Spatial Immune Cell Profiling

Definition Spatial immune cell profiling identifies and characterizes immune cells in a tissue while preserving their physical location. It combines gene/protein expression with spatial information.

• Spatial context of immune cells
• Cell type and functional state
• Preserves tissue architecture

• Tumor microenvironment analysis
• Predicting response to immunotherapy
• Autoimmune diseases and infection
• Cell–cell interaction mapping

• Spatial Transcriptomics – gene expression + coordinates (e.g. 10x Genomics Visium)
• Imaging Mass Cytometry (IMC) – protein markers with subcellular resolution
• Multiplex Immunofluorescence – multiple antibody stains per tissue section (e.g. CODEX)
• RNAscope / MERFISH – in situ RNA detection with spatial precision

In a tumor biopsy, spatial profiling may reveal that CD8+ T cells are present at the invasive margin but absent in the core — indicating an immune-excluded phenotype.