Fig. 5: CelloType performs joint segmentation and cell type classification.

a, A grouped barplot showing mean AP values for cell type predictions by the compared methods. The bar height represents mean values for each cell type from a 10-fold cross-validation experiment. Each grouped barplot is overlaid with ten data points, representing the results of a 10-fold cross-validation. The error bar represents the standard deviation. The average values across cell types are shown in the parentheses. Statistical significance is indicated as follows: ****P < 1 × 10⁻⁴, ***P < 1 × 10⁻³, **P < 1 × 10⁻², *P < 0.05. P values were computed using one-sided Student’s t-test (Supplementary Table 13). b, A line plot showing the relationship between classification accuracy and confidence score threshold by the compared methods. X1, fitted coefficient for linear regression between classification accuracy and confidence score; pval, P value for the coefficient. c, Representative examples of cell segmentation and classification results using the colorectal cancer CODEX dataset. Each row represents a 200 × 200 pixel FOV of a CODEX image. Each FOV shows predicted cell segmentation masks (boxes) and cell types (colors). Ground truth, manually annotated cell types; Cellpose2 + CellSighter, cell segmentation by Cellpose2 followed by cell type classification by CellSighter. Randomly selected confidence scores for cell classification computed by the compared methods are displayed next to the predicted instances.