Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy
Fig 3
UMAP visualizations of image-based embeddings obtained with Cell-DINO
Left column (A,C): Image-based embeddings of the HPA-FoV dataset. Right column (B,D): Image-based embeddings of the Cell Painting datasets. Top row (A,B): unprocessed embeddings. Bottom row (C,D): transformed embeddings for downstream analysis. A) Points are fields of view, and the colors reveal the cell line of the sample. B) Points are single cells, and the colors reveal the source study where the cells come from: LINCS [48] and LUAD [9] are A549 cells, while CDRP [49], TAORF [50], and BBBC022 [51] are U2OS cells. Samples from the five studies were used for training. C) Points are embeddings of fields of view after harmonization [52]; colors are protein localization labels. D) Points are well-level aggregated features after batch correction with sphering [73] from the LINCS dataset. Colors are mechanisms of action; names with a are antagonists and names with i are inhibitors).