| name | slicer |
| description | Search and reason over 3D Slicer source code, dependencies, and community discussions. Use for questions about MRML scene graphs, VTK/ITK/CTK pipelines, Slicer Python scripting, C++ module development, extension development, Qt-based module UI, segmentation, volume rendering, DICOM workflows, the Slicer build system, and guix-systole specific runtime behavior.
|
| version | 5.8.1 |
| requires | [] |
Slicer Skill
This skill provides read-only access to 3D Slicer and its core dependency sources,
installed as Guix packages at content-addressed store paths. All data is
reproducible and version-pinned to the exact commits used by guix-systole.
Data Sources
All paths are baked into the slicer-skill package at build time. Run
slicer-skill status to print the active store paths for the current installation.
| Variable | Content |
|---|
SLICER_SOURCE | 3D Slicer source tree (slicer-source-5.8) |
VTK_SOURCE | VTK source tree (vtk-slicer-source) |
ITK_SOURCE | ITK source tree (itk-slicer-source) |
CTK_SOURCE | CTK source tree (ctk-source) |
SLICER_PATCHES | guix-systole patches applied to Slicer (patches/slicer/) |
Layer 1 — Standard Slicer Development
Project Structure
Inspect $SLICER_SOURCE/ for the top-level layout:
Base/ — Core application framework
Base/Python/slicer/ — The slicer Python package (util.py,
ScriptedLoadableModule.py, parameter node wrapper). Read these to understand
the Python API surface.Base/QTCore/ — Non-GUI logic (settings, I/O manager, module factory)Base/QTGUI/ — Main application GUI (layout manager, module panel)
Libs/ — Shared libraries independent of Qt
Libs/MRML/Core/ — MRML scene graph: node classes, events, serialization.
Header files (vtkMRML*.h) document the node hierarchy.Libs/vtkSegmentationCore/ — Segmentation data structuresLibs/vtkITK/ — VTK/ITK bridge filters
Modules/Loadable/ — C++ modules with Qt UIModules/Scripted/ — Python-only modulesModules/CLI/ — Command-line interface modules (SlicerExecutionModel)
Module Types
Read these reference implementations:
- Scripted modules:
$SLICER_SOURCE/Modules/Scripted/SampleData/ or
SegmentStatistics/. Base classes in
$SLICER_SOURCE/Base/Python/slicer/ScriptedLoadableModule.py.
- Loadable modules (C++ + Qt):
$SLICER_SOURCE/Modules/Loadable/Volumes/ or
Markups/. Pattern: qSlicer*Module, widget, logic, MRML node classes.
- CLI modules:
$SLICER_SOURCE/Modules/CLI/AddScalarVolumes/ — XML descriptor
- C++/Python executable. Note: CLI is disabled in guix-systole (see Layer 2).
MRML Scene Graph
- Conceptual overview:
$SLICER_SOURCE/Docs/developer_guide/mrml_overview.md
- Node hierarchy: headers in
$SLICER_SOURCE/Libs/MRML/Core/vtkMRML*Node.h
- Python API:
$SLICER_SOURCE/Base/Python/slicer/util.py — getNode(),
loadVolume(), arrayFromVolume(), updateVolumeFromArray()
Python API
$SLICER_SOURCE/Base/Python/slicer/util.py — primary utility functions$SLICER_SOURCE/Base/Python/slicer/ScriptedLoadableModule.py — module base classes$SLICER_SOURCE/Base/Python/slicer/parameterNodeWrapper/ — declarative parameters$SLICER_SOURCE/Base/Python/slicer/__init__.py — top-level namespace
Script Repository
The script repository at $SLICER_SOURCE/Docs/developer_guide/script_repository.md
and script_repository/*.md contains working Python recipes. Search here first
before writing code from scratch. Key files:
| File | Topics |
|---|
script_repository/volumes.md | Loading, NumPy access, scalar/vector data |
script_repository/segmentations.md | Segment Editor, effects, import/export |
script_repository/markups.md | Fiducials, curves, planes, ROIs |
script_repository/transforms.md | Linear and non-linear transforms |
script_repository/dicom.md | DICOM loading, exporting, database |
script_repository/gui.md | Layouts, views, keyboard shortcuts |
script_repository/models.md | Surface meshes, polydata |
script_repository/sequences.md | Time sequences |
VTK and ITK
- VTK headers and examples:
$VTK_SOURCE/
- ITK headers and examples:
$ITK_SOURCE/
- Slicer's VTK/ITK bridge:
$SLICER_SOURCE/Libs/vtkITK/
- VTK pipeline patterns in Slicer:
.cxx files in $SLICER_SOURCE/Modules/Loadable/
CTK (Common Toolkit)
CTK provides the Qt-based widget library, plugin framework, and DICOM stack.
