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

Key Investigators

  • Rafael Palomar (Oslo University Hospital and NTNU, Norway)
  • Steve Pieper (Isomics Inc., Cambridge, MA, USA)

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.

Objectives

The main objective for PW38 is the consolidation of the development achieved in PW37 in Virtual Machines and Containers; this will enable researchers and developers to test the system and contribute to its development. This objective includes the generation of documentation to get started with the project.

As secondary objectives we aim to continue advancing on the integration of 3D Slicer:

  • Enabling Python support
  • Porting scripted modules

as well as the integration of allied technologies:

  • Plus Toolkit
  • MONAI Label
  • Total Segmentator

Approach and Plan

  1. Project discussion
  2. Release of the SystoleOS development VMs and Containers
  3. Documentation on how to get started with SystoleOS (gentoo-overlay, containers, VMs)

Progress and Next Steps

Background and References

  1. SystoleOS project in PW37