Fig. 3: Berberine chloride as an example of a reference compound with a clear, interpretable phenotype.

A Feature response reproducibility. Thirteen independent experiments were conducted with U-2 OS cells treated with berberine chloride (10 µM) for 24 h, features were extracted with SPACe and signed Earth Mover’s Distance (signed EMD) is represented as a heatmap. B Signed EMD heatmap showing all the extracted features after a berberine chloride concentration-response (75 nM to 10 µM) at the 24 h time point. C Average ± standard deviation of the top, non-redundant eight features changing after berberine chloride treatment, with EC₅₀ indicated, from the experiments in (A). D Eighteen cell lines were treated with berberine chloride 10 µM for 24 h and the signed EMD of all features is represented as a heatmap. E Stacked bar graph showing a berberine chloride “consensus fingerprint” of the changing features across cell lines. Increased features are in red, decreased in blue, and unchanged in gray. N/A represents shape features and ratios (i.e., nuclear size/cell size). Source data are provided as a Source Data file.