Standardizing spatial transcriptomic analysis for infectious diseases with STID

Spatial transcriptomic studies of infectious diseases still rely on fragmented data analysis processes. Here, we developed STID (spatial transcriptomics toolkit for infectious diseases), a standardized framework for spatial transcriptomic analysis of infectious diseases that leverages the Seurat ecosystem and incorporates Python-based modules. STID provides an extensible infection-specific data structure and supports a full suite of analyses, such as pathogen background correction, infection-associated spot and niche identification, single-sample niche characterization, and multi-sample comparative and temporal analyses. STID is broadly applicable to spatial transcriptomic data from infectious diseases caused by bacteria, viruses, and parasites and enables systematic characterization of the structural features, cellular composition, molecular functions, and host-pathogen interactions within pathogen-infected and/or host-responsive niches. Overall, STID provides an accessible, reproducible, and extensible framework for analyzing infection-associated spatial transcriptomic data and for dissecting host-pathogen interactions in their native spatial microenvironments.