Installation

Contents

Installation#

Quick install#

spatialvi-tools requires Python ≥ 3.12. Install into a fresh virtual environment:

pip install spatialvi-tools

Optional extras#

Extra	Command	Installs
Spatial backends	`pip install "spatialvi-tools[spatial]"`	squidpy, spatialdata
GPU acceleration	`pip install "spatialvi-tools[rapids]"`	cuML, cuPy, cuGraph
Tutorials	`pip install "spatialvi-tools[tutorials]"`	jupyter, matplotlib, seaborn
All	`pip install "spatialvi-tools[all]"`	everything above

Development install#

git clone https://github.com/YosefLab/spatialvi-tools.git
cd spatialvi-tools
pip install -e ".[dev,test]"
pre-commit install

Verifying the installation#

import spatialvi
print(spatialvi.__version__)

GPU support#

RAPIDS-based acceleration (neighbor computation and latent representation) requires a CUDA-capable GPU and the rapids extra. The base package runs on CPU without any GPU dependencies.