title: XPIWIT--an XML pipeline wrapper for the Insight Toolkit.
abstract: 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.
  
  
  METHODS
  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/.
  
  
  BACKGROUND
  johannes.stegmaier@kit.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Bartschat
authors.affiliation: Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Germany.
authors.forename: Eduard
authors.initials: E
authors.lastname: Hübner
authors.affiliation: Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Germany.
authors.forename: Markus
authors.initials: M
authors.lastname: Reischl
authors.affiliation: Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Germany.
authors.forename: Ralf
authors.initials: R
authors.lastname: Mikut
authors.affiliation: Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Germany.
authors.forename: Johannes
authors.initials: J
authors.lastname: Stegmaier
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D004625:Embryo, Nonmammalian / Q000033:anatomy & histology*; D007091:Image Processing, Computer-Assisted; D021621:Imaging, Three-Dimensional / Q000379:methods*; D012984:Software; D015027:Zebrafish / Q000033:anatomy & histology*