A lightweight server-less single-page application for interactive visualization of digital slide microscopy (SM) images and associated image annotations in standard DICOM format. The application is based on the dicom-microscopy-viewer library and can simply be placed in front of a DICOMweb compatible Image Management System (IMS), Picture Archiving and Communication (PACS), or Vendor Neutral Archive (VNA).
The app will search the IMS for studies containing SM images and visualize image instances of the DICOM VL Whole Slide Microscopy Image SOP Storage Class.
The app allows users to create graphical image region of interest (ROI) annotations and store them as DICOM Comprehensive 3D SR documents using SR template TID 1500 "Measurement Report". ROIs are stored as 3D spatial coordinates (SCOORD3D) according to SR template TID 1410 "Planar ROI Measurements and Qualitative Evaluations" together with measurements and qualitative evaluations. Specifically, Image Region is used to store the vector graphic data and Finding is used to describe what has been annotated using a standard medical terminology such as SNOMED CT.
The app will also search the IMS for existing SR documents and display any ROI annotations contained in DICOM Comprehensive 3D SR documents that are structured according to TID 1500.
Users can authenticate and authorize the application to access data via OpenID Connect (OIDC) based on the OAuth 2.0 protocol using either the authorization code grant type (with Proof Key for Code Exchange (PKCE) extension) or the legacy implicit grant type.
The app can be configured via a public/config/{name}.js JavaScript configuration file.
Please refer to the AppConfig.d.ts file for configuration options.
The configuration can be changed at build-time using the REACT_APP_CONFIG environment variable.
The repository provides a Docker compose file to deploy a web server and a dcm4chee-arc-light DICOMweb server on localhost for local app development and testing:
$ docker-compose up -d
Serves the app via an NGINX web server at http://localhost:8008 and exposes the DICOMweb RESTful services at http://localhost:8008/dicomweb.
Local deployment uses the default configuration public/config/local.js.
window.config = {
path: "/",
servers: [
{
id: "local",
url: "http://localhost:8008/dicomweb",
write: true
}
],
annotations: [
{
finding: {
value: '108369006',
schemeDesignator: 'SCT',
meaning: 'Neoplasm'
},
style: {
stroke: {
color: [251, 134, 4, 1],
width: 2
},
fill: {
color: [255, 255, 255, 0.2]
}
}
}
]
};Here is an example configuration public/config/gcp.js for running the app with the Google Healthcare API and OIDC authentication/authorization:
const gcpProject = ""
const gcpLocation = ""
const gcpDataset = ""
const gcpStore = ""
const gcpClientID = ""
window.config = {
path: "/",
servers: [
{
id: "gcp",
url: `https://healthcare.googleapis.com/v1/projects/${gcpProject}/locations/${gcpLocation}/datasets/${gcpDataset}/dicomStores/${gcpStore}/dicomWeb`,
write: true
}
],
oidc: {
authority: "https://accounts.google.com",
clientId: gcpClientID,
scope: "email profile openid https://www.googleapis.com/auth/cloud-healthcare",
grantType: "implicit"
},
annotations: [
{
finding: {
value: '108369006',
schemeDesignator: 'SCT',
meaning: 'Neoplasm'
},
style: {
stroke: {
color: [251, 134, 4, 1],
width: 2
},
fill: {
color: [255, 255, 255, 0.2]
}
}
}
]
};Create an OIDC client ID for web application.
Note that Google's OIDC implementation does currently not yet support the authorization code grant type with PKCE challenge. For the time being, the legacy implicit grand type has to be used.
To install requirements and run the app for local development, run the following commands:
$ yarn install
$ yarn start
This will serve the app via a development server at http://localhost:3000 using the local configuration.
The configuration can be specified using the REACT_APP_CONFIG environment variable, which can be set either in the .env file or directly in the command line:
$ REACT_APP_CONFIG=local yarn start