MilliMap

Interactive spatial omics visualization and analysis in a single code-free desktop application. Explore tissues, run analyses, and discover biology — all without writing a line of code.

Download GitHub Read the Paper

MilliMap is currently under peer review. Please request code or assistance from the developer team.

Features

From data to insight, without switching tools

MilliMap turns analysis results into interactive spatial objects. Click a gene in a DEG table to recolor the tissue. Select cells in UMAP and see them highlighted on the slide. No context switching.

Interactive 3D Visualization

Linked spatial and embedding views. Select cells in one, instantly see them highlighted in the other.

Spatial Selection & ROIs

Lasso, rectangle, or 3D volume selection. Save any region as a named ROI and pass it straight into downstream analysis.

Integrated Analysis Stack

Preprocessing, clustering, DE, spatial stats, enrichment, batch correction — every parameter adjustable without writing code.

Interactive Results

Every result becomes an interactive object. Click a gene or cluster pair and the tissue updates in real time.

Millini AI Agent & Claude MCP

An LLM agent that turns natural-language questions into multi-step analysis, grounded in your live session state — and exposes MilliMap as an MCP server so Claude can drive your workspace directly.

Share Your Session

Hand off your live workspace to collaborators — export as a runnable Jupyter notebook, or save the full session archive so anyone can reopen it exactly where you left off.

Ecosystem

Built on trusted foundations

MilliMap integrates the best tools in the spatial omics ecosystem, connected through a unified GUI.

Single-cell Analysis

Scanpy

Preprocessing, clustering, and differential expression for single-cell genomics workflows.

Spatial Statistics

Squidpy

Moran's I, neighborhood enrichment, and co-occurrence — the spatial side of the scverse ecosystem.

Data Format

AnnData

The standard annotated data container that powers the entire scverse single-cell ecosystem.

3D Rendering

PyVista / VTK

Hardware-accelerated 3D visualization for interactive point clouds and volumetric tissue rendering.

Enrichment

GSEApy

Gene set enrichment analysis with built-in support for MSigDB and custom gene libraries.

Integration

HarmonyPy

Fast batch correction for multi-sample integration across donors, conditions, and platforms.

How to Cite

Citation

If MilliMap is useful in your research, please cite our paper.

Feng, Q., Qian, S.B., Wan, L.J., Starr, Z., Asif, S., Han, H.-S. MilliMap: interactive closed-loop analysis for spatial omics. bioRxiv (2026). doi: 10.64898/2026.05.01.722104.