Pipelines

• Pipeline Overview
  • Overview
  • Data Flow
  • Preprocessing Pipeline
  • 3D Reconstruction Pipeline
  • Algorithmic Details
  • GPU Acceleration
  • Running the Pipelines
  • Quality Metrics and Reporting
  • Error Handling
  • Output Structure
• Nextflow Workflows Guide
  • Overview
  • Available Workflows
  • Prerequisites
  • Preprocessing Workflow
  • 3D Reconstruction Workflow
  • GPU Acceleration
  • CPU Core Management
  • Configuration Files
  • Execution Profiles
  • Monitoring and Debugging
  • Common Issues
  • Best Practices
  • Authoring Notes (linumpy reconstruction workflow)
  • Reference
• 2.5D Reconstruction Workflow
  • Overview
  • When to Use This Workflow
  • Location
  • Input
  • Running
  • Parameters
  • Pipeline Processes
  • Outputs
  • Cluster / Container Configs
  • Differences from the 3D Workflow
• Diagnostic Tools for 3D Reconstruction Troubleshooting
  • Context: Oblique Sample Mounting
  • Common Artifacts and Their Causes
  • Pipeline Diagnostic Options
  • Diagnostic Scripts
  • Troubleshooting Workflow
  • Example: Troubleshooting sub-18 Oblique Brain
  • Parameters Reference
  • Output Directory Structure