fepegar/digital_slide_archive

The official deployment of the Digital Slide Archive and HistomicsTK.

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.

Installation

See here for installation instructions.

There is also a complete docker-compose example.

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

There is a migration guide from the Girder 2 version.

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.

Funding

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