Entomological Label Information Extraction

📚 Getting Started

  • Installation
    • Prerequisites
      • System Requirements
      • Software Dependencies
    • Installation Methods
      • Option 1: Conda Environment (Recommended)
      • Option 2: pip Installation
      • Option 3: Development Installation
      • Option 4: HPC/Cluster Installation (Apptainer)
    • Verification
      • Test Installation
      • Test Basic Functionality
      • Data Directory Setup
    • Troubleshooting
      • Common Issues
      • Getting Help
    • Next Steps
  • Quick Start Guide
    • 🚀 Option 1: Gemini Pipeline (Recommended)
    • 🔧 Option 2: Traditional Pipelines (Offline)
    • 🎯 What Happens Next?
    • 📈 Quick Results Check
    • 🚑 Need Help?
    • Understanding Pipeline Types
      • Multi-Label Images (MLI)
      • Single-Label Images (SLI)
    • Basic Usage Examples
      • Streamlit Interface (Recommended)
      • Command Line Method
      • Pipeline Scripts
    • Understanding Results
      • Multi-Label Results
      • Single-Label Results
      • Key Output Files
    • Common Workflows
      • Museum Digitization
      • Research Data Preparation
      • Quality Assessment
    • Next Steps
    • Tips for Success
      • Image Quality
      • Batch Processing
      • Result Validation
      • Performance Optimization
  • User Guide
    • System Overview
      • Architecture
      • Preprocessing and Thresholds
    • Preparing Your Data
      • Image Requirements
      • Quality Guidelines
      • Multi-Label Images
      • Single-Label Images
      • Directory Structure
    • Using the Interface
      • Starting the Interface
      • Interface Workflow
    • Command Line Usage
      • Gemini Pipeline (Recommended)
      • Traditional Pipeline Commands
      • Advanced Options
    • Manual Pipeline Scripts
      • Direct Script Execution
    • Understanding Results
      • Output Structure
      • Key Output Files
      • Quality Assessment
    • Processing Workflows
      • Complete Museum Digitization
      • Research Data Extraction
      • Batch Processing
    • Troubleshooting
      • Common Issues
      • Getting Help
    • Best Practices
      • Image Preparation
      • Processing Strategy
      • Quality Control
      • Data Management
    • Entity Recognition (Gemini Pipeline)
    • Advanced Features
      • Custom Configuration
      • Programmatic Access
      • Integration

🔧 API Reference

  • API Reference
    • Quick Module Guide
    • Detailed Documentation
      • label_processing Package
      • label_postprocessing Package
      • label_evaluation Package
      • pipelines Package
      • scripts Package
    • Programmatic Usage

🛠️ Help & Info

  • Troubleshooting
    • 🔧 Installation Issues
    • 🖼️ Processing Issues
    • 🎁 Quick Help Commands
    • 📞 Still Need Help?
    • Specific Error Messages
    • Quality Issues
    • Performance Optimization
    • Development Issues
    • Getting More Help
    • Prevention Tips
  • Advanced Configuration
    • Environment Variables
      • Project Path Overrides
      • Pipeline Path Overrides
    • Model Caching
      • Detection Model Caching
    • Rotation Model Configuration
      • Model Search Paths
      • Missing Model Handling
    • Conda Environment Customization
      • Using Custom Environment Name
    • Docker Configuration
      • Custom Port Mapping
      • Custom Volume Mounts
      • Memory and CPU Limits
    • HPC/Apptainer Configuration
      • Environment Variables in HPC
      • Parallel Processing
    • Tesseract Configuration
      • Custom Tesseract Path
      • Language Packs
    • Performance Tuning
      • Multiprocessing
      • Batch Size for Detection
      • GPU Configuration
    • Troubleshooting
      • Cache Issues
      • Path Resolution Issues
      • Permission Issues
    • See Also
  • Rotation Model Setup and Troubleshooting
    • Quick Setup
      • 1. Download Pre-trained Model
      • 2. Verify Model Installation
    • Model Search Order
    • Troubleshooting
      • Error: “Rotation model not found”
      • Error: “Model loading failed”
      • Error: “Legacy optimizer not supported”
      • Pipeline skips rotation or uses unrotated images
    • Training Your Own Model
      • Data Preparation
      • Training Script
      • Model Requirements
    • Advanced Configuration
      • Custom Model Path
      • Skip Rotation Step
    • Performance Notes
      • Rotation Speed
      • Accuracy
      • When Rotation Fails
    • Testing
      • Test Rotation on Sample Images
      • Validate Rotation Accuracy
    • Support
    • See Also
  • Contributing
    • How to Contribute
    • Getting Started
      • Development Setup
    • Code Standards
      • Style Guidelines
      • Code Formatting
    • Testing
      • Running Tests
      • Writing Tests
    • Documentation
      • Documentation Standards
      • Building Documentation
    • Submitting Changes
      • Pull Request Process
      • Pull Request Template
    • Issue Reporting
      • Bug Reports
      • Feature Requests
    • Development Guidelines
      • Architecture Principles
      • Adding New Features
    • Model Contributions
      • Contributing Models
      • Model Standards
    • Community
      • Communication Channels
      • Code of Conduct
    • Recognition
    • Release Process
      • Version Numbering
      • Release Checklist
    • Getting Help
  • Changelog
    • [2.0.0] - 2025-03-13
      • Added
      • Changed
      • Fixed
    • [1.0.0] - 2024-01-01
      • Added
      • Core Features
      • Performance
      • Documentation
      • Development
      • Security
      • Compatibility
      • Known Issues
    • Future Releases
      • Planned Features
      • Version 2.1.0
    • Contributing
    • License
    • Acknowledgments
  • License
    • MIT License
    • Third-Party Licenses
      • Core Dependencies
      • OCR Dependencies
      • Web and GUI Dependencies
      • Development Dependencies
      • Documentation Dependencies
    • Models and Training Data
      • Detection Models
      • Classification Models
    • Usage Terms
      • Commercial Use
      • Academic Use
      • Attribution
    • Disclaimer
    • Contact
    • Legal Notice
Entomological Label Information Extraction
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© Copyright 2025, Margot Belot.

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