Fig. 5

Analytic pipeline and results summary for analyzing the mouse brain MERFISH dataset. A The analytic pipeline built on the SRT-Server. The constructed analytic pipeline uses five analytic modules, with the parameter settings for each module visualized on the panel. B A corresponding annotated brain tissue section from the Allen Brain Atlas. C 20 detected spatial domains from BASS in the CL_jo module. D 40 detected cell types from BASS in the CL_jo module. E The UMAP plot for 30 detected cell types from Seurat in the CT_PCA module. F Thirty detected cell types from Seurat in the CT_PCA module with resolution = 1. G The pseudo-time inference results are obtained from slingshot in the TRAJ module. The left panel shows the pseudo-time of four selected cell types. The right two plots include arrows to display pseudo-time change on the mouse brain: the arrow point from tissue locations with low pseudo-time towards tissue locations with high pseudo-time