ChoroVIST

ChoroVIST is an interface to analyze choroid metrics such as Vascular Index and Thickness and performs choroid region segmentations using a backend code called Choroidalyzer, which is also available on GitHub on https://github.com/justinengelmann/Choroidalyzer . The interface is implemented with a simple database and includes several useful features that make it easy to use and highly relevant for medical professionals.

App Interface Overview

ChoroVIST Welcome Screen

This is the welcome screen of the app, displaying the main icons that reference the app's icon and the educational institutions responsible for supporting its development.

ChoroVIST Main Screen

This is the main screen for daily use by medical professionals, allowing the analysis of new exams as well as searching through the patient's history for previous uploaded exams.

Chorovist DataBase

This is the database with which the app communicates, implemented in Excel to better suit the medical environment and provide easier navigation and interpretation.

Generated Clinical Report

This is an example of a generated medical report from the app, ready for printing and clinically relevant.

🔧 Installation

🛠️ Step 1: Create and Activate a Conda Environment

First, you'll need to create a dedicated conda environment for ChoroVIST. If you haven't installed it on your computer yet, we recommend the lightweight Miniconda.

During installation, make sure to:

. Tick the box that says "Add Miniconda to my PATH environment variable" (if available).

. Choose the option to register Miniconda as your default Python.

The creation of this environment isolates the dependencies for ChoroVIST and ensures they won't conflict with other projects.

1.1 Open your terminal or the Miniconda/Conda PowerShell (depending on what you installed)

• If you're on Windows:

  • Click the Start menu (or press the Windows key).
  • Type and open terminal
  • Open your Conda Prompt

• If you're on macOS or Linux:

  • Open the Terminal application (you can find it via Spotlight or your applications menu).
  • Then type conda commands directly as shown in the next steps.

1.2 Create the Conda Environment

Run the following command to create a new environment named chorovist with Python 3.10:

conda create -n chorovist python=3.10

1.3 Activate the Environment

Once the environment is created, activate it by running:

conda activate chorovist

⚡ Step 2: Install Required Dependencies

After activating the environment, you'll need to install the necessary dependencies to run ChoroVIST.

pip install torch torchvision torchaudio matplotlib tqdm pandas scikit-image scipy openpyxl oct_converter tkcalendar

⚙️ Step 3: Set Up the Application

Once the environment is ready and dependencies are installed, ChoroVIST should be ready to run.

3.1 Navigate to Your Desired Folder

Before cloning the repository, use the terminal to move to the folder where you want ChoroVIST to be saved.

• For example, if you want to place it in your Documents folder:

cd C:\Users\YourName\Documents

3.2 Clone the Repository

⚠️ Make sure Git is installed on your system.
You can check by running:

git --version

If it's not installed, download it from git-scm.com.

If you haven't cloned the repository yet, you can do so by running the following command in your desired directory:

git clone https://github.com/gui305/ChoroVIST.git

3.3 Enter the ChoroVIST Directory

After cloning the repository, navigate into the ChoroVIST folder using the terminal:

cd ChoroVIST

3.4 Run ChoroVIST

Now that you are in the repository directory, you can run the application using Python:

python ChoroVIST.py

🖥️ Optional Step 4: Compile the Application into an Executable App

4.1 Install PyInstaller

First, install PyInstaller using pip:

pip install pyinstaller

4.2 Compile the Application

Run the following PyInstaller command to compile the application into an executable. This will bundle all dependencies, include necessary assets, and create a single executable file. This could take a few minutes.

pyinstaller --onefile --windowed --hidden-import=skimage.measure --icon=coroide.ico --add-data "FMUL.png;." --add-data "Tecnico.png;." --add-data "OLHO.png;." --add-data "coroide.ico;." ChoroVIST.py

4.3 Run the Executable

After compiling, you'll find the ChoroVIST executable inside the dist folder. Simply double-click to run the application like a normal app. You can change the app location understanding that the app will run over the ChoroVIST Database and Datafiles that you have in the directory of the exec.

🩺 Usage and Clinical Application

Everyone is free to use the app for clinical purposes and to edit the code for further investigation or personal changes.