STAPLE: automating spatial transcriptomics analysis and AI interpretation

Spatial transcriptomics workflows often span separate tools for cell typing, neighborhoods, and cell-cell communication, yielding fragmented outputs that hinder scalability, interpretation, and reproducibility. STAPLE systematizes analyses across distinct methods into a modular framework, unifying data structures and cross-tool interoperability. End-to-end analyses are performed unassisted with a single invocation, fostering rigorous, reproducible spatial transcriptomics analysis. Its novel, AI-enabled reporting layer synthesizes quantitative results into summaries of biological findings, facilitating analysis interpretation.