1. NA-MIC National Alliance for Medical Image Computing http://na-mic.org Slicer4 Guided Tour Steve Pieper, Ph.D.

2. National Alliance for Medical Image Computing http://na-mic.org Goals Understanding the Lay of the Land Developing our Common Language Highlighting the Points of Interest http://www.slicer.org/slicerWiki/index.php/Slicer4

3. National Alliance for Medical Image Computing http://na-mic.org The Big Picture Model / View / Controller Style –MRML / GUI / Logic Rules: –MRML: Things that get loaded with a scene file. –GUI: Things that depend on a display. –Logic: Things that operate on MRML.

4. National Alliance for Medical Image Computing http://na-mic.org Overview

5. National Alliance for Medical Image Computing http://na-mic.org MRML Concepts: Nodes Data Containers and Data Helpers –XML (De)Serializable –Issue Events when Changed –Have Pointers to Bulk Data E.g. vtkImageData, vtkPolyData… Have Unique IDs Exist in only one MRML Scene –One MRML Scene for the Application

6. National Alliance for Medical Image Computing http://na-mic.org Coordinate Systems http://www.slicer.org/slicerWiki/index.php/Coordinate_systems Interface Works in Millimeters, Patient Space Volume Nodes have IJKToRAS –IJK is Index Space of Image –RAS is Right/Anterior/Superior vtkImageData is pixel container with origin 0,0,0 and spacing 1,1,1 Annotations, PolyData are RAS mm

7. National Alliance for Medical Image Computing http://na-mic.org MRML: Storable Storable Nodes Reference Storage Nodes Storage Nodes: Bulk Data I/O Storage Nodes allow RemoteIO (URL access to Bulk Data) –HTTP download supported now –Upload handlers still experimental –Scene files can contain URLs

8. National Alliance for Medical Image Computing http://na-mic.org MRML: Displayable Has List of Display Nodes –Tagged by ViewNode IDs: each display node on/off in each view –E.g. FiberBundles with Lines + Glyphs DisplayNode has Parameters and Pipelines to Implement Visualization of Displayable

9. National Alliance for Medical Image Computing http://na-mic.org MRML Transformable Has Reference to TransformNode defining Transform To Parent Transforms are RAS to RAS Linear Transforms are Handled On- the-fly Non-Linear Transforms must be applied using modules

10. National Alliance for Medical Image Computing http://na-mic.org MRML: Hierarchies Grouping Concept Independent of Transform Hierarchy –E.g. Vascular Tree Levels of Detail In Slicer3, Parent Model Display Parameters Override when Collapsed In Slicer4, Plans to Use Hierarchies for Time Series, DICOM, etc.

11. National Alliance for Medical Image Computing http://na-mic.org (Were SceneSnapShots in Slicer3) Retains State of MRML Nodes –Included in MRML Scene File –Optional Image and Text Description Bulk Data Not Copied –Load all Bulk Data Before Making SceneViews –Use Visibility to Control what is Shown MRML: SceneViews

12. National Alliance for Medical Image Computing http://na-mic.org Module GUIs qSlicerAbstractModuleWidget subclasses (are QWidgets) setup() enter() exit() Are MRMLNode Editors –Synchronize MRML Events to/from Widgets

13. National Alliance for Medical Image Computing http://na-mic.org Modules Slicer Loadable Modules –Shared Libraries Discovered at Run- Time –Can use Qt, MRML, VTK, ITK, Teem, etc. –Best Choice for Full Control, Interactivity, Optimized Computation Requires Familiarity with C++ APIs

14. National Alliance for Medical Image Computing http://na-mic.org Command Line Interface (CLI) Modules Just Like Slicer3 Any Executable that Works with –xml can be used (even via wrapper scripts) Shared Library CLI for Better Performance No Slicer API Knowledge Required Interface is Consistent, but Limited

15. National Alliance for Medical Image Computing http://na-mic.org Scripted Modules Most of Qt, VTK, Slicer API Exposed –Only Python Supported –Tcl Legacy Mode to Ease Transition Very Rapid Development Iterations Requires Some Familiarity with APIs More about Slicer4 Python Later…

16. National Alliance for Medical Image Computing http://na-mic.org Extensions Any Module Type can be an Extension Optional User Install –Built to Match Slicer Version –Network Download from within Slicer NA-MIC DBPs, Collaborations are Expected to Deliver Extensions Extension Writing Tutorial Later…

