An Analytical Neighborhood Enrichment Score for Spatial Omics
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arXiv
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| Format: | Preprint |
| Published: |
2025
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| _version_ | 1866916807270465536 |
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| author | Andersson, Axel Nyström, Hanna |
| author_facet | Andersson, Axel Nyström, Hanna |
| contents | 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. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2506_18692 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | An Analytical Neighborhood Enrichment Score for Spatial Omics Andersson, Axel Nyström, Hanna Quantitative Methods 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. |
| title | An Analytical Neighborhood Enrichment Score for Spatial Omics |
| topic | Quantitative Methods |
| url | https://arxiv.org/abs/2506.18692 |