Installation¶
Install PySPIM for development and research use.
Prerequisites¶
- Python 3.8.1 or higher
- CUDA-compatible GPU (optional, for GPU acceleration)
- Git
Installation¶
PySPIM is currently in development. Install from source:
# Clone the repository
git clone https://github.com/matt-black/pyspim.git
cd pyspim
# Install packages (basic usage)
just install
# Or manually with UV
uv pip install -e packages/pyspim
uv pip install -e packages/napari-pyspim
Development Installation¶
For development and contributing:
# Install packages + development tools
just install-dev
# Or manually
uv sync --extra dev
uv pip install -e packages/pyspim
uv pip install -e packages/napari-pyspim
# Install pre-commit hooks
just pre-commit
CUDA Support¶
For GPU acceleration:
Development Workflow¶
# List all available commands
just --list
# Run tests
just test-fast
# Format and lint code
just format
just lint
# Build documentation
just docs-serve
Verification¶
After installation:
# Test core package
import pyspim
print(f"PySPIM version: {pyspim.__version__}")
# Test napari plugin
import napari
import napari_pyspim
viewer = napari.Viewer()
# Check that the plugin appears in the plugins menu
Troubleshooting¶
| Issue | Solution |
|---|---|
| CUDA not found | Install CUDA drivers and correct CuPy version |
| Import errors | Ensure you're in the correct Python environment |
| Plugin not showing | Restart napari after installation |
| Just command not found | Install just: conda install -c conda-forge just |