https://github.com/digitalslidearchive/digital_slide_archive

The official deployment of the Digital Slide Archive and HistomicsTK.
https://github.com/digitalslidearchive/digital_slide_archive

bioimage-informatics digital-slide-archive hacktoberfest histology histomicstk

Last synced: about 1 year ago
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The official deployment of the Digital Slide Archive and HistomicsTK.

• Host: GitHub
• URL: https://github.com/digitalslidearchive/digital_slide_archive
• Owner: DigitalSlideArchive
• License: apache-2.0
• Created: 2015-12-29T20:03:50.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2025-04-04T14:06:55.000Z (about 1 year ago)
• Last Synced: 2025-04-04T15:23:30.206Z (about 1 year ago)
• Topics: bioimage-informatics, digital-slide-archive, hacktoberfest, histology, histomicstk
• Language: Python
• Homepage: https://digitalslidearchive.github.io
• Size: 34.8 MB
• Stars: 117
• Watchers: 15
• Forks: 55
• Open Issues: 25
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

Awesome Lists containing this project

README

          
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 ``_ 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

-----------------------------------------------------------

`Discussions `_ | `Issues `_ | `Contact Us `_

Installation

------------

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

There is a `migration guide <./docs/migration.rst>`_  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 `` 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 `_.