Fig. 3
From: Single-cell spatial explorer: easy exploration of spatial and multimodal transcriptomics
A complex gate pattern was obtained by image analysis. Using ImageJ/Fiji tools, Region Of Interest (ROI, here splenic follicles) were defined, exported and imported in Single-Cell Spatial Explorer (A). Gates previously defined with ImageJ/Fiji were compared in Single-Cell Spatial Explorer on the Reactome pathway (\(> 2500\) pathways) scores computed in Single-Cell Signature Explorer [8], resulting in a P value vs fold change table and volcano plot (B). On the volcano plot, a dot was selected and the corresponding pathway (’CD22-mediated BCR regulation’) visualized on the tissue image