Fig. 6

Giotto Viewer provides an interactive workspace to visualize and compare multiple cell annotations. a Visualization of the Visium brain dataset. Two interlinked panels are displayed, showing the data in the physical (left) and expression space (middle). A zoomed-in view shows underlying cell staining pattern at individual spots (right). b–e Visualization of the seqFISH+ mouse somatosensory cortex dataset. b Four interlinked panels are displayed, showing the spatial domain (top) and cell type (bottom) distribution in both physical (left) and expression space (right). c A zoomed-in view of b focusing on the L1–3 regions. Cells in domain D7 are selected (indicated by red outline in left panels and highlighted in the right panels) to enable comparison between spatial domain and cell type annotations. d Expression patterns of representative domain-specific genes. e Subcellular transcript localization patterns of all (top) or selected genes (middle and bottom) in a representative cell. Each dot represents an individual transcript