{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T00:37:27Z","timestamp":1767832647929,"version":"3.49.0"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2020,12,26]],"date-time":"2020-12-26T00:00:00Z","timestamp":1608940800000},"content-version":"vor","delay-in-days":11,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"FCT\u2014Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","award":["UIDB\/04046\/2020"],"award-info":[{"award-number":["UIDB\/04046\/2020"]}]},{"name":"FCT\u2014Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","award":["UIDP\/04046\/2020"],"award-info":[{"award-number":["UIDP\/04046\/2020"]}]},{"name":"HIT-CF","award":["H2020-SC1-2017-755021"],"award-info":[{"award-number":["H2020-SC1-2017-755021"]}]},{"DOI":"10.13039\/100016077","name":"EU","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100016077","id-type":"DOI","asserted-by":"publisher"}]},{"name":"post-doctoral fellowship","award":["SFRH\/BPD\/93017\/2013"],"award-info":[{"award-number":["SFRH\/BPD\/93017\/2013"]}]},{"DOI":"10.13039\/100016032","name":"Dutch Cystic Fibrosis Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100016032","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Portuguese Platform of BioImaging","award":["PPBI-POCI-01-0145-FEDER-022122"],"award-info":[{"award-number":["PPBI-POCI-01-0145-FEDER-022122"]}]},{"DOI":"10.13039\/100006129","name":"FCT","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006129","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The forskolin-induced swelling (FIS) assay has become the preferential assay to predict the efficacy of approved and investigational CFTR-modulating drugs for individuals with cystic fibrosis (CF). Currently, no standardized quantification method of FIS data exists thereby hampering inter-laboratory reproducibility.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed a complete open-source workflow for standardized high-content analysis of CFTR function measurements in intestinal organoids using raw microscopy images as input. The workflow includes tools for (i) file and metadata handling; (ii) image quantification and (iii) statistical analysis. Our workflow reproduced results generated by published proprietary analysis protocols and enables standardized CFTR function measurements in CF organoids.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>All workflow components are open-source and freely available: the htmrenamer R package for file handling https:\/\/github.com\/hmbotelho\/htmrenamer; CellProfiler and ImageJ analysis scripts\/pipelines https:\/\/github.com\/hmbotelho\/FIS_image_analysis; the Organoid Analyst application for statistical analysis https:\/\/github.com\/hmbotelho\/organoid_analyst; detailed usage instructions and a demonstration dataset https:\/\/github.com\/hmbotelho\/FIS_analysis. Distributed under GPL v3.0.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa1073","type":"journal-article","created":{"date-parts":[[2020,12,14]],"date-time":"2020-12-14T20:22:47Z","timestamp":1607977367000},"page":"5686-5694","source":"Crossref","is-referenced-by-count":14,"title":["An open-source high-content analysis workflow for CFTR function measurements using the forskolin-induced swelling assay"],"prefix":"10.1093","volume":"36","author":[{"given":"Marne C","family":"Hagemeijer","sequence":"first","affiliation":[{"name":"Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht , 3584 EA Utrecht, The Netherlands"},{"name":"Regenerative Medicine Center Utrecht, University Medical Centre Utrecht , 3584 EA Utrecht, The Netherlands"}]},{"given":"Annelotte M","family":"Vonk","sequence":"additional","affiliation":[{"name":"Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht , 3584 EA Utrecht, The Netherlands"},{"name":"Regenerative Medicine Center Utrecht, University Medical Centre Utrecht , 3584 EA Utrecht, The Netherlands"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1560-7991","authenticated-orcid":false,"given":"Nikhil T","family":"Awatade","sequence":"additional","affiliation":[{"name":"BioISI \u2013 Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa , 1749-016 Lisboa, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8062-5558","authenticated-orcid":false,"given":"Iris A L","family":"Silva","sequence":"additional","affiliation":[{"name":"BioISI \u2013 Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa , 1749-016 Lisboa, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3545-5104","authenticated-orcid":false,"given":"Christian","family":"Tischer","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory (EMBL), Centre for Bioimage Analysis (CBA) , 69117 Heidelberg, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2255-2960","authenticated-orcid":false,"given":"Volker","family":"Hilsenstein","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory (EMBL), Advanced Light Microscopy Facility (ALMF) , 69117 Heidelberg, Germany"}]},{"given":"Jeffrey M","family":"Beekman","sequence":"additional","affiliation":[{"name":"Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht , 3584 EA Utrecht, The Netherlands"},{"name":"Regenerative Medicine Center Utrecht, University Medical Centre Utrecht , 3584 EA Utrecht, The Netherlands"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0828-8630","authenticated-orcid":false,"given":"Margarida D","family":"Amaral","sequence":"additional","affiliation":[{"name":"BioISI \u2013 Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa , 1749-016 Lisboa, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4208-1086","authenticated-orcid":false,"given":"Hugo M","family":"Botelho","sequence":"additional","affiliation":[{"name":"BioISI \u2013 Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa , 1749-016 Lisboa, Portugal"}]}],"member":"286","published-online":{"date-parts":[[2020,12,26]]},"reference":[{"key":"2023062504243327100_btaa1073-B1","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1007\/978-1-4939-7021-6_31","article-title":"Quantitative phenotypic image analysis of three-dimensional organotypic cultures","volume":"1612","author":"Akerfelt","year":"2017","journal-title":"Methods Mol. 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