1. Slicer3 Architecture

2. Overview Algorithms ITK VTK Slicer Modules Slicer 3.0 User Desktop
Scripts of
Slicer Mods
VTK Apps
Using ITK
Batch
Programs
Non-NAMIC
Cmd tools
LONI
Pipeline
The FMA is an ontology of canonical human anatomy which represents anatomical structures in terms of Anatomical Entities (AE; e.g., organs, cells, molecules) that are linked to each other by Structural Relationships (SR; e.g., containment, continuity, adjacency). This figure represents a subset of thoracic AEs including the cavities of the proximal aorta (AoP), the left ventricle (LV), the pericarial space (peri), and the pleural space. The AoP and LV cavities contain (vertical arrows) blood. For clarity, a single horizontal arrow represents all other Structural Relationships between this subset of AEs.
Birn Grid
Data/Compute

3. Slicer3 “Observer MVC” Pattern
MRML (Model)
For Scene Description and Application State
MRML Nodes are Persistent and Undoable
Scene and Nodes are Observable
Logic Encapsulate VTK and ITK Pipelines (Controller)
Observe MRML to Configure Pipelines
Help Create/Manage Nodes
No UI Components (no Widgets, Actors, Mappers, Renderers or RenderWindows)
GUI (View)
Observe and Edit MRML
Interact with User and Display Hardware
GUI
Renderers
Widgets
Edit
Observe
Logic
Observe
Edit
Observe
Edit
MRML Nodes
Motivation for this architecture: modularize! Make the parts resuable.
MVC is model/view/controller – often used as an idealized design pattern, but almost always gets customized for any give application
“Observe” means generic event mechanisms are used to pass information.
“Edit” means code can directly call methods.
Example: GUI can call methods in Logic classes, but Logic cannot call GUI methods.
MRML cannot call Logic or GUI methods.
There can be many observers for any event.

4. Execution Model Modules
Slicer 3 Architecture Diagram (updated )
CommandLineModule
Base
(Managed by
Base and communicates
like other Modules)
Logic
Links to:
Base Logic,
MRML
Auto-Generated GUIs from XML Descriptions
GUI
Links to:
KWWidgets
Logic
Links to:
ITK
MRML
VTK (except
Rendering)
GUI
Links to:
VTK Rendering
KWWidgets
Logic
MRML
Mediators
Mediators
Observe Modified
Events
MRML
Provides
Frames for Widgets,
Routing of User Events
Formulates Command Line
and passes data
Observe Modified
Events on Application
State
Edit Mrml
Scene/Nodes
Describe Input options (uses
--xml option)
Back-door to MRML with
MRMLIDImageIO
ITK IO Factory Library
(Otherwise through files,
command line options)
Registers GUI Event Observers
Interactive Module
Execution Model Modules
build as executables or shared libraries
support –xml query
Observe Modified
Events
Logic
Links to:
Base Logic
ITK
MRML
VTK (except
Rendering)
GUI
Links to:
VTK Rendering
KWWidgets
Logic
MRML
Mediators
Edit Mrml
Scene/Nodes
Slicer Daemon communication via server port
External Connections
Use socket connection directly (e.g. MATLAB)
Use slicerget/slicerget utilities (e.g. unu)
Notes:
All classes in the Logic directory should be able to run ‘headless’ without OpenGL or window system for scripting and testing
Base Logic and GUI contain transient application state (cursor location, focus, mrml scene connection…)
Persistent and Undoable state in MRML Nodes
Interactive Modules are ones which interact with the VTK scene and/or User events
Interactive Modules interact with 3D scene by creating objects in MRML scene (not by direct manipulation of the Renderer)
Logic classes encapsulate and manage internal vtk/itk pipelines and provide helper routines to create/manage nodes
GUI classes are implemented as KWWidget subclasses
Each Logic class defines Get/Set methods for internal state and Modified Events that GUI classes can Observe
Code in Base implements “first order” Node types (Volumes, Models, Transforms, Fiducials, Colors, etc).
Code in Modules provides application-specific extensions

5. Slicer3 Slice Coordinates
RASToRAS Transforms
SliceToRAS Matrix
XYToSlice Matrix
RASToIJK Matrix
RAS to RAS Coordinates
Slice Coordinates
XY Image Space Coordinates
In RenderWindow
IJK = XYToIJK * XY
IJK = RASToIJK * RASToRAS * SliceToRAS * XYToSlice * XY
IJK Volume Coordinates
From GUI
VolumeNode
TransformNode
SliceNode
XYToIJK Matrix Calculated by SliceLayerLogic Coordinates are Cell Centered (no VTK flip)

6. Slice Management Volume Display Node Volume Node Foreground
Slice Layer Logic
Volume Display Node
Volume Node
Background
Slice Layer Logic
Slice Node
Slice GUI
Slice Logic
Slice Composite Node
MRML Nodes: Persistent, Undoable State
Logic: Encapsulate VTK Pipelines, Observe MRML Nodes
GUI: Manage Widgets and Rendering; Manipulated Nodes and Logic; Observe Nodes and Logic

