Introduction

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.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/.johannes.stegmaier@kit.eduSupplementary data are available at Bioinformatics online.

Publications

  1. XPIWIT--an XML pipeline wrapper for the Insight Toolkit.
    Cite this
    Bartschat A, Hübner E, Reischl M, Mikut R, Stegmaier J, 2016-01-01 - Bioinformatics (Oxford, England)

Credits

  1. Andreas Bartschat
    Developer

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

  2. Eduard Hübner
    Developer

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

  3. Markus Reischl
    Developer

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

  4. Ralf Mikut
    Developer

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

  5. Johannes Stegmaier
    Investigator

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

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Summary
AccessionBT006565
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionGermany
Submitted ByJohannes Stegmaier