CPPAnalyzer Jupyter notebook

This is is a Jupyter notebook for the normalization and quality control of Cell Painting and Cell Painting PLUS data using a costumized R code (SourceCode4Pipeline-productionV1.R). It requires as input data image analysis results on single cell level, an example data set can be found at Wedler et al. (2026) "Dataset for Cell Painting PLUS: An iterative staining-elution protocol for in vitro phenotypic screenings" (https://doi.org/10.5281/zenodo.18184315).

To specify the analysis, several excel sheets with analysis details are used: A compound layout file (for example Compound_layout_columnbased.xlsx) is used to assign to each well the respective treatment condition. When wells should be excluded from analysis for example due to known experimental errors, this can be done via listing these wells in a respective table to exclude wells (Table_to_exclude_wells.xlsx). A separate excel file states for each plate the optical section (z-plane) that should be analyzed (Table_planes.xlsx).

The use of this Jupyter notebook is described in detail in: Wedler et al., (2026): Cell Painting PLUS: An iterative staining-elution protocol for high-content phenotypic screenings (Current Protocols, doi:10.1002/cpz1.70368).