7. Slice Management Stores: Window/Level Lookup Table (Color Node)
Volume Display Node
Stores:
Window/Level
Lookup Table (Color Node)
Transparency Threshold
Volume Node
Foreground
Slice Layer Logic
Volume Display Node
Volume Node
Background
Slice Layer Logic
Slice Node
Slice GUI
Slice Logic
Slice Composite Node
MRML Nodes: Persistent, Undoable State
Logic: Encapsulate VTK Pipelines, Observe MRML Nodes
GUI: Manage Widgets and Rendering; Manipulated Nodes and Logic; Observe Nodes and Logic

8. Slice Management Stores:
Volume Display Node
Stores:
RAS Location of Slice (Origin and Orientation)
Field of View
Pixel Dimensions
Volume Node
Foreground
Slice Layer Logic
Volume Display Node
Volume Node
Background
Slice Layer Logic
Slice Node
Slice GUI
Slice Logic
Slice Composite Node
MRML Nodes: Persistent, Undoable State
Logic: Encapsulate VTK Pipelines, Observe MRML Nodes
GUI: Manage Widgets and Rendering; Manipulated Nodes and Logic; Observe Nodes and Logic

9. Slice Management Stores: Volume IDs per Layer Opacity of Overlay
Volume Display Node
Stores:
Volume IDs per Layer
Opacity of Overlay
Volume Node
Foreground
Slice Layer Logic
Volume Display Node
Volume Node
Background
Slice Layer Logic
Slice Node
Slice GUI
Slice Logic
Slice Composite Node
MRML Nodes: Persistent, Undoable State
Logic: Encapsulate VTK Pipelines, Observe MRML Nodes
GUI: Manage Widgets and Rendering; Manipulated Nodes and Logic; Observe Nodes and Logic

10. Slice Management Stores: Image Data IJKToRAS Matrix Name…
Volume Display Node
Stores:
Image Data
IJKToRAS Matrix
Name…
Volume Node
Foreground
Slice Layer Logic
Volume Display Node
Volume Node
Background
Slice Layer Logic
Slice Node
Slice GUI
Slice Logic
Slice Composite Node
MRML Nodes: Persistent, Undoable State
Logic: Encapsulate VTK Pipelines, Observe MRML Nodes
GUI: Manage Widgets and Rendering; Manipulated Nodes and Logic; Observe Nodes and Logic

11. Slice Management Pipeline with: vtkImageReslice
Volume Display Node
Volume Node
Pipeline with:
vtkImageReslice
vtkImageMapToWindowLevelColors
vtkImageMapToRGBA
Foreground
Slice Layer Logic
Volume Display Node
Volume Node
Background
Slice Layer Logic
Slice Node
Slice GUI
Slice Logic
Slice Composite Node
MRML Nodes: Persistent, Undoable State
Logic: Encapsulate VTK Pipelines, Observe MRML Nodes
GUI: Manage Widgets and Rendering; Manipulated Nodes and Logic; Observe Nodes and Logic

12. Slice Management Pipeline with: vtkImageBlend Volume Display Node
Volume Node
Pipeline with:
vtkImageBlend
Foreground
Slice Layer Logic
Volume Display Node
Volume Node
Background
Slice Layer Logic
Slice Node
Slice GUI
Slice Logic
Slice Composite Node
MRML Nodes: Persistent, Undoable State
Logic: Encapsulate VTK Pipelines, Observe MRML Nodes
GUI: Manage Widgets and Rendering; Manipulated Nodes and Logic; Observe Nodes and Logic

13. Slice Management GUI: SliceControllerWidget (Menus, Scale, Buttons…)
Volume Display Node
Volume Node
GUI:
SliceControllerWidget (Menus, Scale, Buttons…)
SliceViewer (RenderWidget, ImageMapper, ImageActor…)
Foreground
Slice Layer Logic
Volume Display Node
Volume Node
Background
Slice Layer Logic
Slice Node
Slice GUI
Slice Logic
Slice Composite Node
MRML Nodes: Persistent, Undoable State
Logic: Encapsulate VTK Pipelines, Observe MRML Nodes
GUI: Manage Widgets and Rendering; Manipulated Nodes and Logic; Observe Nodes and Logic

14. Undo Architecture for Slicer3
Versioning “Commit Aside” Strategy Encapsulated within MRML
Store “Initial Scene” (from file) and “Delta Scenes” (scenes containing undoable changes)
Delta Scenes ‘are’ MRML Scenes
Some Nodes are Reference Nodes
Setting the MRML scene in the Application Logic causes the cascade of observer callbacks
=> All Undoable operations must store their data as MRML nodes

15. Undo Implementation MRML Scene Undo Stack Initial Scene Delta1 Scene
Saved Scene N1 N1 N2 N4 N4 N3 N5 N5