Fig. 3

Analytic pipeline and results summary for the anterior mouse brain 10X Visium dataset. A The analytic pipeline built on the SRT-Server. The constructed analytic pipeline uses eight analytic modules, with the parameter settings for each module visualized on the panel. B The H&E staining image displays the general tissue structure of the anterior mouse brain. C A corresponding annotated brain tissue section from the Allen Brain Atlas. D A spatial scatter pie plot displays the inferred cell-type compositions across spatial locations from CARD in the DECON module. E The trajectory inferred by mature neuron whose proportion is estimated by cell2loction. F Fifteen detected spatial domains from SpatialPCA in the SDD module. G Bubble plot displays − log10(p-values) for different pathways from the ORA module (y-axis). Six pathways are colored: GO biological process (red), GO molecular function (yellow), GO cellular component (blue), KEGG (grass-green), Reactome (grass-green), and Wikipathways (purple)