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  • Usage
    • Installation
    • Step-by-step Guide
      • 1- Pipeline Configuration
        • Step 1: Import Libraries and Initialize Configuration
        • Step 2: Set Mandatory Configuration
        • Step 3: Define Raw Data Directory Structure
        • Step 4: Specify Optional Configuration
        • Step 5: Apply Configuration Settings
        • Next Steps
      • 2- Volumetric Alignment
        • Step 1: Load the Configuration
        • Step 2: Execute Volumetric Alignment
        • Next Steps
      • 3- Alignment Evaluation
        • Step 1: Load Configuration Settings
        • Step 2: Additional Configuration for Alignment Evaluation
        • Step 3: Alignment Measurement
        • Step 4: Alignment Evaluation and Confidence Interval Calculation
        • Next Steps
      • 4- Synapses ROI Segmentation
        • Step 1: Load Configuration Settings
        • Step 2: Synapses ROI Segmentation
        • Next Steps
      • 5- Synapses Analysis
        • Step 1: Load Configuration Settings
        • Step 2: Extract Synapse Coordinates from Segmentation Masks
        • Step 3: Define Round-Channel Pairs for Analysis
        • Step 4: Measure Synapse Properties
        • Conclusion

Package Reference

  • Configration Module
    • Pipeline Configration
      • Config
        • Config.create_directory_structure()
        • Config.load_config()
        • Config.print()
        • Config.save_config()
        • Config.set_config()
        • Config.set_permissions()
  • Align Module
    • Volumes Alignment
      • execute_volumetric_alignment()
      • execute_volumetric_alignment_bigstream()
      • transform_ref_round()
      • volumetric_alignment()
    • Volumes Alignment Evaluation
      • calculate_alignment_evaluation_ci()
      • measure_round_alignment_NCC()
      • plot_alignment_evaluation()
      • alignment_NCC()
      • template_matching()
  • Segmentation Module
    • Synapses Segmentation
      • synapses_roi_segmentation()
  • Analysis Module
    • Puncta Analysis
      • extract_synapse_coordinates()
      • measure_synapse_properties()
      • measure_synapse_properties_pairwise()
  • Utils Module
    • Utility Functions
      • calculate_volume_and_surface_area()
      • chmod()
      • subtract_background_rolling_ball()
      • subtract_background_top_hat()
    • Package Logger
      • configure_logger()
  • I/O Module
    • I/O Functions
      • create_folder_structure()
      • load_json()
      • nd2ToVol()
      • save_json()
  • Search

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