Integration of 3D Slicer and BioImage Suite

描述（由申请人提供）：虽然用于医学图像分析的开源软件的日益可用性为复杂任务的不同来源的算法的集成开辟了新的途径，但源代码级的集成是一个重要的过程。 例如，各种算法可以用不同的编程语言编写和/或需要大量的底层库。 这些问题使得这些算法的源代码集成通常是一项不可能的复杂和容易出错的任务。 另一种策略，我们采用的建议的工作是使用二进制集成。 在这种情况下，算法已经以二进制形式预编译，并使用标准接口以类似于在Web浏览器中使用插件的方式集成在一起。 这种策略具有主要的潜在优势，包括代码许可证和开发框架中立性，因为所有需要标准化的是各种算法的调用。 在这项工作中，我们建议推广和标准化现有的二进制接口开发的3D切片机团队，并使用此功能，从耶鲁BioImage套件软件包和3D切片机无缝提供给“其他”包。 为此，我们提出了两个具体的目标：（1）扩展和推广切片执行层，以纳入其他文件格式和对象，以实现集成和（2）扩展耶鲁BioImage套件软件包，以充分实现这一层。 随着这个框架的发展，我们希望为其他图像分析软件包之间的进一步互操作性铺平道路。 这种集成最终将为用户提供大量数据分析所需的工具，并允许开发人员专注于开发新的图像分析算法。 我们预计，通过采用这种类型的接口，门户网站，如NITRC，因此最终可以转化为一个存储库的可互操作的组件，可以很容易地集成到执行复杂的图像分析任务，而不需要所有的开发人员实现他们的算法使用完全相同的底层软件工程框架。 相反，开发人员只需要标准化他们的算法如何被外部应用程序调用，这是一个更容易处理的任务。 这种类型的接口还可以在未来使用互联网服务等算法，从而甚至可能消除对本地软件安装的需求。 公共卫生相关性：与公共卫生的相关性开发用于医学图像分析的标准化集成接口将使研究人员能够容易且无缝地联合收割机组合来自各种来源的图像分析算法，以完成其数据的复杂分析。 特别是，这种集成将使更新和更有效的算法能够被医学成像用户社区采用，而无需正式重新实施并集成到更大的软件包中。 相反，这样的算法可以被设计为可作为标准插件使用，就像插件在Web浏览器中使用一样，并由用户自己集成到他们的定制工作流程中。

DESCRIPTION (provided by applicant): While the increasing availability of open source software for medical image analysis has opened up new avenues for the integration of algorithms from different sources for complex tasks, integration at the source code level is a non-trivial process. For example, the various algorithms may be written in different programming languages and/or require a large assortment of underlying libraries. These issues make the source integration of such algorithms often an impossibly complex and error-prone task. An alternative strategy, which we adopt for the proposed work is the use of binary integration. In this scenario, the algorithms are already precompiled in binary form and are integrated together using a standard interface in a manner similar to the use of plugins in web browsers. This strategy has major potential advantages including code license and development framework neutrality, as all that needs to be standardized is the invocation of the various algorithms. In this work, we propose to generalize and standardize an existing binary interface developed by the 3D Slicer team and use this to make functionality from the Yale BioImage Suite software package and 3D Slicer seamlessly available to the "other" package. To this end, we propose two specific aims: (1) Extend and generalize the Slicer Execution Layer to incorporate additional file formats and objects to enable the integration and (2) Extend the Yale BioImage Suite software package to fully implement this layer. With the development of this framework, we hope to pave the way for further interoperability among other image analysis packages. This integration will eventually provide users with a large collection of tools that they need for data analysis and allow developers to focus on developing novel image analysis algorithms. We anticipate that, with the adoption of this type of interface, a portal such as NITRC could thus be eventually transformed into a repository for interoperable components that could easily be integrated to perform complex image analysis tasks without requiring all developers to implement their algorithms using the exact same underlying software engineering framework. Instead, developers would only need to standardize how their algorithms are invoked by external applications which is a much more tractable task. This type of interface could also enable, in the future, the use of such algorithms as internet services, thus potentially even eliminating the need for local software installation. PUBLIC HEALTH RELEVANCE: Relevance to Public Health The development of standardized integration interfaces for medical image analysis will enable researchers to easily and seamlessly combine image analysis algorithms from a variety of sources to accomplish complex anal- ysis of their data. This integration will, in particular, enable newer and more effective algorithms to be adopted by the medical imaging user community without them having to be officially reimplemented and integrated into larger software packages. Rather, such algorithms could be designed to be available as standard plugins, in the same way that plugins are used in web browsers, and integrated by the users themselves in their customized workflows.