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What is DSA?

The Digital Slide Archive (DSA) is an open-source platform for storing, managing, visualizing, and annotating large microscopy images. It is designed for whole-slide digital pathology, but the same machinery works for other large, tiled image formats.

DSA is not a single application. It is a set of services and plugins that run together:

Piece What it does
Girder Asset and user management, permissions, and the HTTP API.
large_image Reads many slide formats as multi-resolution tiles.
HistomicsUI The slide viewer, annotation tools, and analysis panels.
Slicer CLI Web Runs containerized analysis tasks from the UI and the API.
HistomicsTK A collection of pathology image-analysis algorithms.
MongoDB Stores users, items, metadata, and annotations.
Girder Worker and RabbitMQ Queue and run analysis jobs.
Memcached Caches tile data for faster viewing.

What you can do with it

  • Organize images in collections, folders, and items, with per-user and per-group access control.
  • Store files on a local filesystem or in external assetstores such as Amazon S3.
  • View and navigate whole-slide images in a browser.
  • Draw, edit, and review annotations, including multi-user annotation studies.
  • Run analysis tasks on whole images or selected regions, on one machine or across worker machines.
  • Drive all of the above through the REST API and the Python client.

How the pieces are deployed

The common deployment is a single computer running five containers: Girder, MongoDB, Girder Worker, RabbitMQ, and Memcached. Analysis tasks start additional short-lived containers. For more computing power, you can run workers on other machines while the main server keeps the database and assetstore.

See System Overview for diagrams of both layouts.

Ways to run DSA

  • Use the public demo to explore the interface: Try the demo.
  • Install on one machine with Docker Compose: Install on one machine.
  • Scale out with external workers, Kubernetes, or Apptainer. The repository contains reference deployments under devops/; this slice documents the single-machine Docker Compose path only.

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