Phase 1: Create modular utilities - data_persistence, artifact_cache, image_utils

Fix: Remove redundant LLM call after parallel execution + Command template reuse optimization

Fix multi-channel crop handling and add organoid illumination correction skip

Refactor planner: Remove unnecessary Segmentation->Cropper enforcement, enable intelligent analysis depth decision

Phase 1-4: Complete architecture refactoring with unified image processing

Add multi-channel image processing guide based on best practices