Unsupervised discovery of dynamic cell phenotypic states from transmitted light movies
Fig 4
UPSIDE identifies stem cell-associated morphological states from patient-derived AML leukemic cells.
(A) LSCs (CD34+CD38-) from an acute myeloid leukemia patient were cultured in cytokines with or without AhR inhibitors (UM729 and StemRegnin1) filmed for ~5 days (left). Brightfield images were captured once every 3-5 minutes. αCD34-APC and αCD38-PE antibodies were added in situ, and fluorescent images were captured once every hour (top right). Still frames show representative time lapse images of AML cells (bottom right). Scale bar represents 10 μm. (B) UMAP 2D projection of the UPSIDE generated latent space cell representations. Individual morphological clusters were identified using the Louvain Clustering algorithm, then grouped manually based on their proximity to each other in the latent space (See S6B Fig). Representative cell images from each cluster were also shown. Scale bar represents 10 μm. (C) Clustergram shows Z-scores of the latent mask and texture encodings for each morphological cluster. (D) Decoded images of the four most enriched features for each morphological state. Texture features were visualized using difference maps that were zoomed in around the decoded cells. (E) Area, eccentricity, and edge strength for each cell were calculated and mapped to the UMAP latent space representation. (F) CD34 and CD38 levels were mapped onto the UMAP. (G) Violin plots show distributions of CD34 and CD38 expression levels in different morphological clusters (left). (H) Histograms showing log CD34 levels against CD38 levels for each morphological cluster (right).