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

conda create -n nichemap python=3.10
conda activate nichemap

2. Install NicheMap

Install from PyPI:

pip install nichemap

Or install the development version from GitHub:

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

3. Install notebook dependencies

From this tutorials repository:

pip install -r requirements.txt

4. Add a Jupyter kernel

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

When opening the tutorial notebooks, select:

Python (NicheMap)

5. Prepare tutorial data

The notebooks expect the tutorial dataset at:

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

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.