slicer

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 structures
  • Libs/vtkITK/ — VTK/ITK bridge filters
• Modules/Loadable/ — C++ modules with Qt UI
• Modules/Scripted/ — Python-only modules
• Modules/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

# Find a class definition
grep -rn "class qSlicerMarkupsModule" $SLICER_SOURCE/

# Find CMake macro usage
grep -rn "slicerMacroBuildLoadableModule" $SLICER_SOURCE/Modules/Loadable/

# Find all MRML node headers
find $SLICER_SOURCE/Libs/MRML/Core -name "vtkMRML*Node.h"

# Find VTK class
grep -rn "class VTK_EXPORT vtkMRMLVolumeNode" $VTK_SOURCE/

# Search patch for a specific file
grep -rn "UseSlicer.cmake" $SLICER_PATCHES/

# Find scripted module example
ls $SLICER_SOURCE/Modules/Scripted/