SlicerCBM Guix Channel

This Guix channel provides a package for SlicerCBM — Computational Biophysics for Medicine in 3D Slicer.

Package	Version	Description
slicer-cbm	git	SlicerCBM extension (all 24 scripted modules) built against slicer-5.10 from guix-systole

Installing

Add the channels to ~/.config/guix/channels.scm — systole provides Slicer, this channel provides the extension, and mvox / explicitsim provide native tools that some CBM modules call out to at runtime:

(cons* (channel
         (name 'systole)
         (url "https://github.com/SystoleOS/guix-systole.git")
         (branch "main"))
       (channel
         (name 'slicer-cbm)
         (url "https://github.com/SlicerCBM/Guix-SlicerCBM.git")
         (branch "main"))
       (channel
         (name 'mvox)
         (url "https://github.com/benzwick/guix-mvox")
         (branch "main"))
       (channel
         (name 'explicitsim)
         (url "https://github.com/benzwick/guix-explicitsim")
         (branch "main"))
       %default-channels)

Then pull and install:

guix pull
guix install slicer-cbm
Slicer                    # CBM modules appear under "Physics / CBM.*"

SLICER_ADDITIONAL_MODULE_PATHS (a native search path declared by slicer-5.10) auto-discovers the installed scripted-module directory, so no extra wiring is needed once both packages are in the profile.

Development

Build from a local checkout without adding the channel:

git clone https://github.com/SystoleOS/guix-systole
git clone https://github.com/SlicerCBM/Guix-SlicerCBM

guix build -L guix-systole/systole -L Guix-SlicerCBM slicer-cbm

Lint the package:

guix lint -L guix-systole/systole -L . slicer-cbm

Related channels

• guix-systole — 3D Slicer and its full dependency tree (VTK, ITK, CTK, Qt5, …) packaged for Guix. This channel is a hard dependency.
• guix-mvox — MFEM and MVox mesh voxeliser. Required at runtime for SlicerCBM modules that call out to MVox (e.g. MVoxMeshGenerator).
• guix-explicitsim — ExplicitSim explicit PDE solver (GPL-3-or-later). Required at runtime for CBM modules that launch explicit dynamics simulations (e.g. MTLEDSimulator, TumorResectionAndBRainRemodelling).

License

The package definitions in this repository are BSD-3-Clause, matching upstream SlicerCBM. See SlicerCBM's LICENSE.