EMSegmentation in Slicer 3 B Davis S Barre

EMSegmentation in Slicer 3 B. Davis, S. Barre, Y. Yuan, W. Schroeder, P. Golland, K. Pohl

Goals n Design automatic segmenter that n n Easy to use Adaptable to new segmentation problem Applicable large data sets Open to integration of new technology Slicer 2 Slicer 3

Wizard Interface Parameter Set Tree Atlas Target Intensity n Parameters Registration Run n n Separates a complex task into a sequence of manageable steps Checks correctness of user input before each transition Provides consistent access to help

Parameter Set Tree Atlas Parameter set defines segmentation scenario: n Atlas, Images, Algorithm parameters n Target Intensity Parameters Registration Run n Create new parameter set Apply/modify existing parameter set

Parameter Set Tree Atlas Target Intensity Parameters Registration Run Defines a hierarchy of anatomical structures

Parameter Set Assign atlas to anatomical structures Tree Atlas white matter csf grey matter background Target Intensity Parameters Registration Run

Parameter Set Choose input channels Tree Atlas Target Intensity T 1 Parameters Registration Run T 2

Parameter Set Tree Atlas Target Intensity Parameters Registration Run Define intensity distribution for each structure

Parameter Set Tree Specify node-based segmentation parameters n n Atlas n n Target n Intensity Parameters Registration Run Influence of n Input channels Atlas Smoothing Relative weight to other structures Stopping conditions

Parameter Set Specify atlas-to-input channel registration Tree Atlas white matter csf grey matter background Target Intensity Parameters Registration Run T 1 T 2

Parameter Set Tree Atlas Target Intensity Parameters Registration Run Segment input channels using parameters

n n Slicer 2 -> Slicer 3 Improve usability n GUI n Workflow Engineering Goals n Future development n Parameters n MRML structure

Design MRML • Global Parameters • Hierarchical parameters • Image data • Segmentation output Logic • Manage MRML nodes • API for access to parameters • Manage hierarchy • Segmentation algorithm GUI • Window to parameter set • Wizard • Interaction with images