Single-cell multi-omics captures more than one molecular layer (RNA + protein, or RNA + chromatin) from the same cell; doing it spatially keeps that multi-layer picture tied to the cell's actual position in the tissue.
joint_signal(x,y) = integration * (rna(x,y) + protein(x,y)) - noise
- Spatial resolution — how many resolvable spots/cells the tissue section is divided into for joint profiling.
- Modality integration — how well RNA and protein readouts from the same spot are computationally cross-referenced.
- Signal strength — raw capture efficiency of transcripts and epitopes at each spatial location.
- Cross-modal noise — measurement noise/dropout that can misalign the two data modalities.
Spatial multi-omics let researchers map, for the first time in situ, which immune cell states (by protein) sit next to which transcriptional tumor states (by RNA) — resolving biology that single-modality profiling missed entirely.