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.

Availability and implementation

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

Supplementary data are available at Bioinformatics online.

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