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arXiv · 2506.18692

An Analytical Neighborhood Enrichment Score for Spatial Omics

Axel Andersson·Hanna Nyström
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Abstract

The neighborhood enrichment test is used to quantify spatial enrichment and depletion between spatial points with categorical labels, which is a common data type in spatial omics. Traditionally, this test relies on a permutation-based Monte Carlo approach, which tends to be computationally expensive for large datasets. In this study, we present a modified version of the test that can be computed analytically. This analytical version showed a minimum Pearson correlation of 0.95 with the conventional Monte Carlo-based method across eight spatial omics datasets, but with substantial speed-ups. Additional experiments on a large Xenium dataset demonstrated the method's ability to efficiently analyze large-scale data, making it a valuable tool for analyzing spatial omics data.

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Axel Andersson, Hanna Nyström. 2025-06-23. An Analytical Neighborhood Enrichment Score for Spatial Omics. https://arxiv.org/abs/2506.18692

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