NA-MIC Project Weeks

Systole OS: an operating system for development/deployment of medical devices.

Key Investigators

Rafael Palomar (Oslo University Hospital and NTNU, Norway)
Andras Lasso (Queen’s University, Kingston, Canada)
Steve Pieper (Isomics Inc., Cambridge, MA, USA)
Jean-Christophe Fillion-Robin (Kitware Inc., Carrboro, NC, USA)
Sam Horvath (Kitware Inc.)

Project Description

For more than a decade, 3D Slicer has been enabling world-class biomedical research. The great success of 3D Slicer is now pushing the boundaries of research, making some research groups and companies regard 3D Slicer as a viable software for building medical devices that not only could support regular clinical workflows but also become commercial products. While the development of 3D Slicer has been tailored towards research, its modular architecture makes the development of industrial prototypes possible.

The vision of Systole OS is the integration of 3D Slicer and related software (e.g, Plus Toolkit, MONAI Label and more!) in a free and open-source operating system based on GNU/Linux, with the aim to support the development and deployment of medical devices.

Systole

Here are some of the features that we would like to leverage in Systole OS:

Cutting-edge software

Systole OS is based on Gentoo Linux, which follows a rolling-release model providing up-to-date support out of box.

Installable Slicer…

Slicer, together with all the required dependencies will be installable with a simple command (e.g., emerge sci-medical/slicer). No SuperBuild! No Slicer-Launcher!

…and Modular Slicer

The base installation of 3D Slicer will include only the components needed to run the application (e.g., emerge slicer-modules/models can be done separately).

Source-based

Systole OS is a source-based distribution, which means that all packages will be built from source. Having the flexibility to make decisions on compile-time allows:

Tighter hardware integration
Highly configurable packages (e.g., flaggie sci-medical/slicer -python +opencl; emerge sci-libs/slicer will install Slicer without python support and with opencl support)
Portability to hardware architectures other than amd64 (e.g., arm, risc-v).

Extensible

Systole OS works on the Gentoo overlay system which allows you to extend the system with your own ovelay or override packages provided by Systole.

Objective

In PW37 we aim to take the first steps towards the creation of the Systole overlay, which is a set of packages containing an installable version of 3D Slicer and its dependences.

Approach and Plan

Project discussion
Review of dependencies and -DSlicer_SUPERBUILD=OFF
Development of the packages for the dependencies and 3D Slicer
Development of the packages for the 3D Slicer default modules

Progress and Next Steps

First full installation of a minimal 3D Slicer!

SystoleOS gentoo overlay has been made public at https://github.com/SystoleOS/gentoo-overlay.
Simple 3D Slicer installation with a -DSlicer_SUPERBUILD=OFF approach (-python). There are still some glitches and workarounds even for the simplest version, but this shows the feasibility of the project.

Systole OS, by nature, is a continuous project that needs to keep up with the developments of 3D Slicer and the developments of the underlying software packages itself. It is necessary to establish infrastructure for testing that can help us on the development process (next step). In addition we need to establish infrastructue to support a community documentation, containers, communication channels, etc (next step).

When it comes to the development of Systole OS itself, the first efforts will go on the direction of fixing bugs, enable new configurations of 3D Slicer (e.g, +python). To engage more users, it is important that Systole OS shows utility. We are planning to integrate a Slicer custom application (to be decided) as a deployment prototype.