Coordination Interface Framework (CIF): Universal Analysis Protocol v1.0

This document defines the Coordination Interface Framework (CIF) Universal Analysis Protocol v1.0, a reproducible computational specification for spatial transcriptomics analysis of immune–stromal coordination. The protocol formalizes the operational implementation of the Coordination Interface Framework developed in earlier framework versions, including standardized gene programs, parameter settings, spatial gradient computation, transition-interface detection, and geometry metrics. This specification provides a stable and reproducible analysis workflow for applying the CIF framework across spatial transcriptomics datasets. Implementation note: Quality-control metrics were computed using Scanpy's`calculate_qc_metrics` function. In this implementation, the mitochondrialfilter `pct_counts_mt ≤ 20` corresponds to the protocol definition of amitochondrial fraction threshold of 0.2.