PUBLICATION
XPIWIT—an XML pipeline wrapper for the Insight Toolkit
- Authors
- Bartschat, A., Hübner, E., Reischl, M., Mikut, R., Stegmaier, J.
- ID
- ZDB-PUB-150930-9
- Date
- 2016
- Source
- Bioinformatics (Oxford, England) 32(2): 315-7 (Journal)
- Registered Authors
- Mikut, Ralf
- Keywords
- none
- MeSH Terms
-
- Animals
- Computational Biology/methods*
- Embryo, Nonmammalian/anatomy & histology*
- Image Processing, Computer-Assisted
- Imaging, Three-Dimensional/methods*
- Software*
- Zebrafish/anatomy & histology*
- PubMed
- 26415725 Full text @ Bioinformatics
Citation
Bartschat, A., Hübner, E., Reischl, M., Mikut, R., Stegmaier, J. (2016) XPIWIT—an XML pipeline wrapper for the Insight Toolkit. Bioinformatics (Oxford, England). 32(2):315-7.
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.
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: Exemplary XML pipelines and a quick start guide are provided at the journal's web site.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping