in Dr. Minoru Ko's stem-cell characterization project, which involves over-expression or repression of selected genes, followed by imaging using in-situ or antibody probes or live cells. All of these experimental parameters including genes being manipulated and genes used for detection can be displayed simultaneously using this table viewer. This year, we also continued to improve the MATLAB interface to OME, and have used it extensively to compute the image descriptors for our imaging projects. Over 1,000 image descriptors have been computed on over 20,000 images. Finally, the entire WND-CHARM classification system has been implemented in OME, allowing end-users to use this without having to program in MATLAB. A detailed description of using WND-CHARM is available on-line on the OME site (http://openmicroscopy.org).