Overview

The My Data project is a web-based portal for KPMP biopsy participants to view whole slide images from their biopsy. Users begin with a walk-through of the biopsy, slide prep, and staining process that leads to the images they are about to view. Users then choose images to view by selecting their 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. In most ways, the My Data project is identical to early releases of the Digital Pathology Repository (DPR).

Repositories

List of the repositories required to run this application.
Repository Description
cassiopeia-data This is the service layer for the My Data project.
cassiopeia-web This is the GUI layer for the My Data project.
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 My Data and DPR runtimes, 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 cassiopeia-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 cassiopeia-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.