- Widget catalog:
$CTK_SOURCE/Libs/Visualization/VTK/Widgets/ and
$CTK_SOURCE/Libs/Widgets/
- Python scripting manager:
$CTK_SOURCE/Libs/Scripting/Python/
- DICOM:
$CTK_SOURCE/Libs/DICOM/
Segment Editor
- Module and widget:
$SLICER_SOURCE/Modules/Scripted/SegmentEditor/
- Python effects (templates for custom effects):
$SLICER_SOURCE/Modules/Loadable/Segmentations/EditorEffects/Python/SegmentEditorEffects/
- Abstract base classes:
AbstractScriptedSegmentEditorEffect.py in same dir
Extension Development
- Developer guide:
$SLICER_SOURCE/Docs/developer_guide/extensions.md
- Extension Wizard (scaffolding tool):
$SLICER_SOURCE/Modules/Scripted/ExtensionWizard/
- Real extension examples: well-structured extensions live in the Extensions Index
Common Pitfalls
arrayFromVolume returns a view. After in-place modification call
slicer.util.arrayFromVolumeModified(node) to notify the display pipeline.- Node names are not unique. Use
node.GetID() for reliable identification.
- Long operations block the UI. Use
slicer.app.processEvents() or a background
thread.
- Coordinate systems. Slicer uses RAS internally; many formats use LPS. Sign
flips are a common source of bugs.
arrayFromVolume axis order is KJI (slice, row, column), not IJK.
Layer 2 — guix-systole Slicer Differences
This section documents how guix-systole Slicer diverges from upstream behavior.
Read this when upstream documentation gives conflicting or confusing results.
Runtime Differences
bin/Slicer is a direct ELF binary symlink
bin/Slicer → bin/SlicerApp-real. There is no launcher wrapper script. You can
run gdb bin/SlicerApp-real directly. See patch 0045–0048 in $SLICER_PATCHES.
Module discovery via environment variable
Modules are discovered through SLICER_ADDITIONAL_MODULE_PATHS (a Guix
native-search-path), not via --additional-module-path CLI flags. The env var
scans both qt-loadable-modules and qt-scripted-modules directories in the
profile. The CLI flag --additional-module-path (singular) only keeps the last
value and should not be used for multiple paths. Patch: 0045.
LD_LIBRARY_PATH extended at startup
At process startup, Slicer extends LD_LIBRARY_PATH with every directory listed in
SLICER_ADDITIONAL_MODULE_PATHS. This ensures dlopen can find side-libraries of
loadable modules. Patch: 0046.
PYTHONPATH assembled at startup
PYTHONPATH is prepended with CTK_LIBRARY_DIR:vtkAddon_LIB_DIR:SLICER_PYTHONPATH
at startup. CTK_LIBRARY_DIR and vtkAddon_LIB_DIR are compile-time constants
baked into vtkSlicerConfigure.h. SLICER_PYTHONPATH is a Guix native-search-path
that scans bin/Python, lib/Slicer-5.8, and lib/python3.11/site-packages in the
profile. Patches: 0046, 0048.
Qt plugin path registered at startup
QCoreApplication::addLibraryPath(CTK_LIBRARY_DIR) is called in
preInitializeApplication(), making CTK's Qt plugins available. QTWEBENGINE_DISABLE_SANDBOX=1
is also set. Patch: 0047.
