Open Topology A Toolkit for Brain Isosurface Correction
Open Topology: A Toolkit for Brain Isosurface Correction Sylvain JAUME(1), Patrice RONDAO(2), Benoit MACQ(2) (1) Oct 30, 2005 Kitware Inc. , (2) University of Louvain Sylvain Jaume 1
Visualization of the Brain Speech, vision, etc. lie in the outer layer. surface visualization Oct 30, 2005 Sylvain Jaume 2
Visualization of the Brain 3 D Image Segmentation Marching Cubes Smoothing Mesh Oct 30, 2005 Sylvain Jaume 3
Visualization of the Brain 3 D Image Segmentation Marching Cubes Smoothing Mesh Oct 30, 2005 Sylvain Jaume 4
Visualization of the Brain 3 D Image Segmentation Marching Cubes Smoothing Mesh Oct 30, 2005 Sylvain Jaume 5
Visualization of the Brain 3 D Image Segmentation Marching Cubes Smoothing Mesh with Handles Oct 30, 2005 Sylvain Jaume 6
Visualization of the Brain 3 D Image Segmentation Marching Cubes Smoothing Mesh with Handles Oct 30, 2005 Sylvain Jaume 7
Visualization of the Brain 3 D Image Segmentation Marching Cubes Smoothing Mesh with Handles Oct 30, 2005 Sylvain Jaume 8
Visualization of the Brain 3 D Image Segmentation Marching Cubes Smoothing Mesh with Handles Oct 30, 2005 Sylvain Jaume 9
Visualization of the Brain 3 D Image Segmentation Marching Cubes Smoothing Mesh with Handles Oct 30, 2005 Sylvain Jaume 10
Visualization of the Brain • Where do handles come from ? Limited resolution Scanner artifacts Segmentation errors Oct 30, 2005 Sylvain Jaume 11
Visualization of the Brain • Does it really matter ? ? ? For 3 D visualization For distance measurements For EEG source localization Oct 30, 2005 Sylvain Jaume 12
State of the Art • Image methods – Malandain 93, Shattuck 01, Kriegeskorte 01 • Mesh methods – Fischl 01, Guskov 01, Wood 04, Segonne 05 • Graph methods – Han 02, Segonne 03 • Level-Set methods – Han 01, Bischoff 02 Oct 30, 2005 Sylvain Jaume 13
Contributions No region is left out Fast (less than 2 min) Open Source Oct 30, 2005 Sylvain Jaume 14
Algorithm Overview 3 D Image Marching Cubes Handle Detection Handle Correction Oct 30, 2005 Sylvain Jaume Triangle Mesh Contours Corrected 3 D Image 15
Algorithm Overview 3 D Image Marching Cubes Handle Detection Handle Correction Oct 30, 2005 Sylvain Jaume Triangle Mesh Contours Corrected 3 D Image 16
Algorithm Overview 3 D Image Marching Cubes Handle Detection Handle Correction Oct 30, 2005 Sylvain Jaume Triangle Mesh Contours Corrected 3 D Image 17
Algorithm Overview 3 D Image Marching Cubes Handle Detection Handle Correction Oct 30, 2005 Sylvain Jaume Triangle Mesh Polylines Corrected 3 D Image 18
Algorithm Overview 3 D Image Marching Cubes Handle Detection Handle Correction Oct 30, 2005 Sylvain Jaume Triangle Mesh Contours Corrected 3 D Image 19
Algorithm Overview 3 D Image Marching Cubes Handle Detection Handle Correction Oct 30, 2005 Sylvain Jaume Triangle Mesh Contours Corrected 3 D Image 20
Algorithm Overview 3 D Image Marching Cubes Handle Detection Handle Correction Oct 30, 2005 Sylvain Jaume Triangle Mesh Contours Corrected 3 D Image 21
Algorithm Overview 3 D Image Marching Cubes Handle Detection Handle Correction Marching Cubes Oct 30, 2005 Sylvain Jaume Triangle Mesh Contours Corrected 3 D Image Corrected Mesh 22
Algorithm Overview 3 D Image Marching Cubes Handle Detection Handle Correction Marching Cubes Oct 30, 2005 Sylvain Jaume Triangle Mesh Contours Corrected 3 D Image Corrected Mesh 23
Key Points Oct 30, 2005 Sylvain Jaume 24
1. Embracing the Handle Oct 30, 2005 Sylvain Jaume 25
