Napari Plugin Usage

Process dual-view SPIM data through an interactive napari interface.

Quick Start

1. Launch napari: napari
2. Open plugin: Plugins → PySPIM → DiSPIM Pipeline
3. Follow the 5-step workflow in the tabs

Video Tutorial

Complete Workflow Demonstration

Workflow Steps

1. Data Loading

• Browse to μManager folder containing a.tif and b.tif
• Set parameters: Step size (0.5 μm), Pixel size (0.1625 μm), Theta (45°)
• Click "Load Data"

2. ROI Detection

• Choose channels: Both A & B, or single channel
• Select method: Otsu (automatic) or Manual (draw rectangle)
• Click "Detect and Apply ROI"

3. Deskewing

• Select cropped A and B layers
• Verify parameters from metadata
• Click "Deskew Data"

4. Registration

• Select deskewed A and B layers
• Choose transform: t+r+s (translation + rotation + scaling)
• Enable phase correlation
• Click "Register Data"

5. Deconvolution

• Load PSF files for both channels (.npy format)
• Select algorithm: "Efficient" (recommended)
• Set iterations: 20, regularization: 1e-6
• Click "Deconvolve Data"

Supported Formats

• μManager acquisitions (standard folder structure)
• TIFF files (individual files per channel)
• HDF5 files (hierarchical data format)
• Zarr arrays (compressed format)

Troubleshooting

Issue	Solution
Plugin not appearing	Restart napari after installation
CUDA errors	Check GPU availability with nvidia-smi
Memory errors	Reduce chunk size in deconvolution
Registration failures	Try different transform types

Advanced Features

• GPU Acceleration: Automatic when available
• Background Processing: Non-blocking operations
• Memory Management: Automatic cleanup and chunking
• Data Flow: Parameters automatically passed between steps