NA-MIC National Alliance for Medical Image Computing Slicer3 Update

National Alliance for Medical Image Computing When last we saw you… Steve took a beating on Slicer 2.6 Steve presented Slicer3 Execution Model Calmer heads prevailed “There must be something wrong with this…” - Polina

National Alliance for Medical Image Computing Review of base architecture Logic MRML Nodes GUI WidgetsRenderers Edit Observe Edit

National Alliance for Medical Image Computing Gratuitous screenshots

National Alliance for Medical Image Computing Status MRML Slices 3D View Data GUI Volumes Models Transforms Application GUI Fiducials Execution model Colors Model maker Editor Slicer2 modules Build/Package Testing Bug tracking Grid system System

National Alliance for Medical Image Computing

June 2006

National Alliance for Medical Image Computing September 2006 GUI Thread Processing Thread

National Alliance for Medical Image Computing AHM 2007 Many Core 1 presentations with 2D plotting –Key component of clinical analysis Slicer 3 had no 2D plotting –VTK very lacking in 2D plotting

National Alliance for Medical Image Computing February 2007 Python, SciPy, PyLab, Matplotlib

National Alliance for Medical Image Computing March 2007 Large scale experiment control Scenario #1 –Use Slicer3 interactively to select parameters –Run across N datasets Scenario #2 –Use Slicer3 interactively to select some parameters –Design of experiments across remaining parameters Assumptions –Single computer, cluster, grid –No direct access to compute nodes –Staged data –Staged programs –Experiment scheduling –Job submission –Experiment control –Job execution robustness –Platform Options Loopy launcher BatchMake Grid tools

National Alliance for Medical Image Computing Current Slicer3 activities Performance –Resampling, observer madness, intervention Visualization breadth –Cine, lightbox, tensors, plots, CSV, tables Interaction breadth –Tracked cursors, editors, measurements, WWidgets, SWidgets Execution model breadth –Scenes, transforms, coordinate frames, CSV, MRMLImageIO, … MRML breadth –Model hierarchies, grouping, CSV, tables Modules –IGT

National Alliance for Medical Image Computing Three integration strategies Base Slicer3 modules (interactive modules) –Tight integration with GUI and Visualization subsystems –Need MRML Node, Logic class, GUI class Command line modules (execution model modules) –XML descriptions of executable and shared library modules Wizard based modules –Sophisticated wizard to guide user to setting parameters –Need many MRML, Logic, and GUI classes –EM Segmenter

National Alliance for Medical Image Computing Interactive module

National Alliance for Medical Image Computing Command line module

National Alliance for Medical Image Computing Wizard based module