FIGURE 1:

Data processing and modeling approach. (a) Example images and workflow from the Cell Health assays. We apply a series of manual gating strategies (see Materials and Methods) to isolate cell subpopulations and to generate cell health readouts for each perturbation. (Top) In the “Cell Cycle” panel, in each nucleus we measure Hoechst, EdU, PH3, and gH2AX. (Bottom) In the “Viability” panel, we capture DPC images, measure Caspase 3/7, DRAQ7, and CellROX. (b) Example Cell Painting image across five channels, plus a merged representation across channels. The image is cropped from a larger image and shows ES2 cells. Scale bars are 20 µm. Below are the steps applied in an image-based profiling pipeline, after features have been extracted from each cell’s image. (c) Modeling approach where we fit 70 different regression models using CellProfiler features derived from Cell Painting images to predict Cell Health readouts. Model weights refer to the coefficients derived from each regression model.