Fig. 3: Evaluation of soScope on a spatial chromatin accessibility dataset from a mouse embryo using spatial-CUT&Tag.

a H&E image of the mouse embryo and four major regions (defined in the original publication¹⁸) analyzed in this study. b Evaluation of resolution enhancement performance using Pearson correlation and MSE with simulated low-resolution peak data (“Methods” section). Percentage indicates the improvement/error reduction ratio between soScope and the second-best approach. Boxplot: same format as in Fig. 2d. c Left in each column: spatial visualization of peak counts from four organs using original profiles or enhanced profiles. Right in each column: characterization of high and low expression regions by clustering profiles in the left figure into two groups using \(k\)-means. Results of all comparing methods are provided in Supplementary Fig. 5a; additional peaks are shown in Supplementary Fig. 6. d Detailed investigation of the embryo heart region. Left: high-resolution H&E image reveals two subregions with distinct morphological patterns in the heart region. Right: comparison of marker gene activities from original and enhanced peak expressions. e Spatial visualization of enhanced peak activities from comparing approaches. Results of all comparing methods are provided in Supplementary Fig. 5d. f Validation of the heart structure using a Spatial Transcriptomics dataset from a human embryonic heart section. Left: H&E image with regional annotations. Right: spatial patterns of human orthologous genes. g Quantitative comparison between gene activities in the mouse (left) and gene expressions in the human (right) for heart subregions. Two-sided t-tests were used. n.s.: 0.05 ≤ p; *1E-2 ≤ p < 0.05; **1E-3 ≤ p < 1E-2; ***p < 1E-3 using a two-sided rank-sum test. For Fhl2 in trabecular ventricular myocardium vs. compact ventricular myocardium, Spatial linear: p = 0.020; Image MLP: p = 2.6 × 1E-16; Joint MLP: p = 1.4 × 1E-24; soScope: p = 7.6 × 1E-26; For FHL2, p = 1.1 × 1E-6. For Ldha in trabecular ventricular myocardium vs. compact ventricular myocardium, Spatial linear: p = 0.0012; Image MLP: p = 0.72; Joint MLP: p = 0.60; soScope: p = 1.2 × 1E-10. For LDHA, p = 6.5 × 1E-6. Boxplot: same format as in Fig. 2d. Results of all comparing methods are provided in Supplementary Fig. 5e. Source data are provided as a Source Data file.