# Welcome to NicheMap Tutorials

## Spatial tissue architecture and neighborhood analysis with NicheMap

```{toctree}
:maxdepth: 1
:caption: Contents:

Installation
Tutorial 1: Step-by-step Xenium lung data analysis <Tutorial_1_step_by_step>
Tutorial 2: End-to-end Xenium lung data workflow <Tutorial_2_full_workflow>
Tutorial 3: Cell-type neighborhood analysis <Tutorial_3_neighborhood_analysis>
```

```{image} Figures/Overview.png
:width: 100%
:align: center
```

## 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.