{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,25]],"date-time":"2026-02-25T06:36:19Z","timestamp":1772001379063,"version":"3.50.1"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: 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.<\/jats:p>\n               <jats:p>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\/.<\/jats:p>\n               <jats:p>Contact: \u00a0johannes.stegmaier@kit.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv559","type":"journal-article","created":{"date-parts":[[2015,9,29]],"date-time":"2015-09-29T01:59:04Z","timestamp":1443491944000},"page":"315-317","source":"Crossref","is-referenced-by-count":31,"title":["XPIWIT\u2014an XML pipeline wrapper for the Insight Toolkit"],"prefix":"10.1093","volume":"32","author":[{"given":"Andreas","family":"Bartschat","sequence":"first","affiliation":[{"name":"Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eduard","family":"H\u00fcbner","sequence":"additional","affiliation":[{"name":"Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Markus","family":"Reischl","sequence":"additional","affiliation":[{"name":"Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ralf","family":"Mikut","sequence":"additional","affiliation":[{"name":"Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Johannes","family":"Stegmaier","sequence":"additional","affiliation":[{"name":"Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,9,28]]},"reference":[{"key":"2023020110282188400_btv559-B1","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1038\/nmeth.2084","article-title":"Biological imaging software tools","volume":"9","author":"Eliceiri","year":"2012","journal-title":"Nat. Methods"},{"key":"2023020110282188400_btv559-B2","volume-title":"The ITK Software Guide","author":"Ibanez","year":"2005"},{"key":"2023020110282188400_btv559-B3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/srep08601","article-title":"An ensemble-averaged, cell density-based digital model of zebrafish embryo development derived from light-sheet microscopy data with single-cell resolution","volume":"5","author":"Kobitski","year":"2015","journal-title":"Sci. Rep."},{"key":"2023020110282188400_btv559-B4","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1089\/zeb.2013.0886","article-title":"Automated processing of zebrafish imaging data\u2014a survey","volume":"10","author":"Mikut","year":"2013","journal-title":"Zebrafish"},{"key":"2023020110282188400_btv559-B5","doi-asserted-by":"crossref","first-page":"e90036","DOI":"10.1371\/journal.pone.0090036","article-title":"Fast segmentation of stained nuclei in terabyte-scale, time resolved 3D microscopy image stacks","volume":"9","author":"Stegmaier","year":"2014","journal-title":"PLoS One"},{"key":"2023020110282188400_btv559-B6","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1038\/nmeth.2062","article-title":"Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy","volume":"9","author":"Tomer","year":"2012","journal-title":"Nat. Methods"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/2\/315\/49016476\/bioinformatics_32_2_315.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/2\/315\/49016476\/bioinformatics_32_2_315.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T19:53:29Z","timestamp":1675281209000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/2\/315\/1744077"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,9,28]]},"references-count":6,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2016,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv559","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,1,15]]},"published":{"date-parts":[[2015,9,28]]}}}