17. National Alliance for Medical Image Computing http://na-mic.org Slicer4 Views LayoutNode Defines Interface Layout Manager Creates View Widget Instances to Match Layout ViewNodes Describe 3D Views SliceNodes + SliceCompositeNodes Describe 2D Slice Views

18. National Alliance for Medical Image Computing http://na-mic.org DisplayableManagers DisplaybleManagers Link DisplayableNodes to VTK Actors/Mappers/Props/Widgets –Must Synchronize Events from Either Source (like Module GUIs) Modules Can Register DisplayableManagers with Factory –DisplayableManagers are Instanced as Views are Created

19. National Alliance for Medical Image Computing http://na-mic.org Overview Revisited

20. National Alliance for Medical Image Computing http://na-mic.org Functional Decomposition Reusable Components with Only Needed Dependencies –CTK for Non-Slicer-Specific Qt+DICOM (+VTK) –Reusable MRML: MRMLLogic, qMRMLWidgets –Module Support: SlicerExecutionModel, QTCLI –Slicer: QTCore, QTGUI –Modules: QTCoreModules, QTModules, QTScriptedModules Extensions

21. National Alliance for Medical Image Computing http://na-mic.org DICOM Interface Slicer3 –File Based, Limited Write –Special Purpose Converters (e.g. DWI) Slicer4 (in Development) –Networking and Database (Q/R, Store) –Ron’s “Lollipop” Model (MRMLScene in Private Tags) Community Input Needed

22. National Alliance for Medical Image Computing http://na-mic.org Collaborating Groups CTK, DCMTK, ITKv4, VTK, CMake, Python, Qt… “SuperBuild Philosophy” –Slicer Organization on github.com patched versions as needed –Edits “Belonging” in Package Go in git –Avoid Workarounds/Duplicates in Slicer

23. National Alliance for Medical Image Computing http://na-mic.org svn and git http://svn.slicer.org/Slicer4/trunk –For Nightly builds, releases, collaboration http://www.slicer.org/slicerWiki/index. php/Slicer:git-svn –Developers can choose to use git for topic branches Extensions can use git/svn/cvs

24. National Alliance for Medical Image Computing http://na-mic.org Coding Conventions http://www.slicer.org/slicerWiki/index. php/Slicer:Style_and_Conventions –Use Style of Parent Class VTK Classes use VTK Style Qt Classes use Qt Style Python Code uses Python Style –Comments and Testing –Communicate with your Colleagues

25. National Alliance for Medical Image Computing http://na-mic.org Python in Slicer4 Scripted Modules as Slicelets Python Console PythonQt Slicer in External Python.slicerrc.py Python testing Scripted Access to Modules

26. National Alliance for Medical Image Computing http://na-mic.org Slicer4: What Works (mostly) Main GUI, Toolbars, Menus Scene/Data Load/Save Slice and 3D Visualization (pan/zoom, overlays, models…) Command Line Modules Python Wrapping, Python Scripted Modules Loadable Modules Editor Annotations (Evolution of Fiducials and Measurements) Nightly Builds Volume Rendering Many things…

27. National Alliance for Medical Image Computing http://na-mic.org Slicer4: What’s Missing Some Core Modules Need Work Hierarchies Need Elaboration IGT Modules Performance Optimization Your Extensions! Please help identify what is needed to support your work.

28. National Alliance for Medical Image Computing http://na-mic.org Developer Decision Tree Working on the Slicer Core? –Focus on Qt Transition Working on a Module? –Build it as an Extension Command Line Module? –Develop and Test with Slicer3.6 or Slicer4 GUI Project with Deadlines in early 2011? –Develop with KWWidgets for 3.6.X –Keep your Logic and MRML Distinct from the GUI –Ongoing Support will be Provided Longer-Term Project that Needs a Custom GUI? –Start working with developer builds of Slicer4 –Talk with dev team about any key missing features –Consider doing some or all coding in Python Just use Slicer4 for New Projects

29. National Alliance for Medical Image Computing http://na-mic.org Implementation Strategies Non-Interactive Algorithm –Write ITK Class –Use Slicer Execution Model –Add as Extension Interactive Segmentation –Add Effect to Editor Module –Add as Extension (coming soon) Custom GUI? –Loadable Module