Build Configuration Differences
| Option | guix-systole value | Upstream default |
|---|
Slicer_BUILD_CLI | OFF | ON |
Slicer_BUILD_CLI_SUPPORT | ON | ON |
Slicer_BUILD_EXTENSIONMANAGER_SUPPORT | OFF | ON |
Slicer_BUILD_QTLOADABLEMODULES | OFF (built separately) | ON |
Slicer_BUILD_QTSCRIPTEDMODULES | OFF (built separately) | ON |
Slicer_USE_PYTHONQT | ON | ON |
Slicer_BUILD_ITKPython | OFF | varies |
Slicer_BUILD_DICOM_SUPPORT | ON | ON |
Implication of Slicer_BUILD_CLI=OFF: CLI module executables are not available.
The CLI support library (vtkSlicerCLIModuleLogic) IS built (via
Slicer_BUILD_CLI_SUPPORT=ON), but no CLI executables exist. Modules that depend
on vtkSlicerCLIModuleLogic.h (e.g., CropVolume) cannot be built standalone.
Standalone Module Development with guix-systole
When building a loadable module as a standalone Guix package (not inside Slicer's
superbuild), the module's top-level CMakeLists.txt must include this preamble
before any Slicer macros:
cmake_minimum_required(VERSION 3.16.3...3.19.7 FATAL_ERROR)
project(<ModuleName>)
set(CMAKE_CXX_STANDARD "17")
find_package(Slicer REQUIRED)
include(${Slicer_USE_FILE})
if(NOT Slicer_INSTALL_QTLOADABLEMODULES_SHARE_DIR)
set(Slicer_INSTALL_QTLOADABLEMODULES_SHARE_DIR
"./share/Slicer-${Slicer_VERSION}/qt-loadable-modules")
endif()
if(NOT Slicer_INSTALL_QTLOADABLEMODULES_LIB_DIR)
set(Slicer_INSTALL_QTLOADABLEMODULES_LIB_DIR
"./lib/Slicer-${Slicer_VERSION}/qt-loadable-modules")
endif()
The install directory guards are needed because Slicer_BUILD_QTLOADABLEMODULES=OFF
in the install tree leaves those variables empty. Patch 0037 in $SLICER_PATCHES
explains the root cause.
Add LINK_DIRECTORIES ${EXTRA_MODULE_LIB_DIRS} to all CMake macro calls when the
module depends on other standalone modules (see existing loadable modules in
guix-systole for examples).
Reading the Patches
The patches directory $SLICER_PATCHES contains all modifications applied to the
upstream Slicer source. Each patch is a git commit on the
guix-systole-slicer-5.8 branch. Key patches:
| Patch | What it does |
|---|
0037-COMP-Fix-module-install-dir-variables-for-install-tr.patch | Exposes QTLOADABLEMODULES_* install-dir variables in the install tree; guards recalculation in UseSlicer.cmake |
0045-ENH-Read-SLICER_ADDITIONAL_MODULE_PATHS-env-var.patch | Module discovery from env var |
0046-ENH-Extend-LD_LIBRARY_PATH-and-PYTHONPATH.patch | Runtime library and Python path setup |
0047-ENH-Register-CTK-plugin-path.patch | Qt plugin path and WebEngine sandbox |
0048-ENH-Prepend-CTK-and-vtkAddon-lib-dirs-to-PYTHONPATH.patch | Compile-time lib dir constants in vtkSlicerConfigure.h.in |
Per-module patches live in subdirectories: $SLICER_PATCHES/markups/,
$SLICER_PATCHES/segmentations/, $SLICER_PATCHES/subjecthierarchy/, etc.
Searching Effectively
grep -rn "class qSlicerMarkupsModule" $SLICER_SOURCE/
grep -rn "slicerMacroBuildLoadableModule" $SLICER_SOURCE/Modules/Loadable/
find $SLICER_SOURCE/Libs/MRML/Core -name "vtkMRML*Node.h"
grep -rn "class VTK_EXPORT vtkMRMLVolumeNode" $VTK_SOURCE/
grep -rn "UseSlicer.cmake" $SLICER_PATCHES/
ls $SLICER_SOURCE/Modules/Scripted/
