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Napari Plugin Installation

Install the PySPIM napari plugin for interactive SPIM data processing.

Prerequisites

  • Python: 3.8.1 or higher
  • napari: 0.4.0 or higher
  • CUDA-compatible GPU (optional, for GPU acceleration)

Installation

PySPIM is currently in development. Install from source:

# Clone the repository
git clone https://github.com/matt-black/pyspim.git
cd pyspim

# Install with UV (recommended)
uv pip install -e packages/pyspim
uv pip install -e packages/napari-pyspim

# Or with just
just install

GPU Support

For GPU acceleration:

# Install CuPy with CUDA support
pip install cupy-cuda12x

Verification

  1. Launch napari: 

    napari

  2. Check Plugin:

  3. Go to Plugins menu

  4. Look for PySPIM → DiSPIM Pipeline

  5. Test Loading: 

    import napari
from napari_pyspim import DispimPipelineWidget

viewer = napari.Viewer()
widget = DispimPipelineWidget(viewer)
print("Plugin loaded successfully!")

Troubleshooting

Issue Solution
Plugin not appearing Restart napari after installation
CUDA errors Check GPU availability with nvidia-smi
Import errors Ensure you're in the correct Python environment

Next Steps