Stereopy: modeling comparative and spatiotemporal cellular heterogeneity via multi-sample spatial transcriptomics.

ABSTRACT: Understanding complex biological systems requires tracing cellular dynamic changes across conditions, time, and space. However, integrating multi-sample data in a unified way to explore cellular heterogeneity remains challenging. Here, we present Stereopy, a flexible framework for modeling and dissecting comparative and spatiotemporal patterns in multi-sample spatial transcriptomics with interactive data visualization. To optimize this framework, we devise a universal container, a scope controller, and an integrative transformer tailored for multi-sample multimodal data storage, management, and processing. Stereopy showcases three representative applications: investigating specific cell communities and genes responsible for pathological changes, detecting spatiotemporal gene patterns by co

SUBMITTER: Fang S 

PROVIDER: S-EPMC12012134 | biostudies-literature | 2025 Apr

REPOSITORIES: biostudies-literature