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Leaf Damage Evaluation Macro

This repository contains a Fiji macro designed to evaluate leaf damage caused by salt stress treatment, a critical part of my PhD research. The macro processes images of leaves to determine the total leaf area and the damaged (senesced) area, outputting the data in a tabular format. This data can be further analyzed and visualized using tools like R or Python.

To date,with some modification in the paremeters, this macro can also be used for evaluating Leaf Senescence Index (LSI), Greenness Index (GI) and Leaf Area Index (LAI) etc.

Repository Contents

  • Standalone Macro: Process a single photo of a leaf.
  • Batch Processing Macro: Process a list of files, each containing a single photo of a leaf.
  • R Visualization Script: Visualize the proportion of damaged (senesced) areas.

Example output figures

An example of the analyzed figure.

Sample fig

Usage Instructions

Prerequisites

  • Fiji (ImageJ): Make sure you have Fiji installed. You can download it here.
  • R: For data visualization, R needs to be installed. You can download it here.

Photo Guidelines

  • Photos should be taken in a consistent environment (e.g., same background). It is highly recommended to use a dedicated camera instead of a phone to ensure unified image quality.
  • In the example above, three paper with an area of 1 $cm^2$ were used as controls (white, blue and red). This approach is recommended because it allows for precise area calculation and reduces bias associated with manual photography.

Parameters

TBC.

Running the Macros

  1. Standalone Macro:
  • Open Fiji.
  • Load the standalone macro.
  • Open a single leaf photo.
  • Run the macro to evaluate the total and damaged areas.
  1. Batch Processing Macro:
  • Open Fiji.
  • Load the batch processing macro.
  • Provide a directory of leaf photos.
  • Run the macro to process all photos and generate a table of results.
  1. R Visualization Script:
  • Open R or RStudio.
  • Load the provided R script.
  • Import the table generated by the macro.
  • Run the script to visualize the proportion of damaged (senesced) areas.

Output

The output from the macro includes:

  • Total leaf area
  • Damaged (senesced) area
  • Proportion of damaged area

This data is saved in a table format, which can be used for further analysis and visualization.

Note

If you encounter any issues or have suggestions for improvement, feel free to open an issue or submit a pull request.