{"id":"https://openalex.org/W2177729144","doi":"https://doi.org/10.1093/bioinformatics/btv559","title":"XPIWIT\u2014an XML pipeline wrapper for the Insight Toolkit","display_name":"XPIWIT\u2014an XML pipeline wrapper for the Insight Toolkit","publication_year":2015,"publication_date":"2015-09-28","ids":{"openalex":"https://openalex.org/W2177729144","doi":"https://doi.org/10.1093/bioinformatics/btv559","mag":"2177729144","pmid":"https://pubmed.ncbi.nlm.nih.gov/26415725"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv559","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv559","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/2/315/49016476/bioinformatics_32_2_315.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/2/315/49016476/bioinformatics_32_2_315.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045144723","display_name":"Andreas Bartschat","orcid":null},"institutions":[{"id":"https://openalex.org/I102335020","display_name":"Karlsruhe Institute of Technology","ror":"https://ror.org/04t3en479","country_code":"DE","type":"education","lineage":["https://openalex.org/I102335020","https://openalex.org/I1305996414"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Andreas Bartschat","raw_affiliation_strings":["Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Germany","institution_ids":["https://openalex.org/I102335020"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012783693","display_name":"Eduard H\u00fcbner","orcid":null},"institutions":[{"id":"https://openalex.org/I102335020","display_name":"Karlsruhe Institute of Technology","ror":"https://ror.org/04t3en479","country_code":"DE","type":"education","lineage":["https://openalex.org/I102335020","https://openalex.org/I1305996414"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Eduard H\u00fcbner","raw_affiliation_strings":["Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Germany","institution_ids":["https://openalex.org/I102335020"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049462585","display_name":"Markus Reischl","orcid":"https://orcid.org/0000-0002-7780-6374"},"institutions":[{"id":"https://openalex.org/I102335020","display_name":"Karlsruhe Institute of Technology","ror":"https://ror.org/04t3en479","country_code":"DE","type":"education","lineage":["https://openalex.org/I102335020","https://openalex.org/I1305996414"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Markus Reischl","raw_affiliation_strings":["Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Germany","institution_ids":["https://openalex.org/I102335020"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001459055","display_name":"Ralf Mikut","orcid":"https://orcid.org/0000-0001-9100-5496"},"institutions":[{"id":"https://openalex.org/I102335020","display_name":"Karlsruhe Institute of Technology","ror":"https://ror.org/04t3en479","country_code":"DE","type":"education","lineage":["https://openalex.org/I102335020","https://openalex.org/I1305996414"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ralf Mikut","raw_affiliation_strings":["Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Germany","institution_ids":["https://openalex.org/I102335020"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062748514","display_name":"Johannes Stegmaier","orcid":"https://orcid.org/0000-0003-4072-3759"},"institutions":[{"id":"https://openalex.org/I102335020","display_name":"Karlsruhe Institute of Technology","ror":"https://ror.org/04t3en479","country_code":"DE","type":"education","lineage":["https://openalex.org/I102335020","https://openalex.org/I1305996414"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Johannes Stegmaier","raw_affiliation_strings":["Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Applied Computer Science (IAI), Karlsruhe Institute of Technology, Germany","institution_ids":["https://openalex.org/I102335020"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5062748514"],"corresponding_institution_ids":["https://openalex.org/I102335020"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.6985,"has_fulltext":true,"cited_by_count":43,"citation_normalized_percentile":{"value":0.90767622,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"32","issue":"2","first_page":"315","last_page":"317"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.42730000615119934,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.42730000615119934,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11685","display_name":"Zebrafish Biomedical Research Applications","score":0.41749998927116394,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.023399999365210533,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8719857931137085},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5869582891464233},{"id":"https://openalex.org/keywords/unix","display_name":"Unix","score":0.567866861820221},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.522213339805603},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4986579418182373},{"id":"https://openalex.org/keywords/implementation","display_name":"Implementation","score":0.4812335968017578},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.4758201241493225},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.4714782238006592},{"id":"https://openalex.org/keywords/microsoft-windows","display_name":"Microsoft