[EXP] Analysis, Denoising and Segmentation Pipeline

[patrickcleeve2]

Core

• Core salami acquistion / milling loop
• Configuration tools

Analysis

• Read sweep configuration
• Generate parameter sweep
• Run collection
• Run analysis
• FRSC implementation
• Visualisation

Denoising

• Training
• Pre-process (Tile, Align)
• Inference
• Post-process (Restack / Align)

Segmentation

• Labelling + Training
• Inference
• Visualisation
• Diagnostics

Pipeline

• Configuration
• cmd line program
• Segmentation
• Denoising

Visualisation

• Napari Visusalisation (All layers)
• Onboard Diagnostics and Statistics

Performance

• Denoise Inference: ~45s
• Segmentation Inference: ~2s