A versatile tool to rapidly process and analyze leaf photos

Leaf area is an important morphological metric than can be useful for comparing plants, phenotyping, understanding growth over time and for calculating things like ET, as examples. While measuring leaf area is a rather straightforward process, it is also hands on and error prone using most techniques. To address this issue we have developed an image processing pipeline that allows users to take individual photos of the leaves for which an area is needed, then automatically extract leaf area from each image file.

What once took days or weeks, now takes minutes or hours.

Input

Directory with photo(s) of any leaf on reference paper

Output

CSV data table containing ID info for each leaf and leaf area

Recommended installation process

Clone the repository to your local system using git, in terminal (macOS and Linux) or cmd (Windows):

git clone https://github.com/mattjenkins3/Automated-Leaf-Area-Detection.git

Pro tip: We recommend navigating to the directory where you'd like to store this software before cloning.

Using software

1. Create a virtual environment

Note: first Install virtualenv if not already installed

Navigate to the root directory 'Automated-Leaf-Area-Detection/' of the cloned repository.

Use the following commands to create a new virtual environment and then activate it:

$ python3 -m venv myenv

This will create the virtual Python environment called myenv. Replace myenv with a different name if you prefer.

Activate the virtual environment called myenv using:

$ source myenv/bin/activate

2. Install dependencies

(myenv) $ python -m pip install -r requirements.txt

3. Open a Jupyter notebook

(myenv) $ jupyter notebook

4. Start exploring the Leaf Area Tool notebook

This tool allows users to process large batches of images quickly.

5. When you're done, don't forget to deactivate your virtual environment using

$ deactivate

Requirements

• Python 3.7: There are many ways to install Python on your local machine, but we recommend downloading the official installer for your specific operating system, directly from Python.

Citing this repository

To cite this repository:

@software{Leaf-Area-Tool,
  author = {Matthew Jenkins, Dylan Lenczewski-Jowers, Fabiola Chavez Lamas},
  title = {{Leaf Area Detect}: Automated Leaf Area Tool},
  url = {https://github.com/mattjenkins3/Automated-Leaf-Area-Detection.git},
  version = {0.1.4},
  year = {2023},
}