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Root Quantify: Python-Based Root System Image Processing Tool

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Liangchao Deng
Liangchao Deng
Ph.D. Candidate @ SHZU @CAS-Cemps

Overview​

Root Quantify is a Python-based tool designed for processing root system images. It provides a complete pipeline for analyzing root images with the following capabilities:

Key Features:​

  • Batch Processing: Automatically iterates through all images in a selected folder
  • Interactive ROI Selection: Users click to select polygon vertices to define the region of interest (ROI)
  • Digital Image Processing: Performs background estimation, shadow removal, binarization, and inversion
  • Manual Correction: Allows manual editing of processed ROI with adjustable brush size
  • Dual-Window Preview: Left window shows original image, right window handles ROI selection and processing
  • Automatic Archiving: Saves processed images and moves originals to prevent reprocessing

Key Features in Detail​

Batch Processing​

  • Automatically processes all images in the selected folder
  • No need to manually select images one by one
  • Supports multiple image formats

Interactive ROI Selection​

  • Polygon-based selection allows precise definition of irregular regions
  • Visual feedback during selection
  • Reset capability for correcting mistakes

Digital Image Processing Pipeline​

  1. Background Estimation: Identifies and estimates background intensity
  2. Shadow Removal: Reduces uneven lighting effects
  3. Binarization: Converts image to black and white
  4. Inversion: Ensures roots appear black on white background

Manual Correction Tools​

  • Draw Mode: Add black pixels (roots) to the image
  • Erase Mode: Remove black pixels (background)
  • Adjustable Brush: Fine-tune correction precision
  • Undo Function: Revert last operation if needed

Automatic Archiving​

  • Prevents reprocessing of already processed images
  • Maintains organized file structure
  • Preserves original images for reference

Use Cases​

Root System Analysis​

  • Quantify root length, density, and distribution
  • Compare root systems across different treatments
  • Extract morphological parameters for research

Agricultural Research​

  • Study root development patterns
  • Analyze root responses to environmental conditions
  • Support breeding programs for root architecture

Educational Purposes​

  • Demonstrate image processing techniques
  • Teach root system analysis methods
  • Support student research projects

Root Quantify is an open-source tool designed to simplify root system image analysis. For questions, issues, or contributions, visit the GitHub repository.

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