Prapillyzer

Prapillyzer (Profile + Papilla) is an innovative software tool designed to extend and enhance the traditional Cup-to-Disc Ratio (CDR) measurement used in ophthalmic imaging. Unlike conventional methods that typically provide a single vertical or horizontal CDR value, this tool offers a comprehensive profile of CDR values around the entire optic disc.

Installation

We'll use Anaconda to create a new Python environment and handle all the required dependencies.

1. Install Anaconda following the official guidelines.

2. Clone this repo to your machine.

3. Open a new Anaconda terminal (Windows) or a normal terminal window (Linux/MacOS) and cd to the directory of the cloned repo: cd <repo_directory>

4. Open a new Anaconda terminal and create a new environment: conda create -n pcdr python=3.12

5. Activate your newly create environment: conda activate pcdr

6. Install the required libraries to run Prapillyzer: pip install -r requirements.txt

7. Install Pytorch using pip

Usage

1. Modify the configuration parameters found in cfg/config.ini to suit your needs.

2. Download the model weights from here (disc.pth, cup.pth, fovea.pth) and place those files in src/models

3. Place all your images in the input folder you've set in the previous step. The software uses data/ as the default folder to look for input images.

4. Run main.py

5. Check the ouput folder (default is results/) for the results. The folder should contain a file called results.csv with all the measurements. Images with the segmentations and CDR-Profiles will also be saved there if saving the result image is set as True in the config file.

Sample results

Disclaimer

Current implementation uses automatic segmentation of fovea, disc and cup. In future releases, the software will accept user generated masks.