Fig. 3: Cell-type deconvolution specificity comparison on spatially registered Visium spots to GeoMx AOI labels. | Nature Communications

Fig. 3: Cell-type deconvolution specificity comparison on spatially registered Visium spots to GeoMx AOI labels.

From: Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneity

Fig. 3

a Image registration between GeoMx fluorescent image and Visium spot coordinates. Image above is representative of 1 sample. b Density plot of overlapping area between Visium spots and each GeoMx AOI. A threshold of > 70% was applied to select spots registered to a GeoMx AOI label. Number of mapped spots: n total (n passed 70% threshold)—Malignant: n = 1422 (116 AOIs); Other: n = 1676 (342 AOIs); T cells: n = 701 (5 AOIs); Macrophage: n = 395 (0 AOIs). (c) For registered GeoMx segments and Visium spots in (b), using matched Level 1.5 Chromium reference from Fig. 2a to deconvolute cell type fraction. Boxes represent the quartiles of the data, while the whiskers extend to data points within 1.5x the interquartile range from the lower and upper quartiles. The horizontal black line within each box represents the median. Outliers are indicated as individual data points. Malignant: GeoMx (n = 28 AOIs), Visium (n = 116 spots); Other: GeoMx (n = 29 AOIs), Visium (n = 342 spots); T cells: GeoMx (n = 3 AOIs), Visium (n = 5 spots). Source data are provided as a Source Data file.

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