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Digital Slide Archive

The Digital Slide Archive is a system for working with large microscopy images.

  • Organize images from a variety of assetstores, such as local file systems and S3.
  • Provide user access controls.
  • Image annotation and review.
  • Run algorithms on all or parts of images.

Website

See https://digitalslidearchive.github.io/digital_slide_archive/ for information about the system.

Demo Instance

http://demo.kitware.com/histomicstk/histomicstk.

License

The Digital Slide Archive is made available under the Apache License, Version 2.0. For more details, see LICENSE

Community

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Installation

For installation instructions, see the complete docker compose example.

For local development including HistomicsUI, there are some devops scripts.

There is a migration guide from the Girder 2 version or from the deploy_docker.py script.

Adding Docker Tasks

Docker tasks conforming to the slicer_cli_web module's requirements can be added. These tasks appear in the HistomicsUI interface and in the Girder interface. An administrator can add a Docker image by going to the slicer_cli_web plugin settings and entering the Docker image name there. For instance, to get the HistomicsTK tasks, add dsarchive/histomicstk:latest.

To use a docker image from a docker repository that requires authentication, see the comments on how to pass through authenticaition in the docker-compose.yml file. On the host machine (and the worker machines if they are separate), login to the docker repository, saving credentials. This could be done with the command docker login <repository> which will then prompt for username and password. Other docker config values can be set this way, too.

Funding

This work was funded in part by the NIH grant U24-CA194362-01.