Installation

Installation#

Requirements#

  • Python >= 3.11

  • PyTorch >= 2.0

  • scvi-tools >= 1.1.0

Installing spatialvi-tools#

From source#

git clone https://github.com/yoseflab/spatialvi-tools.git
cd spatialvi-tools
pip install -e .

Development installation#

pip install -e ".[dev,doc,test]"

Optional Dependencies#

JAX support (for Tangram, VIVS)#

pip install spatialvi-tools[jax]

GPU support#

spatialvi-tools automatically uses GPU if available. Make sure you have the correct PyTorch version installed for your CUDA version:

pip install torch --index-url https://download.pytorch.org/whl/cu121

Verifying Installation#

import spatialvi
print(spatialvi.__version__)
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