1. Embracing the Handle • Init Oct 30, 2005 Sylvain Jaume 26
1. Embracing the Handle • Init Oct 30, 2005 Sylvain Jaume 27
1. Embracing the Handle • Init Oct 30, 2005 Sylvain Jaume 28
1. Embracing the Handle • Init Oct 30, 2005 Sylvain Jaume 29
1. Embracing the Handle • Split Oct 30, 2005 Sylvain Jaume 30
1. Embracing the Handle • Split Oct 30, 2005 Sylvain Jaume 31
1. Embracing the Handle • Split Oct 30, 2005 Sylvain Jaume 32
1. Embracing the Handle • Merge Oct 30, 2005 Sylvain Jaume 33
1. Embracing the Handle • Merge Oct 30, 2005 Sylvain Jaume 34
1. Embracing the Handle • Merge Oct 30, 2005 Sylvain Jaume 35
1. Embracing the Handle • Merge Oct 30, 2005 Sylvain Jaume 36
1. Embracing the Handle • Merge Oct 30, 2005 Sylvain Jaume 37
1. Embracing the Handle • Merge Oct 30, 2005 Sylvain Jaume 38
1. Embracing the Handle • Finalize Oct 30, 2005 Sylvain Jaume 39
1. Embracing the Handle • Finalize Oct 30, 2005 Sylvain Jaume 40
1. Embracing the Handle • Finalize Oct 30, 2005 Sylvain Jaume 41
2. Holding it Tight • Distance Oct 30, 2005 Sylvain Jaume 42
2. Holding it Tight • Distance Oct 30, 2005 Sylvain Jaume 43
2. Holding it Tight • Distance Oct 30, 2005 Sylvain Jaume 44
2. Holding it Tight • Distance Oct 30, 2005 Sylvain Jaume 45
2. Holding it Tight • Distance Oct 30, 2005 Sylvain Jaume 46
2. Holding it Tight • Distance Oct 30, 2005 Sylvain Jaume 47
2. Holding it Tight • Distance Oct 30, 2005 Sylvain Jaume 48
2. Holding it Tight • Distance Oct 30, 2005 Sylvain Jaume 49
2. Holding it Tight • Distance Oct 30, 2005 Sylvain Jaume 50
3. Filling the Handle • New pixel intensity inside the loop Oct 30, 2005 Sylvain Jaume 51
Putting it Together 1. Handle Detection – Embracing the handle 2. Handle Localization – Holding it tight 3. Handle Correction – Filling the handle Oct 30, 2005 Sylvain Jaume 52
Performance Euler Characteristic • • • g: genus, i. e. number of handles V: number of vertices E: number of edges F: number of faces C: number of connected components Oct 30, 2005 Sylvain Jaume 53
Data Structures vtk. Points vtk. Cell. Array vtk. Cell. Links Oct 30, 2005 Sylvain Jaume 54
Data Structures vtk. Points vtk. Cell. Array Half-Edge • Edge to Polygon • Edge to Start Point • Edge to End Point Oct 30, 2005 Sylvain Jaume 55
Data Structures vtk. Points vtk. Cell. Array Half-Edge Detection • Edge to Reverse Edge • Edge to Parent Edge Localization Oct 30, 2005 Sylvain Jaume 56
Data Structures vtk. Points vtk. Cell. Array Half-Edge Detection Localization Oct 30, 2005 • Edge to Contour • Edge to Distance Sylvain Jaume 57
Data Structures Extended Half-Edge Structure: • • Edge to Polygon Edge to Start Point Edge to End Point Edge to Reverse Edge to Parent Edge to Contour Edge to Distance Oct 30, 2005 Sylvain Jaume 58
Code • vtk. Handle. Detection – Half-edge structure – Area growing – Shortest loop • vtk. Handle. Correction – Loop to image – Water-tight region Oct 30, 2005 Sylvain Jaume 59
Goal Correct EVERY handle FAST! Oct 30, 2005 Sylvain Jaume 60
Perspectives Visualization, measurements, source localization Benchmarking with other methods Half-Edge algorithms Integration into CARET Software Oct 30, 2005 Sylvain Jaume 61
MICCAI Open Source Workshop • "Open Topology: A Toolkit for Brain Isosurface Correction", Jaume, Rondao, Macq, MICCAI WS 2005. • • Oct 30, 2005 Sylvain Jaume Article Code Data Demo 62
www. Open. Topology. org • • Algorithm Source code Documentation Data • Updates Oct 30, 2005 Sylvain Jaume 63
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