Running Digital Slide Archive + OpenSlide with iSyntax support

1. Login to docker github: docker login ghcr.io -u <YOUR-USERNAME>. See Github docs for reference.
2. Run DSA as usual, cd devops/dsa && DSA_USER=$(id -u):$(id -g) docker-compose up. It will pull the prebuilt image.

Building Digital Slide Archive + OpenSlide with iSyntax support

1. You must be in linux shell/wsl2 shell. Checking out with git on windows will introduce windows endlines (^M) and will break scripts & patches.
2. python -m venv venv && source ./venv/bin/activate && pip install packaging requests
3. git submodule update --init - to get openslide with isyntax-support.
4. cd large_image_wheels/ && ./rebuild.sh - this will take a long while (1 hour on a good machine, more on a weaker one). For repeated builds, can use ./build.sh, but need to run ./rebuild.sh at least once to get package version checking. (Note: most of the built wheels will be unused, but I was not brave enough to untangle those dependencies and remove unneeded stuff.)
5. Build the dsa container: docker build -t ghcr.io/innovationcore/dsa_common_isyntax . in root directory.
6. Run DSA as usual, cd devops/dsa && DSA_USER=$(id -u):$(id -g) docker-compose up.

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

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.

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.