Getting Started

The Eyened platform is a modern web platform for visualization and annotation of ophthalmic images with features like:

• Loading of various image formats including DICOM.
• Convenient system for browsing / filtering loaded studies and images.
• Task system for managing grading tasks.
• Drawing tools for 2D image segmentation of enface images and OCT B-scans
• Images and annotations are rendered in the browser, making it very responsive and easy to set up.
• Authentication system secures the viewer, images, thumbnails and annotations.
• Image enhancements such as CLAHE can be applied on the fly.
• Integrated tools for registration of enface images.
• Automated ETDRS grid placement via AI-based bounds detection and landmark detection (fovea, optic disc) upon insertion of CFI images.

Quick Setup

The easiest way to get started with the eyened platform is by configuring and running our docker-compose. The platform will then be accessible from any machine within your network.

With this setup you will be able to:

• Run the client / viewer, initially on an empty database.
• Run our import script to import local images and associated metadata into the system.

You can set up the Eyened platform in two ways:

Option 1: Automated Setup (Recommended)

We provide a setup script that automates the installation process and includes enhanced security features: Prerequisite: ensure docker and docker-compose is installed

1. Clone our repository:

   git clone https://github.com/Eyened/eyened-platform.git

2. Run the setup script:

   cd eyened-platform/docker
   chmod +x setup.sh
   ./setup.sh

The setup script will:

• Prompt you for configuration settings or use defaults
• Create and configure the .env file
• Create necessary directories for images, storage, and database
• Build and start the containers
• Display the URLs for accessing the platform

Note

Running Multiple Instances: If you want to run multiple instances of the platform on the same host:

• Change the name in docker-compose.yaml to something unique for every project
• Change the port of adminer in docker-compose.yaml (or remove this service) to avoid conflicts
• Assign different folders for storage for each instance
• Assign different ports to expose mysql docker

Option 2: Manual Setup

If you prefer to set up manually:

1. Clone our repository:

   git clone https://github.com/Eyened/eyened-platform.git

2. Navigate to the docker directory:

   cd eyened-platform/docker

3. Create a .env file with the following variables:

   Variable	Description
   PORT	Port the app will be served on
   ADMIN_USERNAME	Username for the default admin user
   ADMIN_PASSWORD	Password for the default admin user
   SECRET_KEY	Secret key for JWT token generation
   IMAGES_BASEPATH	Local folder to serve images from (may be read-only)
   SEGMENTATIONS_ZARR_STORE	Local path to store segmentations (zarr format)
   THUMBNAILS_PATH	Local path to store generated thumbnails
   DATABASE_PATH	Path to the database files
   DATABASE_PORT	Port to access the database from outside
   DATABASE_ROOT_PASSWORD	Root password for external database access
   DATABASE_USER	Username for database access
   DATABASE_PASSWORD	Password for database access

4. Create the necessary directories:

   mkdir -p $HOME/eyened-platform/{images,storage,database}

5. Start the platform:

   USERID=$(id -u) GROUPID=$(id -g) docker-compose up -d

Accessing the Platform

Once the platform is running:

1. The viewer will be available at http://<HOSTNAME>:<PORT> from within your network
2. Adminer (database management) will be available at http://<HOSTNAME>:8080

To manage the platform:

• To view logs: docker-compose logs -f
• To stop the platform: docker-compose down
• To start the platform: USERID=$(id -u) GROUPID=$(id -g) docker-compose up -d

Caution

Make sure to set up regular back ups for both the MySQL database and storage folders.

Tip

Using eyened_orm python package

The eyened_orm python package can be installed by running:

cd orm
pip install -e .

To use the eyened_orm package for database access, copy the .env file from the docker folder to the eyened_orm/environments folder:

cp docker/.env orm/eyened_orm/environments

Multiple Database Environments

You can create different environment files to connect to different databases or use different database users. For example, to set up a read-only database user:

1. Copy the existing environment file:

cp orm/eyened_orm/environments/.env orm/eyened_orm/environments/read-only.env

2. Update the database credentials in read-only.env:

DATABASE_USER=readonly_user
DATABASE_PASSWORD=your_password

3. Use the environment in your code:

from eyened_orm import Database
database = Database("read-only")  # Will automatically read from 'eyened_orm/environments/read-only.env'

Next Steps

To import data into the platform, follow the Importing Data guide.

For more details about the platform’s architecture and services, see the Platform Design documentation.