Feng, Q.; Qian, S. B.; Wan, J.; Starr, Z. R.; Asif, S.; Han, H.-S.

Spatial omics analysis requires iterative interplay between statistical computation and tissue-context interpretation, yet current workflows fragment these steps across disconnected environments. We present MilliMap, an interactive framework that unifies statistical analysis with spatial exploration. By closing the analysis-visualization loop, MilliMap empowers biologists to steer parameters, refine ROIs, and validate findings within a single environment. We demonstrate its utility by delineating complex neuroanatomy and identifying niche-restricted functional states in tumor microenvironments.