Overview

The Digital Pathology Repository (DPR) is a web-based portal for viewing whole slide images from KPMP participants. Users choose images to view by selecting a KPMP case ID and then panning, zooming, and saving images of the slides in our web viewer. The whole slide image web viewer is based on the OpenSeadragon library and consumes the Deep Zoom Image (DZI) pyramidal image format.

Repositories

List of the repositories required to run this application.
Repository Description
delphinus-data This is the service layer for the Digital Pathology Repository.
delphinus-web This is the GUI layer for the Digital Pathology Repository.
heavens-docker This repository holds all of the docker containers and docker-compose scripts for running our applications.
wsi-worker This is the dockerized script to convert an SVS (our preferred WSI format) into assets for the DPR runtime, including database updates and DZI pyramidal image output.

Data Stores

MongoDB
knowledgeEnvironment
Collection Name Description
patients A list of cases with viewable slides, each with a contained array of slide images belonging to the case. Slides have a `stain` property, which is a mongodb dbref object to the `stains` collection. The items in the slides array are the principal objects in this document. For an example document in this collection with all available data attributes, see delphinus-data/data/samples/patients.json.
stains A list of whole slide image stains, each with a `type`, `title`, and `description`. For an example document in this collection, see delphinus-data/data/samples/stains.json.
File System
The application can be configured to point to any location on disk for the file system. Inside that directory, the `dataLake` and `deepZoomImages` directories are used to serve DZI image pyramids to users. The `wsi-worker` script is responsible for creating the web-ready assets for storage in the `dataLake` directory and symlinking them by file UUID into the `deepZoomImages` folder for web access. For more information on this storage and linking scheme, see the wsi-worker README.md.