MilliMap

Features

Visualization meets analysis

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

GPU-accelerated point clouds with bidirectionally linked spatial and embedding views. Select in one, see it in the other.

📊

Integrated Analysis Stack

Scanpy preprocessing, Leiden clustering, differential expression, Squidpy spatial statistics, GSEA, and batch correction — all from the GUI.

🎯

Interactive Results

Analysis outputs are spatial objects. Click a gene, a cell-type pair, or a statistic and the tissue view updates instantly.

🗺️

Spatial Selection & ROIs

Freeform lasso, rectangle, cluster-based, and 3D volume selection. Save, merge, and use ROIs directly in downstream analyses.

🤖

Millini AI Agent

A built-in LLM-powered assistant that translates natural-language biological questions into reproducible analysis operations.

📓

Session Export

Every operation is logged. Export your entire analysis session as a reproducible Jupyter notebook with executable Scanpy/Squidpy code.

Get Started

Up and running in minutes

Download the standalone app for macOS or Windows — no Python environment required. Or install from source with pip or conda.

      # Clone the repository

      git clone https://github.com/milliomics/MilliMap.git

      cd MilliMap

      # Option 1: Conda (recommended)

      conda env create -f setup/environment.yml

      conda activate millimap

      # Option 2: pip

      pip install -r requirements.txt

      # Launch MilliMap

      python src/millimap/main.py

Ecosystem

Built on trusted foundations

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

Scanpy

Preprocessing, clustering, and differential expression

Squidpy

Spatial statistics: Moran's I, neighborhood enrichment, co-occurrence

AnnData

Standard data container from the scverse ecosystem

PyVista / VTK

Hardware-accelerated 3D rendering

GSEApy

Gene set enrichment analysis

HarmonyPy

Batch correction for multi-sample integration

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 spatial omics visualization and analysis. Manuscript in preparation (2026).