IBEX: an open infrastructure software platform to facilitate collaborative work in radiomics.
IBEX: an open infrastructure software platform to facilitate collaborative work in radiomics.
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DOI：
10.1118/1.4908210
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发表时间：
2015-03-01
期刊：
影响因子：
3.8
通讯作者：
Court, Laurence E
中科院分区：
文献类型：
--
作者：
Zhang, Lifei;Fried, David V;Court, Laurence E
目的：放射组学是定量图像特征的高通量提取和分析，已被证明在定量肿瘤表型方面具有相当大的潜力。然而，目前，软件基础设施的缺乏阻碍了放射组学及其应用的发展。因此，作者开发了成像生物标志物探索者（IBEX），这是一个开放的基础设施软件平台，可以灵活地支持常见的放射组学工作流程任务，如多模态图像数据导入和审查，特征提取算法的开发，模型验证以及多个机构之间的一致数据共享。方法：采用MATLAB和c/c++编程语言开发IBEX软件包。软件架构部署了现代的模型-视图-控制器、单元测试和函数处理编程概念，以隔离每个定量成像分析任务，验证其相关数据和算法是否适合使用，并插入新的模块。一方面，IBEX是自包含的，可以随时使用：它实现了通用的数据导入器、通用的图像过滤器和通用的特征提取算法。另一方面，IBEX提供了一个基于MATLAB和c/c++的集成开发环境，因此用户不局限于其内置功能。在IBEX开发人员工作室中，用户可以插入、调试和测试新算法，扩展IBEX的功能。IBEX还支持数据和特征算法的质量保证：图像数据、感兴趣的区域和特征算法相关的数据可以被审查、验证和/或修改。更重要的是，数据共享的一致性和计算结果的可重复性这两个协同工作流程的关键要素被嵌入到IBEX工作流程中：图像数据、特征算法和模型验证，包括来自不同用户的新开发的模型验证，可以轻松一致地共享，从而更容易在机构之间复制结果。结果：具有不同技术水平的研究人员，包括放射肿瘤学家、物理学家和计算机科学家，都发现IBEX软件直观、功能强大且易于使用。IBEX可以在任何有windows操作系统和1GB内存的计算机上运行。作者充分验证了所有导入器、预处理算法和特征提取算法的实现。Windows 1.0测试版的独立IBEX和IBEX的源代码可以下载。结论：作者成功实现了IBEX，这是一个开放式基础设施软件平台，可以简化常见的放射组学工作流程任务。它的透明性、灵活性和便携性可以大大加快放射组学研究的步伐，并为成功的临床转化铺平道路。
PURPOSE: Radiomics, which is the high-throughput extraction and analysis of quantitative image features, has been shown to have considerable potential to quantify the tumor phenotype. However, at present, a lack of software infrastructure has impeded the development of radiomics and its applications. Therefore, the authors developed the imaging biomarker explorer (IBEX), an open infrastructure software platform that flexibly supports common radiomics workflow tasks such as multimodality image data import and review, development of feature extraction algorithms, model validation, and consistent data sharing among multiple institutions.METHODS: The IBEX software package was developed using the MATLAB and c/c++ programming languages. The software architecture deploys the modern model-view-controller, unit testing, and function handle programming concepts to isolate each quantitative imaging analysis task, to validate if their relevant data and algorithms are fit for use, and to plug in new modules. On one hand, IBEX is self-contained and ready to use: it has implemented common data importers, common image filters, and common feature extraction algorithms. On the other hand, IBEX provides an integrated development environment on top of MATLAB and c/c++, so users are not limited to its built-in functions. In the IBEX developer studio, users can plug in, debug, and test new algorithms, extending IBEX's functionality. IBEX also supports quality assurance for data and feature algorithms: image data, regions of interest, and feature algorithm-related data can be reviewed, validated, and/or modified. More importantly, two key elements in collaborative workflows, the consistency of data sharing and the reproducibility of calculation result, are embedded in the IBEX workflow: image data, feature algorithms, and model validation including newly developed ones from different users can be easily and consistently shared so that results can be more easily reproduced between institutions.RESULTS: Researchers with a variety of technical skill levels, including radiation oncologists, physicists, and computer scientists, have found the IBEX software to be intuitive, powerful, and easy to use. IBEX can be run at any computer with the windows operating system and 1GB RAM. The authors fully validated the implementation of all importers, preprocessing algorithms, and feature extraction algorithms. Windows version 1.0 beta of stand-alone IBEX and IBEX's source code can be downloaded.CONCLUSIONS: The authors successfully implemented IBEX, an open infrastructure software platform that streamlines common radiomics workflow tasks. Its transparency, flexibility, and portability can greatly accelerate the pace of radiomics research and pave the way toward successful clinical translation.