xOpat Deployment

To deploy xOpat, we need to configure it statically,

Clone repository and install development dependencies: git clone https://github.com/RationAI/xopat.git cd xopat npm install

Create env.json in env directory (can be also created - but unpersonalised - by using grunt env):

note

This env.json file is suitable for WSI-Server. If you have your own image server you need to configure your own.

env.json
{
    "core": {
        // This configuration file supports JSON with comments
        "gateway": "/",
        // Active configuration key from 'client'
        "active_client": "localhost",
        "client": {
            "localhost": {
                // Viewer url, so that it is accessible at domain+path url
                "domain": "http://localhost:8000",
                "path": "/",
                // Named slide-protocol registry. Each entry is a backtick template
                // resolving a scalar DataID to a tile-source URL; the server URL is
                // embedded directly in the template. The `default_*_protocol` keys
                // pick which entry is used by default for background / visualization
                // slides. Protocols can also be added at runtime by plugins via
                // `window.SLIDE_PROTOCOLS.register(...)` — e.g. the dicom plugin
                // registers a "dicom" factory protocol that builds a DICOMWebTileSource.
                "slide_protocols": {
                    "wsi_service": "`http://localhost:8080/v3/slides/info?slide_id=${data}`"
                },
                "default_background_protocol":    "wsi_service",
                "default_visualization_protocol": "wsi_service",
                "headers": {},
                "js_cookie_expire": 365,
                "js_cookie_path": "/",
                "js_cookie_same_site": "",
                "js_cookie_secure": "",
                "secureMode": false
            }
        },
        // Setup can configure much more default parameters for the viewer
        "setup": {
            "locale": "en",
            "theme": "auto"
        }
    },
    // We do not re-define any plugin configuration
    "plugins": {},
    // We force-load module for communication with WSI-Service
    "modules": {
        "rationai-wsi-tile-source": {  // the module id
            "permaLoad": true          // the built-in parameter for force-loading
        }
    }
}

run server node: npm run s-node

Now you should see xOpat running. However, to open the viewer, you must tell it what data is to be viewed in a what way, and possibly also other things (active plugins and their configuration, etc.).

Accessing WSIs

The simples way of opening a slide is through URL parameters.

Go to image server deployment and inspect "cases" to the url: http://localhost:8080/v3/cases
Fetch desired case ID and use it to get its slides: http://localhost:8080/v3/cases/slides?case_id=*CASE_ID
Find desired slide ID and add it to the xOpat deployment url: http://localhost:9000/?slides=*SLIDE_ID*

Now you should have working xOpat instance.

Accessing WSIs​

Accessing WSIs