XPIWIT——用于 Insight Toolkit 的 XML 管道包装器。

XPIWIT--an XML pipeline wrapper for the Insight Toolkit.

机构信息

Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Germany.

出版信息

Bioinformatics. 2016 Jan 15;32(2):315-7. doi: 10.1093/bioinformatics/btv559. Epub 2015 Sep 28.

DOI:10.1093/bioinformatics/btv559

PMID:26415725

Abstract

UNLABELLED

The Insight Toolkit offers plenty of features for multidimensional image analysis. Current implementations, however, often suffer either from a lack of flexibility due to hard-coded C++ pipelines for a certain task or by slow execution times, e.g. caused by inefficient implementations or multiple read/write operations for separate filter execution. We present an XML-based wrapper application for the Insight Toolkit that combines the performance of a pure C++ implementation with an easy-to-use graphical setup of dynamic image analysis pipelines. Created XML pipelines can be interpreted and executed by XPIWIT in console mode either locally or on large clusters. We successfully applied the software tool for the automated analysis of terabyte-scale, time-resolved 3D image data of zebrafish embryos.

AVAILABILITY AND IMPLEMENTATION

XPIWIT is implemented in C++ using the Insight Toolkit and the Qt SDK. It has been successfully compiled and tested under Windows and Unix-based systems. Software and documentation are distributed under Apache 2.0 license and are publicly available for download at https://bitbucket.org/jstegmaier/xpiwit/downloads/.

CONTACT

johannes.stegmaier@kit.edu

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

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Insight Toolkit 提供了大量多维图像分析功能。然而，当前的实现常常存在以下问题：由于针对特定任务的硬编码 C++ 管道，缺乏灵活性；或者执行速度较慢，例如由于实现效率低下或单独的滤波器执行的多次读写操作。我们为 Insight Toolkit 提供了一个基于 XML 的包装应用程序，它将纯 C++ 实现的性能与易于使用的动态图像分析管道图形设置相结合。创建的 XML 管道可以在控制台模式下由 XPIWIT 本地或在大型集群上进行解释和执行。我们成功地将该软件工具应用于自动化分析斑马鱼胚胎的兆字节规模、时间分辨的 3D 图像数据。

可用性和实现

XPIWIT 是使用 Insight Toolkit 和 Qt SDK 用 C++ 编写的。它已经在 Windows 和基于 Unix 的系统中成功编译和测试。软件和文档根据 Apache 2.0 许可证分发，可在 https://bitbucket.org/jstegmaier/xpiwit/downloads/ 处公开下载。