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Installation

We provide pretrained weights for the multimodal autoencoder (AE) and graph convolutional masked autoencoder (GCN) under data/.

SpatialFusion depends on PyTorch and DGL, which have different builds for CPU and GPU systems. You can install it using pip or inside a conda/mamba environment.

1. Create mamba environment

mamba create -n spatialfusion python=3.10 -y
mamba activate spatialfusion
# Then install GPU or CPU version below

2. Install platform-specific libraries (GPU vs CPU)

GPU (CUDA 12.4)

pip install "torch==2.4.1" "torchvision==0.19.1" \
  --index-url https://download.pytorch.org/whl/cu124
conda install -c dglteam/label/th24_cu124 dgl

Note: TorchText issues exist for this version: https://github.com/pytorch/text/issues/2272 — this may affect scGPT.

pip install torch==2.3.0 torchvision==0.18.0 torchaudio==2.3.0 \
  --index-url https://download.pytorch.org/whl/cu121
conda install -c dglteam/label/th21_cu121 dgl

# Optional: embeddings used by scGPT
pip install --no-cache-dir torchtext==0.18.0 torchdata==0.9.0

# Optional: UNI (H&E embedding model)
pip install timm

CPU-only

pip install "torch==2.4.1" "torchvision==0.19.1" \
  --index-url https://download.pytorch.org/whl/cpu
conda install -c dglteam -c conda-forge dgl

# Optional, used for scGPT
pip install --no-cache-dir torchtext==0.18.0 torchdata==0.9.0

# Optional, used for UNI
pip install timm

💡 Replace cu124 with the CUDA version matching your system (e.g., cu121).

3. Install SpatialFusion package

cd spatialfusion/
pip install -e .

Includes: pytest, black, ruff, sphinx, matplotlib, seaborn.

cd spatialfusion/
pip install -e ".[dev,docs]"

4. Verify Installation

python - <<'PY'
import torch, dgl, spatialfusion
print("Torch:", torch.__version__, "CUDA available:", torch.cuda.is_available())
print("DGL:", dgl.__version__)
print("SpatialFusion OK")
PY

5. Notes

  • Default output directory is:

$HOME/spatialfusion_runs

Override with:

export SPATIALFUSION_ROOT=/your/path * CPU installations work everywhere but are significantly slower.