Extended Data Fig. 2: Comparison of cell segmentation and cell type annotation results from different segmentation methods. | Nature Genetics

Extended Data Fig. 2: Comparison of cell segmentation and cell type annotation results from different segmentation methods.

From: Spatially resolved analysis of pancreatic cancer identifies therapy-associated remodeling of the tumor microenvironment

Extended Data Fig. 2: Comparison of cell segmentation and cell type annotation results from different segmentation methods.

a, Overlap of cell boundaries identified by Cellpose (red) and Baysor (blue). b, Barplot showing the adjusted mutual information score across transcripts for each sample. U, untreated; T, treated; b, base panel; a, augmented panel. c, UMAP visualization of the non-malignant cells segmented by Cellpose (left) and Baysor (right). d, Two representative FOVs showing the spatial distributions of all annotated cells (left, Cellpose; right, Baysor). e, Bubble heatmap showing expression levels of select marker genes for annotated cell types (top, Cellpose; bottom, Baysor). f, Comparison of cell type counts (top) and proportions (bottom) between Cellpose (red) and Baysor (blue). g, Heatmap showing the confusion matrix of cell types annotated for cells segmented with Cellpose (x axis) and Baysor (y axis).

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