Image Server Deployment

The first thing, to have working xOpat instance is to have deployed image server. We will use image server we are maintaining: WSI-Service.

note

If you already have your own Image Server deployed, you can skip this part.

How to deploy WSI-Service?

Download some WSI test slides. It does not matter where the slides come from, but they must be compatible with the image server used. Test data can be found for example on openslide.org
note
the Simple Mapper we will be using needs to have slides in certain hiearchy:
root-folder ├── case1 │ ├── slide1_1 │ └── slide1_2 ├── case2 │ └── slide2_1 ...
tip
The server state cached. If you want to add new slides, you need to go to visit http://localhost:8080/refresh_local_mapper to revalidate the cache.

Clone WSI-Service repository (note the --recursive flag: there are submodules):

git clone --recursive https://github.com/RationAI/WSI-Service.git

Create .env file in the root folder of repository. Make sure COMPOSE_DATA_DIR points to the folder with downloaded slides, root-folder.

.env
    # if true, it will allow logging functionality
    WS_DEBUG=False
    # if true, it will make OpenAPI sites available
    WS_DISABLE_OPENAPI=True
    # url of service which maps slide ids to path. We use build in service
    WS_MAPPER_ADDRESS=http://localhost:8080/slides/storage?slide={slide_id}
    # How the mapper resolves slide paths
    WS_LOCAL_MODE=wsi_service.simple_mapper:SimpleMapper
     
    # Auth of a choice, here we request no auth
    WS_API_V3_INTEGRATION=wsi_service.api.v3.integrations.disable_auth:DisableAuth

    # this variables are configuring docker compose file
    COMPOSE_RESTART=no
    COMPOSE_NETWORK=default
    COMPOSE_WS_PORT=8080
    # directory where the test slides are saved
    COMPOSE_DATA_DIR=path/to/slides

    # server API configuration
    WS_CORS_ALLOW_CREDENTIALS=False
    WS_CORS_ALLOW_ORIGINS=["*"]

    # Timeouts and size settings
    WS_INACTIVE_HISTO_IMAGE_TIMEOUT_SECONDS=600
    WS_MAX_RETURNED_REGION_SIZE=25000000
    WS_MAX_THUMBNAIL_SIZE=500
    WS_ENABLE_VIEWER_ROUTES=False

Make sure that Docker and Docker Compose is installed on your machine.

info

If you do not have these applications, the easiest way is to use Docker Desktop. The commands can be different based on used docker distribution.

Example of the docker compose yaml used by the environment configuration:

docker-compose.yml

version: "3.8"

services:
wsi_service:
    build:
    context: "."
    target: wsi_service_production
    network: "${COMPOSE_NETWORK}"
    restart: "${COMPOSE_RESTART}"
    environment:
    - WS_CORS_ALLOW_CREDENTIALS=${WS_CORS_ALLOW_CREDENTIALS}
    - WS_CORS_ALLOW_ORIGINS=${WS_CORS_ALLOW_ORIGINS}
    - WS_DEBUG=${WS_DEBUG}
    - WS_DISABLE_OPENAPI=${WS_DISABLE_OPENAPI}
    - WS_MAPPER_ADDRESS=${WS_MAPPER_ADDRESS}
    - WS_LOCAL_MODE=${WS_LOCAL_MODE}
    - WS_ENABLE_VIEWER_ROUTES=${WS_ENABLE_VIEWER_ROUTES}
    - WS_INACTIVE_HISTO_IMAGE_TIMEOUT_SECONDS=${WS_INACTIVE_HISTO_IMAGE_TIMEOUT_SECONDS}
    - WS_MAX_RETURNED_REGION_SIZE=${WS_MAX_RETURNED_REGION_SIZE}
    - WS_API_V3_INTEGRATION=${WS_API_V3_INTEGRATION}
    volumes:
    - ${COMPOSE_DATA_DIR}:/data
    ports:
    - ${COMPOSE_WS_PORT}:8080

Finally run the docker container by:
```
docker compose up
```
tip
you can add -d flag, for program to detach from your terminal.

This should make WSI server running on localhost:8080. For more information feel free to check the repository of WSI-Service.

How to deploy WSI-Service?​

How to deploy WSI-Service?