The Visium CytAssist Spatial Gene Expression for FFPE assay is designed to analyze mRNA in tissue sections derived from formalin fixed & paraffin embedded (FFPE) tissue samples. The Visium CytAssist instrument requires a glass slide with intact tissue sections as input. This protocol outlines deparaffinization, decrosslinking, immunofluorescence (IF) staining, and imaging of tissue for use with 10x Genomics Visium CytAssist Spatial Gene Expression for FFPE assay. Deparaffinized, decrosslinked, and stained tissue sections are inputs for the downstream Visium Spatial Gene Expression for FFPE workflow.