Digital Slide Archive documentation

The Digital Slide Archive (DSA) stores, manages, visualizes, and annotates large whole-slide microscopy images. It combines a Girder-based data server, the HistomicsUI viewer and annotation interface, and containerized analysis tasks from HistomicsTK and other Slicer CLI Web tools.

This documentation site is being rebuilt in focused slices. The Get Started path, the task tutorials, the controls reference, and the new Administration section are ready to use. Each page records its source and verification date in a collapsible note at the bottom.

Start here

• New to DSA?

  Understand what the platform is and how its pieces fit together.

  What is DSA?

• Want to look around first?

  Open the public demo and explore a slide without installing anything.

  Try the demo

• Ready to install?

  Run DSA on one machine with Docker Compose. The verified Ubuntu 24.04 walkthrough covers the DSA 5 stack with screenshots.

  Install on one machine

  Ubuntu 24.04 walkthrough

• Already installed?

  Upload a slide and open it in the viewer.

  Upload and view your first slide

• Running an instance?

  Manage accounts, storage, plugins, and jobs, and know which changes need a restart.

  Administration overview

Everyday tutorials

Short, task-based walkthroughs for the actions people need first:

• Connect to a DSA server
• Create a collection
• Create a folder
• Upload or import images
• Copy an item
• Edit metadata
• Annotate a slide
• Run an analysis

Administration

For the person who runs the DSA instance, rather than the researcher using it:

• Administration overview — the web console, the provision and Compose files, and the container runtime.
• Admin console tour — users, groups, collections, plugins, system configuration, assetstores, and jobs.
• Users, groups, and roles — creating accounts, the site-admin flag, disabling accounts, and group roles.
• Assetstores and storage — the assetstore/ bind mount, registering storage, permission pitfalls, and what a backup must include.
• Plugin and system settings — the settings an operator actually touches, and which changes need a restart.

Reference and help

• User guide — viewer controls, annotations, style groups, and permissions.
• System overview — single-computer and distributed-worker layouts.
• REST API cookbook and Python client — drive DSA from scripts.
• Troubleshooting and FAQ — fixes for install, sign-in, viewing, upload, permissions, annotations, and analysis jobs.

BDSA-specific documentation

GutmanLab/BDSA additions to DSA stay on this site for now, so everything remains linkable from this landing page. More BDSA-specific guides will be added here as they are written.

• UI components (bdsa-react-components) — the shared React component library used by BDSA front ends.

Project background

• About the project — history, license, funding, and community.
• Release and upgrade notes — what changed in the current date-stamped image, how to upgrade, and how to roll back.
• Success stories — collaborative annotation and TCGA.
• Papers and publications — work that uses DSA and its components.
• Migration guide — moving from deploy_docker.py or Girder 2.

About this site

• This repository is a staging area for consolidating DSA information and tutorials in one place. Some pages replicate material that still lives upstream; each page records its source and version in a collapsible note at the bottom.
• The documentation source lives in Gutman-Lab/dsa-docs. Build and link-check instructions are in the repository README.md, and SOURCES.md tracks where each page came from and what is still queued.
• The site is built with MkDocs Material and published from main at https://gutman-lab.github.io/dsa-docs/. The upstream project website remains the Jekyll site under DigitalSlideArchive/digital_slide_archive; this preview is the consolidation area, not a replacement for it.