Fig. 2: Cell-type-specific morphological signatures.

a Representative image of cell types included in this study. Scale bar = 50 μm. b Accuracy of Random Forest classifiers in predicting cell type from image-based features. Each point represents the mean classification accuracy from 5-fold cross-validation using all features, grouped by cell type. Error bars represent 95% confidence intervals obtained from n = 1000 bootstrap replicates. c Barplot of feature categories for the 100 most important features based on our Random Forest classifier. The fractions of the features marked as important are indicated for each category. d Classification accuracy for each feature category, calculated as in (b). e Violin plot for Nuclei_RadialDistribution_MeanFrac_Mito_1of4 across cell types (p = 1.37e-35, ANOVA, n = 176 per cell type, two-sided). Feature values are INT scores for each morphology trait. f Violin plot for Cytoplasm_Correlation_RWC_AGP_ER across cell types (p = 1.64e-15, ANOVA, n = 176 per cell type, two-sided), presented like Fig. 2e. In both panels (e, f), boxplots within violins show the median (line), first and third quartiles (box limits), and whiskers extend to the most extreme data point within 1.5 times the interquartile range (IQR) from the box. g Schematic representation of two distinguishing cell morphology characteristics across the four cell types. (top) Nuclei_RadialDistribution_MeanFrac_Mito_1of4 is related to the intensity of the mitochondrial dye near the inner-most region of the cell. A greater value for this feature indicates more of a cell’s mitochondria are present near the nucleus. (bottom) Cytoplasm_Correlation_RWC_AGP_ER refers to the co-presence of the AGP and ER dyes for a given location in the cytoplasm of the cell. A greater feature value indicates that there is stronger overlap for the AGP and ER stains when compared to lower values.