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.
See https://digitalslidearchive.github.io/digital_slide_archive/ for information about the system.
http://demo.kitware.com/histomicstk/histomicstk.
The Digital Slide Archive is made available under the Apache License, Version 2.0. For more details, see LICENSE
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For installation instructions, see the complete docker-compose example.
There is an older method that doesn't use docker-compose. See here.
For local development including HistomicsUI, there are some devops scripts.
There is a migration guide from the Girder 2 version and from the deploy_docker.py script.
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.
This work was funded in part by the NIH grant U24-CA194362-01.