Root Quantify

Overview

Root Quantify is a Python-based tool designed for processing root system images. It supports:

• Batch Processing: Automatically iterates through all images in a selected folder.
• Interactive ROI Selection: In the right window, users click to select polygon vertices to define the region of interest (ROI). Press c to confirm or r to reset the selection.
• Digital Image Processing: The tool performs background estimation, shadow removal, binarization, and inversion on the selected ROI so that the roots appear black on a white background.
• Manual Correction: In the right window, users can manually correct the processed ROI by drawing or erasing. The brush size is adjustable (using +/-), and you can undo the last operation by pressing u. Press q when finished.
• Dual-Window Preview: The left window displays the original image along with its filename, while the right window handles ROI selection, image processing, and manual correction.
• Automatic Archiving: Processed images are saved in an output folder, and the original images are moved to a processed_original folder to prevent reprocessing.

System Requirements

• Python 3.12 (or another compatible version)
• OpenCV (opencv-python)
• NumPy
• Tkinter (usually included with Python)
• macOS or Windows

Installation

1.Clone the Repository Open your terminal and run:

git clone https://github.com/smiler488/RootQuantify.git
cd RootQuantify

2.Install Dependencies Use the provided requirements.txt file to install necessary libraries, Open your terminal and run:

pip install -r requirements.txt

How to Use

1.Run the Application Launch the script from your command line:

python RootImager.py      

2.Select the Image Folder

When the program starts, a folder selection dialog will appear. Choose the folder containing the images you want to process. Supported image formats include JPG, JPEG, PNG, BMP, TIF, and TIFF.

3.Dual-Window Workflow

• Left Window (“Original Image”):Displays the original image along with its filename.
• ROI Selection:Click in the right window to select polygon vertices that define your ROI.Press c to confirm the selection, or press r to reset.
• Automatic Processing:Once confirmed, the selected ROI is processed (background estimation, shadow removal, thresholding, inversion) so that roots appear black on a white background.
• Manual Correction:The right window then enters manual correction mode. You can:Press d to switch to draw mode (black).Press e to switch to erase mode (white).Use + or - to adjust the brush size (a green circle indicates the current brush size at the mouse pointer).Press u to undo the last operation.Press q to finish manual correction.
• 5Once manual correction is complete, press any key to proceed to the next image.

4.Output and Archiving

• The corrected ROI is automatically saved in the output folder with a filename prefixed by processed-.
• The original image is moved to a processed_original folder to avoid processing it again.

5.Completion

When all images have been processed, the terminal will display “Batch processing completed!” You can then close the application.