Definitions and Applications of Spatial Niches in Spatial Omics Data Analyses: A Summary and Discussion

Thomas M. Menino Convention & Exhibition Center 

"Spatial niche" is widely used in spatial omics yet inconsistently defined, obscuring resolution, components, and analytic purpose. We summarize how the term maps to three distinct concepts: (i) a proximity-based neighborhood around an anchor cell/spot; (ii) a computationally derived spatial domain (mutually exclusive or overlapping) grouping spots with shared molecular or contextual features; and (iii) a biologically grounded microenvironment that includes cellular and non-cellular elements (e.g., vasculature, ECM, ligands) supporting resident cells. We organize methods and datasets under this taxonomy and clarify two application modes: using niches as covariates for spot-level modeling versus using niches as spatial clusters for within- and between-niche inference (composition, differential expression, ligand–receptor signaling). We provide reporting standards and selection guidance, and recommend reserving "niche" for the biological microenvironment while using "neighborhood" and "spatial domain" for the other cases to reduce ambiguity and enable rigorous, comparable analyses.