Visium Spatial Gene Expression for FFPE Imaging Guidelines

Technical Note, Last Modified on June 30, 2021, Permalink


The Visium Spatial Gene Expression for FFPE workflow assays RNA levels by using probes against the whole transcriptome in intact formalin fixed paraffin embedded (FFPE) tissue sections and maps the location(s) where gene activity is occuring. Immuno-staining tissue sections with fluorescent antibodies enables simultaneous protein detection. Successful gene expression and protein visualization is highly dependent on good imaging practices.

This Technical Note provides hardware recommendations, general image acquisition and analysis guidelines, and examples of images that are suitable for downstream analysis with Space Ranger. Individual results may vary depending on the specific imaging system, and/or sample characteristics.