Hi all,
I try to do cell type annotation for a visium data from middle temporal gyrus, so I follow seurat tutorial here:
The reference has these cell types in subclass_label column: “Pax6”, “L5/6 NP”, “L5 IT”, “L6 CT”, “L4 IT”, “Astrocyte”, “L2/3 IT”, “Vip”, “Sst Chodl”, “L6 IT Car3”, “L6 IT”, “Sncg”, “Pvalb”, “Oligodendrocyte”, “Lamp5 Lhx6”, “Sst”, “VLMC”, “Lamp5”, “Microglia-PVM”, “OPC”, “L6b”, “Endothelial”, “L5 ET”, “Chandelier”, “max”
However, when using SpatialFeaturePlot(), I got no signal of cell types that should have such as microglia
I use the data from this paper: Spatially resolved transcriptomics reveals genes associated with the vulnerability of middle temporal gyrus in Alzheimer’s disease | Acta Neuropathologica Communications | Full Text
Would you please have a suggestion?