Pipelines#
- Pipeline Overview
- Nextflow Workflows Guide
- 2.5D Reconstruction Workflow
- Reconstruction Parameter Tuning Guide
- How to approach tuning
- Quick orientation: which stage produces which artifact?
- Profiles before parameters
- Stage 1: Tile stitching
- Stage 2: Slice quality assessment
- Stage 3: Common-space alignment
- Stage 4: Missing-slice interpolation
- Stage 5: Pairwise registration
- Stage 6: Stacking
- Stage 7: Bias field correction (optional)
- Stage 8: Atlas registration (optional)
- Reference parameter sets
- See also
- Reconstruction Tuning — Quick Reference
- Diagnostic Tools for 3D Reconstruction Troubleshooting