Add comprehensive plan to reduce jagged/discontinuous slice registration

[Copilot]

Current registration produces jagged, discontinuous slices in the Z-axis. Added analysis and implementation roadmap.

Root Cause Analysis

Independent per-slice registration without explicit Z-axis smoothness constraints. Critical findings:

• Final stack smoothing disabled at line 349: across_slice_smoothing_sigma = 0
• Minimal deformation field smoothing: syn_total_sigma = 0
• No post-registration transform processing

Documentation Added

Quick Start (QUICK_QUALITY_IMPROVEMENTS.md)

• Top 3 fixes: enable final smoothing, increase SyN parameters, add deformation field smoothing
• Expected 40-60% improvement same-day
• Code snippets with exact parameters

Visual Guide (VISUAL_IMPROVEMENT_GUIDE.md)

• ASCII visualizations of problem/solution
• Parameter impact diagrams
• Quality assessment checklist
• Validation script

Technical Plan (REGISTRATION_QUALITY_IMPROVEMENT_PLAN.md)

• 11 prioritized strategies from quick wins to advanced (sliding window, 3D regularization)
• 3-phase roadmap with effort/impact estimates
• Parameter tuning guidelines
• Risk mitigation

Master README (README_QUALITY_IMPROVEMENTS.md)

• Navigation hub and decision matrix
• Timeline options (same day → 2 weeks)
• Expected cumulative improvements by phase

Improvement Strategies

Phase 1: Quick Wins (same day, 40-60% improvement)

# Enable disabled smoothing
final_stack_smoothing_sigma = 2  # Currently 0

# Increase deformation smoothing
syn_flow_sigma = 4      # From 3
syn_total_sigma = 2     # From 0 (disabled)

Phase 2: Transform Processing (2-3 days, 60-75% cumulative)

• Gaussian smoothing of deformation fields across Z-axis
• Median filtering to remove registration outliers

Phase 3: Advanced Methods (1-2 weeks, 75-85% cumulative)

• Bilateral filtering (edge-preserving)
• Adaptive regularization based on MI scores
• Optional: Sliding window registration, 3D global regularization

Implementation Status

Documentation only. No code changes. Ready for phased implementation starting with Phase 1 quick wins.

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