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 <http://demo.kitware.com/histomicstk/histomicstk#?image=5c74528be62914004b10fd1e>_.

License

The Digital Slide Archive is made available under the Apache License, Version 2.0. For more details, see LICENSE <https://github.com/DigitalSlideArchive/digital_slide_archive/blob/master/LICENSE>_

Community

Discussions <https://github.com/DigitalSlideArchive/digital_slide_archive/discussions>_ | Issues <https://github.com/DigitalSlideArchive/digital_slide_archive/issues>_ | Contact Us <https://www.kitware.com/contact-us/>_

Installation

For installation instructions, see the complete docker-compose example <./devops/dsa>_.

There is an older method that doesn't use docker-compose. See here <./ansible>_.

For local development including HistomicsUI, there are some devops <./devops>_ scripts.

There is a migration guide <./ansible/migration.rst>_ from the Girder 2 version and from the deploy_docker.py script.

Adding Docker Tasks

Docker tasks conforming to the slicer_cli_web <https://github.com/girder/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 <http://grantome.com/grant/NIH/U24-CA194362-01>_.