# Installation

`NicheMap` is a Python package for spatial tissue architecture and neighborhood analysis in spatial transcriptomics.

We recommend installing NicheMap in a clean conda environment.

## 1. Create an environment

```bash
conda create -n nichemap python=3.10
conda activate nichemap
```

## 2. Install NicheMap

Install from PyPI:

```bash
pip install nichemap
```

Or install the development version from GitHub:

```bash
git clone https://github.com/yihe-csu/NicheMap.git
cd NicheMap
pip install -e .
```

## 3. Install notebook dependencies

From this tutorials repository:

```bash
pip install -r requirements.txt
```

## 4. Add a Jupyter kernel

```bash
pip install ipykernel
python -m ipykernel install --user --name=nichemap --display-name "Python (NicheMap)"
```

When opening the tutorial notebooks, select:

```text
Python (NicheMap)
```

## 5. Prepare tutorial data

The notebooks expect the tutorial dataset at:

```text
data/SSc_1_1_2_tutorial.h5ad
```

Create a local `data/` directory in the tutorials repository and place `SSc_1_1_2_tutorial.h5ad` there before running the notebooks.

## 6. Open tutorials

```bash
jupyter lab docs/source/
```

## Notes

The notebooks may produce small numerical or visualization differences across software environments. For reproducible analysis, use a fixed Python environment and keep package versions consistent.