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bioRxiv · 10.64898/2026.05.01.722104

MilliMap: interactive closed-loop analysis for spatial omics

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

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.

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Feng, Q., Qian, S. B., Wan, J., Starr, Z. R., Asif, S., Han, H.-S.. 2026-05-05. MilliMap: interactive closed-loop analysis for spatial omics. https://doi.org/10.64898/2026.05.01.722104

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