Capturing cell heterogeneity in representations of cell populations for image-based profiling using contrastive learning
Fig 7
CytoSummaryNet profiles show a better ability to distinguish similar samples than average-aggregated profiles (cpg0001 dataset).
UMAP of the average- (left column) and CytoSummaryNet- (right column) aggregated profiles of the top 15 mechanisms of action, based on CytoSummaryNet’s mAP scores for mechanism of action retrieval, from all used cpg0001 Stain3 plates (Table C in S1 Text). The UMAP was created using n_neighbors = 15 and cosine similarity as a distance measure. The profiles are colored based on their corresponding annotated mechanism of action, compound, plate, and well position from top to bottom, respectively. Same mechanism of action profile clusters that were visible for multiple n_neighbors values are annotated in green ellipses, respectively. Note that Compound2 and Compound5 are intentionally anonymized.