Nature Genetics perspective unifies the fuzzy definition of 'spatial niche' in spatial omics
lucapinello · x · 2026-11-15
A UCLA team led by Jingyi Jessica Li published a Perspective in Nature Genetics addressing the inconsistent use of 'spatial niche' in spatial omics.
The paper surveys the literature and distills three distinct meanings: proximity-based spatial neighborhoods, computationally derived spatial domains, and biologically grounded ecosystems of cellular and non-cellular components.
It also separates two analytical roles — niches as spot-level covariates for local context, and niches as spot clusters for compositional/molecular comparisons — and provides a five-step decision framework (Ask, Select, Match, Analyze, Validate). The recommendation: reserve 'niche' for biological ecosystems and use the computational terms for the derived constructs.
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