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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.
Here are some of the features that we would like to leverage in Systole OS:
Systole OS is based on Gentoo Linux, which follows a rolling-release model providing up-to-date support out of box.
Slicer, together with all the required dependencies will be installable with a simple
emerge sci-medical/slicer). No SuperBuild! No Slicer-Launcher!
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
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:
flaggie sci-medical/slicer -python +opencl; emerge sci-libs/slicerwill install Slicer without python support and with opencl support)
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.
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:
as well as the integration of allied technologies:
Systole Overlay ├── dev-libs │ └── qRestAPI #OK ├── dev-python │ └── PythonQt_CTK #Needs update ├── metadata ├── profiles ├── sci-libs │ ├── itk #OK │ ├── SimpleITK #Needs update │ ├── vtk #OK │ └── vtkAddon #OK ├── sci-medical │ ├── ctk #OK │ ├── CTKAppLauncherLib #OK │ ├── elastix #Needs update │ ├── gdcm #OK │ ├── Slicer #Work-in-progress │ ├── teem #OK │ └── vmtk #Needs update ├── Slicer-CLI #Needs update │ ├── ACPCTransform | │ ├── AddScalarVolumes | │ ├── ExtractSkeleton | │ ├── ModelMaker | │ └── SlicerExecutionModel | ├── Slicer-Loadable │ ├── Annotations #Remove │ ├── Cameras #Needs update │ ├── Colors | │ ├── Data | │ ├── DoubleArrays | │ ├── Markups | │ ├── Models | │ ├── Plots | │ ├── Reformat | │ ├── SceneViews | │ ├── Segmentations | │ ├── SlicerWelcome | │ ├── SubjectHierarchy #Work-in-progress │ ├── Tables | │ ├── Terminologies #OK │ ├── Texts #Needs update │ ├── Transforms | │ ├── Units | │ ├── ViewControllers | │ ├── VolumeRendering | │ └── Volumes | ├── Slicer-Scripted #Needs update │ ├── DataProbe | │ ├── Editor | │ ├── EditorLib | │ ├── Endoscopy | │ ├── LabelStatistics | │ ├── PerformanceTests | │ ├── SampleData | │ ├── ScreenCapture | │ └── SegmentEditor | └── x11-libs #OK └── gdk-pixbuf
Some of the work done for SystoleOS can be used to improve the Slicer code base and help on the future modularization of Slicer. We will coordinate with the Slicer core developers to include as much as possible in Slicer.
baea9d1dc3 * origin/Systole-patches/Slicer ENH: Provide an install version ov vtkSlicerConfigure.h 11e3802dcc * ENH: Fix qt-loadable-modules installation dirs 016d426ec2 * ENH: Enable installation of SLicerBase header files f242cb635c * ENH: Update SlicerInstallConfig 138aaed6e3 * ENH: Add templates infrastructure de7ff279d1 * ENH: Installation and setup qSlicerExport.h.in 2dca449c7b * ENH: Remove extension/launcher cmake code from UseSlicer.cmake 97ba113555 * ENH: Add vtkAddon as a requirement in UseSlicer.cmake 27be7571e8 * ENH: Add CTK as requirement in UseSlicer.cmake 3e8d0cbaf6 * ENH: Make installed CMake files available c49f8f1dff * ENH: Generate and Install SlicerConfig (install tree) 3781a3682c * ENH: Add variable install dirs for Libs dev files 01f68e9856 * ENH: Use slicer installation dirs for base dev components ec5d1bc8e3 * ENH: Use CMake GNUInstallDirs in Slicer directories 63ff5e26b9 * ENH: Remove the 'App-real' suffix from Slicer executable feb34841e8 * ENH: Install testing data only with testing support 5d8961c414 * ENH: Limit CPack on non-superbuild mode e0cebde590 * ENH: Remove conditional code for old VTK fc6ff2f72f * ENH: Make optional the use of Slicer ITK cb2a0161ce * COMP: Adapt to new qRestAPI cmake ae6e0617bd * COMP: Find Eigen (required) 70dc2afdb2 * COMP: Add vtk CommonSystem component as requirement
For reference, here is a discussion where this support can be used for the generation of a GNU/Linux Flatpak: https://discourse.slicer.org/t/interest-to-create-flatpak-for-3d-slicer-have-issue-with-guisupportqtopengl-not-found/16532
Our most pressing issue right now is to integrate all the core modules and release testing virtual machines and containers. After this, more software packages like MONAI Label, Plus Toolkit, TotalSegmentator, VMTK and Elastix will be integrated. Contributions welcome!!