Extended Data Fig. 7: Assesment of Cell Painting performance when using various combinations of channel features.

Mean percent replicating of eight JUMP-MOA plates stained with the final staining conditions after dropping out all feature names containing individual channel names before performing feature selection and calculation of percent replicating. ‘None’ means that only AreaShape features are present. To create a sufficiently compact data representation, the eight channels present were split four each onto the X (AGP, DNA, ER and Mito) and Y (RNA, Brightfield, BFHigh and BFLow) axes; this allows visualization of the 256 possible unique combinations. Note that these results are not the same as truly having the stains not present, because (i) a channel still may have been used in creating the initial segmentation results, and (ii) it does not account for cross-talk between stains. An alternate representation of these data is presented in Extended Data Fig. 8. For more information including the plates represented in this figure, see the Source Data file for this figure; expanded experimental details for each plate may be found in Supplementary Data File 1. AGP, actin golgi plasma membrane; BF, brightfield; Mito, mitochondria.