Fig. 7: Cell type annotation performance of the ST platforms using the ICON2 TMA. | Nature Communications

Fig. 7: Cell type annotation performance of the ST platforms using the ICON2 TMA.

From: Comparison of imaging based single-cell resolution spatial transcriptomics profiling platforms using formalin-fixed paraffin-embedded tumor samples

Fig. 7: Cell type annotation performance of the ST platforms using the ICON2 TMA.The alternative text for this image may have been generated using AI.

a UMAP and spatial locations of manually annotated cell type clusters across the platforms. Clusters are labeled with their corresponding cell types based on top-expressed genes. Each color represents a cell type. b Box plots of the F1-scores display performance of cell segmentation and cell type annotations in ST platforms. Each dot represents number of tissue cores in CosMx (blue) ICON2 (n = 14), MERFISH (purple) ICON2 (n = 21), Xenium-MM (orange) ICON2 (n = 21). The center of the box plot is denoted by the median, a horizontal line dividing the box into two equal halves. The bounds of the box are defined by the lower quartile (25th percentile) and the upper quartile (75th percentile). The whiskers extend from the box and represent the data points that fall within 1.5 times the interquartile range (IQR) from the lower and upper quartiles. Any data point outside this range is considered an outlier and plotted individually. Source data are provided as a Source Data file.

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