spinal-cord-toolbox

Spinal Cord Toolbox (SCT) is a comprehensive, free and open-source set of command-line tools dedicated to the processing and analysis of spinal cord MRI data see the GitHub Repo for more information. This service provides a User Interface, the FSLeyes image viewer.

Basic concept

An osparc-ui module consists of two services, a web proxy web and the actual application app. The web service acts only as a proxy for integration into the osparc platform. The app service consists of the X11 based GUI application that should be accessible via the osparc iframe and some additional supporting programs:

• supervisord: to control the processes in the container
• xtigervnc: VNC client/server application with embedded X-server
• novnc: opensource javascript vnc client
• openbox: Minimal window manager

Usage

Build the module:

$ make build

To run locally at and visit http://127.0.0.1:28080

make run-local

To publish in local throw-away registry:

make publish-local

Workflow

1. The application should be installed via modification of the Dockerfile in spinal-cord-toolbox/app
2. The [program:app] section in supervisord.conf in spinal-cord-toolbox/app/config needs to be modified to accomodate to the correct command line for the program.

Versioning

Two versions:

• integration version (e.g. spinal-cord-toolbox/VERSION_INTEGRATION) is updated with make version-integration-*
• service version (e.g. spinal-cord-toolbox/VERSION) is updated with make version-service-*

CI/CD Integration

A template ci config file is created in ```.github/workflows/check-image.yml``) that just builds the image.

Deployment to oSPARC

The required CI is already packaged. To build and push to the internal registry you must add it to the oSparc/docker-publisher-osparc-services repository.