Starfysh integrates spatial transcriptomic and histologic data to reveal heterogeneous tumor-immune hubs.

ABSTRACT: Spatially resolved gene expression profiling provides insight into tissue organization and cell-cell crosstalk; however, sequencing-based spatial transcriptomics (ST) lacks single-cell resolution. Current ST analysis methods require single-cell RNA sequencing data as a reference for rigorous interpretation of cell states, mostly do not use associated histology images and are not capable of inferring shared neighborhoods across multiple tissues. Here we present Starfysh, a computational toolbox using a deep generative model that incorporates archetypal analysis and any known cell type markers to characterize known or new tissue-specific cell states without a single-cell reference. Starfysh improves the characterization of spatial dynamics in complex tissues using histology images and enable

SUBMITTER: He S 

PROVIDER: S-EPMC11415552 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature