Unified integration of spatial transcriptomics across platforms with LLOKI.

ABSTRACT: Spatial transcriptomics (ST) has transformed our understanding of tissue architecture and cellular interactions, but integrating ST data across platforms remains challenging due to differences in gene panels, data sparsity, and technical variability. Here, we introduce LLOKI, a novel framework for integrating imaging-based ST data from diverse platforms without requiring shared gene panels. LLOKI addresses ST integration through two key alignment tasks: feature alignment across technologies and batch alignment across data sets. Optimal transport-guided feature propagation adjusts data sparsity to match scRNA-seq references through graph-based imputation, enabling single-cell foundation models such as scGPT to generate unified features. Batch alignment then refines scGPT-transformed embeddi

SUBMITTER: Haber E 

PROVIDER: S-EPMC12667708 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature