MetaChrome

Introduction

  • Getting Started
    • Overview
    • What is MetaChrome?
    • Key Features
    • Who Should Use This?
    • Image Requirements
    • Typical Workflow
    • Use Cases
    • Output and Results
    • Performance
    • Getting Help
    • Citation
    • License

Tutorial

  • Installation
    • Requirements
    • Dependencies
    • Installation Steps
    • GPU Support
    • Troubleshooting
  • Tutorial
    • Prerequisites
    • Launch the Application
    • Complete Analysis Workflow
      • Step 1: Configure Channel Identifiers
      • Step 2: Load Your Images
      • Step 3: Segment and Detect
      • Step 4: Find Common Regions
      • Step 5: Get Results
    • Quick Workflow Using “Run All”
    • Batch Processing Multiple Images
    • Understanding the Interface
      • Viewing Your Data
    • Manual Corrections (Optional)
      • Merging Chromosomes
      • Removing Chromosomes
    • Example Workflow Summary
    • Tips for Best Results
    • Common Issues
    • Next Steps

User Guide

  • Basic Workflow
    • Workflow Overview
    • Step 1: Channel Identifier Configuration
    • Step 2: Loading Images
    • Step 3: Chromosome Segmentation
    • Step 4: Spot Detection
      • Adjusting Thresholds
      • Detecting Channel 1 Spots
      • Detecting Channel 2 Spots
    • Step 5: Finding Common Regions
    • Step 6: Measuring Intensities
    • Step 7: Saving and Exporting
    • Analysis Without Segmentation
    • One-Click Analysis: Run All
    • Parameters Reference
    • Best Practices
    • Next Steps
  • Batch Processing
    • Overview
    • When to Use Batch Processing
    • Setup for Batch Processing
    • Running Batch Processing
      • Step 1: Load Image Folders
      • Step 2: Configure Settings
      • Step 3: Start Batch Processing
    • Monitoring Progress
    • Output Files
      • Individual Results
      • Combined Summary
      • Intermediate Files
    • Handling Errors During Batch Processing
    • Post-Processing Batch Results
    • Optimizing Batch Performance
    • Best Practices
    • Troubleshooting
    • Next Steps
  • Manual Corrections
    • Overview
    • Manual Correction Workflow
    • Merging Chromosomes
      • Step-by-Step Process
    • Removing Chromosomes
      • Step-by-Step Process
    • Deleting Spots
      • Deleting Channel 1 Spots (DNA-FISH)
      • Deleting Channel 2 Spots (CENP-C)
    • Drawing Tools and Tips
      • Napari Drawing Tools
      • Drawing Best Practices
      • Common Drawing Issues
    • Saving and Loading Corrections
      • Saving Corrections
      • Loading Previous Corrections
      • Reverting Corrections
    • Correction Workflow for Batch Processing
    • Best Practices
    • Limitations and Considerations
    • Next Steps
  • Advanced Features
    • Parameter Optimization
      • Threshold Optimization Strategy
      • Post-Processing Options
    • Data Export Options
      • CSV File Customization
      • Image Export
    • Integration with Other Tools
      • Python Scripting
      • Jupyter Notebook Integration
      • External Analysis Tools
    • Performance Optimization
      • GPU Acceleration
      • Memory Management
      • Parallel Processing
    • Custom Trained Models
      • Using Your Own Cellpose Model
      • Model Performance Evaluation
    • Advanced Batch Processing
      • Conditional Processing
      • Parameter Sweeps
    • Custom Metrics
      • Calculating Additional Measurements
      • Statistical Analysis Integration
    • Quality Control Metrics
      • Automated QC Checks
    • Troubleshooting Advanced Issues
    • Next Steps
  • Troubleshooting
    • Installation Issues
      • Python Version Errors
      • Dependency Installation Failures
      • CUDA/GPU Issues
      • Qt/GUI Issues
    • Image Loading Problems
      • No Images Found
      • File Format Not Supported
      • Incorrect Number of Channels
    • Segmentation Problems
      • Segmentation Failed
      • Too Many/Few Chromosomes Detected
      • Segmentation is Very Slow
    • Spot Detection Issues
      • No Spots Detected
      • Too Many False Positives
      • Spots Don’t Match Visual Inspection
    • Intensity Measurement Problems
      • Negative or Zero Intensities
      • Unrealistic Intensity Values
      • Missing Intensity Data
    • Batch Processing Problems
      • Batch Processing Stops Unexpectedly
      • Some Folders Skipped
      • Inconsistent Results Across Batch
    • Performance Issues
      • Application is Slow or Unresponsive
      • High Memory Usage
      • Application Crashes
    • Data and File Issues
      • CSV File Empty or Malformed
      • Can’t Find Output Files
      • Unable to Save Corrections
    • Error Messages Reference
      • Common Error Messages and Solutions
    • Getting Additional Help
      • Before Contacting Support
      • Contact Information
      • Community Resources
    • Next Steps
  • Citation
    • Paper Reference
    • BibTeX Entry
    • Contact Information
    • Acknowledgments
    • License

API Reference

  • API Documentation
    • Core Classes
      • ImageProcessor
        • ImageProcessor
      • BatchProcessor
        • BatchProcessor
      • SegmentationPostprocessing
        • SegmentationPostprocessing
    • GUI Components
      • Control Widgets
      • Main Functions
    • Usage Examples
      • Basic Usage
      • Batch Processing
      • Custom Analysis
    • Parameters Reference
      • Segmentation Parameters
      • Spot Detection Parameters
    • Data Structures
      • Spot DataFrames
      • Segmentation Masks
      • Intensity Results
    • Error Handling
    • Extension Points
      • Custom Models
      • Custom Post-processing
      • Custom Visualization
  • API Reference
    • Main Module
    • Image Processor
      • ImageProcessor
        • ImageProcessor.load_images()
        • ImageProcessor.get_spots_in_common_regions()
        • ImageProcessor.load_images1()
        • ImageProcessor.segment_image_BU()
        • ImageProcessor.segment_image()
        • ImageProcessor.segment_image_BU_original()
        • ImageProcessor.find_peaks()
        • ImageProcessor.detect_spots1()
        • ImageProcessor.detect_spots2()
        • ImageProcessor.detect_spots()
        • ImageProcessor.ndi
        • ImageProcessor.detect_spots_cent()
        • ImageProcessor.detect_spots_cent_BU()
        • ImageProcessor.detect_spots_no_segmentation()
        • ImageProcessor.detect_spots_no_segmentation_BU()
        • ImageProcessor.find_common()
        • ImageProcessor.find_common_BU()
        • ImageProcessor.find_common2()
        • ImageProcessor.get_spot_location()
        • ImageProcessor.measure_intensity_at_spots()
        • ImageProcessor.gen_intensity_from_df()
        • ImageProcessor.calculate_intensity_all_cenpc()
        • ImageProcessor.calculate_intensity_all_dna_fish()
        • ImageProcessor.get_centroids_from_labels()
        • ImageProcessor.merge_nuclei_with_line()
        • ImageProcessor.remove_nuclei_with_line()
        • ImageProcessor.split_chromosome_with_line()
        • ImageProcessor.delete_dna_fish_spots_with_line()
        • ImageProcessor.delete_cenpc_spots_with_line()
        • ImageProcessor.split_chromosome_with_line_BU()
    • Batch Processor
      • BatchProcessor
        • BatchProcessor.batch_processing()
    • Segmentation Post-processing
      • SegmentationPostprocessing
        • SegmentationPostprocessing.set_current_folder()
        • SegmentationPostprocessing.save_segmentation()
        • SegmentationPostprocessing.remove_chromosome()
        • SegmentationPostprocessing.split_chromosome()
        • SegmentationPostprocessing.merge_chromosomes()
        • SegmentationPostprocessing.show_info()
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