Extended Data Fig. 6: Robustness to measurement location misalignment.
From: Super-resolved spatial transcriptomics by deep data fusion
a, Hematoxylin and eosin stain of a section from the ileum of the human small intestine. Representative close-up of a small area of the brush border. The brush border in the section measures approximately 7 mm in length. b, Conceptual illustration of the measurement locations on the Visium array. Dark circles indicate test locations withheld during training. Light circles indicate training locations over three misalignment levels: 0.0 (light green), 1.0 (green), and 2.0 (blue) radii of the measurement locations (r = 55 μm). The direction of the misalignment is uniformly random. c,d, Gene-wise Pearson correlation between predicted and ground truth expression (c) and coefficient of determination (d) over the test locations of the n = 100 highest-expressed genes for increasing offsets. Boxes show 25th, 50th, and 75th percentiles. Outliers are represented by points and defined as observations further than 1.5 interquartile ranges from the hinges. Whiskers indicate the extent of all non-outlier observations. Pairwise p-values are based two-sided Wilcoxon signed-rank tests. Exact p-values (top to bottom): c, 2.98 × 10−7 and 8.30 × 10−1; d, 3.45 × 10−9 and 8.14 × 10−1. e–g, Predicted expression of CDHR5 when the training set has 0.0 (e), 1.0 (f), or 2.0 (g) radii misalignment. Close-ups of the same area as in a. h, Reference antibody staining for CDHR5 in the small intestine from the Human Protein Atlas12.
