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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. 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. All workflow components are open-source and freely available: the htmrenamer R package for file handling; CellProfiler and ImageJ analysis scripts/pipelines; the Organoid Analyst application for statistical analysis; detailed usage instructions and a demonstration dataset Distributed under GPL v3.0. Supplementary information and a stepwise guide for software installation and data analysis for training purposes are available at Bioinformatics online. © The Author(s) (2020). Published by Oxford University Press. All rights reserved. For Permissions, please email:


Marne C Hagemeijer, Annelotte M Vonk, Nikhil T Awatade, Iris A L Silva, Christian Tischer, Volker Hilsenstein, Jeffrey M Beekman, Margarida D Amaral, Hugo M Botelho. An open-source high-content analysis workflow for CFTR function measurements using the forskolin-induced swelling assay. Bioinformatics (Oxford, England). 2020 Dec 26

PMID: 33367496

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