articleNature GeneticsFeb 27, 2024HYBRID OA

BANKSY unifies cell typing and tissue domain segmentation for scalable spatial omics data analysis

VSVipul SinghalNCNigel ChouJLJoseph LeeYYYifei YueJLJinyue Liu

Agency for Science, Technology and Research · Genome Institute of Singapore · +7 more institutions

PubMed
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Abstract

Spatial omics data are clustered to define both cell types and tissue domains. We present Building Aggregates with a Neighborhood Kernel and Spatial Yardstick (BANKSY), an algorithm that unifies these two spatial clustering problems by embedding cells in a product space of their own and the local neighborhood transcriptome, representing cell state and microenvironment, respectively. BANKSY's spatial feature augmentation strategy improved performance on both tasks when tested on diverse RNA (imaging, sequencing) and protein (imaging) datasets. BANKSY revealed unexpected niche-dependent cell states in the mouse brain and outperformed competing methods on domain segmentation and cell typing benchmarks. BANKSY can…

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Topics
Keywords
  • Biology
  • Computational biology
  • Segmentation
  • Domain (mathematical analysis)
  • Scalability
  • Spatial analysis
  • Evolutionary biology
  • Computer science
UN Sustainable Development Goals
  • Sustainable cities and communities
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