Supplementary Figure 13: Application to MERFISH data.

(A) In a MERFISH study of an osteosarcoma cell culture of 139 probes from Moffitt et al, the SpatialDE test identified the majority of the probes as spatially variable (66%, FDR<0.05, dashed line, Q-value adjusted). 21 of 92 significant SV genes were assigned to a periodic function by the model, and nine genes had linear functions. Red labels indicate negative control probes. Genes indicated as enriched in proliferating cells in the original study are marked in green, and depleted genes in blue. (B) Visualization of the MERFISH data by plotting general RNA probes in pink and MALAT1 probes in blue on two 512 x 512 virtual pixel grids at different scales. The original imaged region was 5.2 mm wide and 8.2 mm high totaling 38,594 cells (upper). We analyzed a region of 1 mm x 1 mm in the middle of the cell culture with 1,056 cells (lower). (C) Expression levels in the cell culture region visualized for selected SV genes with various fitted periods and length scales (significance levels and colors as in Fig. 2). Black scale bar correspond to 200 μm. Stars next to gene names denote significance levels (* FDR < 0.05, ** FDR < 0.01, *** FDR < 0.001, Q-value adjusted). (D) Fraction of gene probes and control probes detected as significant SV genes as a function of the family-wise error rate (FWER). The number of significant control probes was in line with the FWER.