Welcome to NicheMap Tutorials

Spatial tissue architecture and neighborhood analysis with NicheMap

Contents:

• Installation
• Tutorial 1: Step-by-step Xenium lung data analysis
• Tutorial 2: End-to-end Xenium lung data workflow
• Tutorial 3: Cell-type neighborhood analysis

Overview

NicheMap is a Python toolkit for spatial transcriptomics analysis. It supports spatial domain and tissue-structure analysis, graph-based spatial workflows, and cell-type neighborhood analysis around annotated tissue regions.

These tutorials use Xenium lung data to demonstrate the main NicheMap workflows, from step-by-step analysis to a compact end-to-end pipeline and neighborhood-level cell-type composition analysis.

Tutorials

Tutorial 1 provides a step-by-step walkthrough of the Xenium lung data analysis workflow.

Tutorial 2 provides a streamlined end-to-end version of the same analysis.

Tutorial 3 demonstrates the neighborhood analysis module, including target tissue regions, hop-based neighbor expansion, cell-type composition summaries, spatial topology plots, and trend plots across hops.

Citation

If you use NicheMap in your work, please cite the NicheMap repository and related publication information when available.