Windows","score":0.4435606598854065},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.34595197439193726},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.31387266516685486}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8719857931137085},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5869582891464233},{"id":"https://openalex.org/C112968700","wikidata":"https://www.wikidata.org/wiki/Q11368","display_name":"Unix","level":3,"score":0.567866861820221},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.522213339805603},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4986579418182373},{"id":"https://openalex.org/C26713055","wikidata":"https://www.wikidata.org/wiki/Q245962","display_name":"Implementation","level":2,"score":0.4812335968017578},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.4758201241493225},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.4714782238006592},{"id":"https://openalex.org/C508378895","wikidata":"https://www.wikidata.org/wiki/Q1406","display_name":"Microsoft Windows","level":3,"score":0.4435606598854065},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.34595197439193726},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.31387266516685486}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004625","descriptor_name":"Embryo, Nonmammalian","qualifier_ui":"Q000033","qualifier_name":"anatomy & histology","is_major_topic":false},{"descriptor_ui":"D004625","descriptor_name":"Embryo, Nonmammalian","qualifier_ui":"Q000033","qualifier_name":"anatomy & histology","is_major_topic":false},{"descriptor_ui":"D004625","descriptor_name":"Embryo, Nonmammalian","qualifier_ui":"Q000033","qualifier_name":"anatomy & histology","is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015027","descriptor_name":"Zebrafish","qualifier_ui":"Q000033","qualifier_name":"anatomy & histology","is_major_topic":false},{"descriptor_ui":"D015027","descriptor_name":"Zebrafish","qualifier_ui":"Q000033","qualifier_name":"anatomy & histology","is_major_topic":false},{"descriptor_ui":"D015027","descriptor_name":"Zebrafish","qualifier_ui":"Q000033","qualifier_name":"anatomy & histology","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btv559","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv559","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/2/315/49016476/bioinformatics_32_2_315.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26415725","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26415725","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/2/315","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/2/315","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv559","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv559","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/2/315/49016476/bioinformatics_32_2_315.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.4099999964237213}],"awards":[{"id":"https://openalex.org/G4279291631","display_name":null,"funder_award_id":"MI 1315/4","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2177729144.pdf","grobid_xml":"https://content.openalex.org/works/W2177729144.grobid-xml"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W1970480709","https://openalex.org/W1971831631","https://openalex.org/W2055680969","https://openalex.org/W2073057651","https://openalex.org/W2138476437","https://openalex.org/W2605479038"],"related_works":["https://openalex.org/W2033889310","https://openalex.org/W644889988","https://openalex.org/W2086577855","https://openalex.org/W2119018183","https://openalex.org/W1575418055","https://openalex.org/W2496732697","https://openalex.org/W189459719","https://openalex.org/W1564198055","https://openalex.org/W1486643006","https://openalex.org/W2161927223"],"abstract_inverted_index":{"UNLABELLED:":[0],"The":[1],"Insight":[2,58,127],"Toolkit":[3,59,128],"offers":[4],"plenty":[5],"of":[6,21,64,74,108,114],"features":[7],"for":[8,28,46,56,104,158],"multidimensional":[9],"image":[10,76,112],"analysis.":[11],"Current":[12],"implementations,":[13],"however,":[14],"often":[15],"suffer":[16],"either":[17,92],"from":[18],"a":[19,29,65],"lack":[20],"flexibility":[22],"due":[23],"to":[24],"hard-coded":[25],"C++":[26,67,124],"pipelines":[27,81],"certain":[30],"task":[31],"or":[32,42,94],"by":[33,39,87],"slow":[34],"execution":[35],"times,":[36],"e.g.":[37],"caused":[38],"inefficient":[40],"implementations":[41],"multiple":[43],"read/write":[44],"operations":[45],"separate":[47],"filter":[48],"execution.":[49],"We":[50,98],"present":[51],"an":[52,70],"XML-based":[53],"wrapper":[54],"application":[55],"the":[57,62,101,105,126,130],"that":[60],"combines":[61],"performance":[63],"pure":[66],"implementation":[68],"with":[69],"easy-to-use":[71],"graphical":[72],"setup":[73],"dynamic":[75],"analysis":[77,107],"pipelines.":[78],"Created":[79],"XML":[80],"can":[82],"be":[83],"interpreted":[84],"and":[85,129,138,142,146,154],"executed":[86],"XPIWIT":[88,120],"in":[89,123],"console":[90],"mode":[91],"locally":[93],"on":[95],"large":[96],"clusters.":[97],"successfully":[99,136],"applied":[100],"software":[102],"tool":[103],"automated":[106],"terabyte-scale,":[109],"time-resolved":[110],"3D":[111],"data":[113,167],"zebrafish":[115],"embryos.":[116],"AVAILABILITY":[117],"AND":[118],"IMPLEMENTATION:":[119],"is":[121],"implemented":[122],"using":[125],"Qt":[131],"SDK.":[132],"It":[133],"has":[134],"been":[135],"compiled":[137],"tested":[139],"under":[140,150],"Windows":[141],"Unix-based":[143],"systems.":[144],"Software":[145],"documentation":[147],"are":[148,155,168],"distributed":[149],"Apache":[151],"2.0":[152],"license":[153],"publicly":[156],"available":[157,169],"download":[159],"at":[160,170],"https://bitbucket.org/jstegmaier/xpiwit/downloads/.":[161],"CONTACT:":[162],"johannes.stegmaier@kit.edu":[163],"SUPPLEMENTARY":[164],"INFORMATION:":[165],"Supplementary":[166],"Bioinformatics":[171],"online.":[172]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}