open topology: a toolkit for brain isosurface correction-776
DESCRIPTION
http://hdl.handle.net/1926/50TRANSCRIPT
![Page 1: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/1.jpg)
Oct 30, 2005 Sylvain Jaume 1
Open Topology:A Toolkit for Brain
Isosurface Correction
Sylvain JAUME(1), Patrice RONDAO(2), Benoit MACQ(2)
(1) Kitware Inc., (2) University of Louvain
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Oct 30, 2005 Sylvain Jaume 2
Visualization of the Brain
Speech, vision, etc. lie in the outer layer.
surface visualization
![Page 3: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/3.jpg)
Oct 30, 2005 Sylvain Jaume 3
Visualization of the Brain3D Image
Segmentation
Marching Cubes
Smoothing
Mesh
![Page 4: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/4.jpg)
Oct 30, 2005 Sylvain Jaume 4
Visualization of the Brain3D Image
Segmentation
Marching Cubes
Smoothing
Mesh
![Page 5: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/5.jpg)
Oct 30, 2005 Sylvain Jaume 5
Visualization of the Brain3D Image
Segmentation
Marching Cubes
Smoothing
Mesh
![Page 6: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/6.jpg)
Oct 30, 2005 Sylvain Jaume 6
Visualization of the Brain3D Image
Segmentation
Marching Cubes
Smoothing
Mesh with Handles
![Page 7: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/7.jpg)
Oct 30, 2005 Sylvain Jaume 7
Visualization of the Brain3D Image
Segmentation
Marching Cubes
Smoothing
Mesh with Handles
![Page 8: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/8.jpg)
Oct 30, 2005 Sylvain Jaume 8
Visualization of the Brain3D Image
Segmentation
Marching Cubes
Smoothing
Mesh with Handles
![Page 9: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/9.jpg)
Oct 30, 2005 Sylvain Jaume 9
Visualization of the Brain3D Image
Segmentation
Marching Cubes
Smoothing
Mesh with Handles
![Page 10: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/10.jpg)
Oct 30, 2005 Sylvain Jaume 10
Visualization of the Brain3D Image
Segmentation
Marching Cubes
Smoothing
Mesh with Handles
![Page 11: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/11.jpg)
Oct 30, 2005 Sylvain Jaume 11
Visualization of the Brain
• Where do handles come from ?
Limited resolution
Scanner artifacts
Segmentation errors
![Page 12: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/12.jpg)
Oct 30, 2005 Sylvain Jaume 12
Visualization of the Brain
• Does it really matter ???
For 3D visualization
For distance measurements
For EEG source localization
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Oct 30, 2005 Sylvain Jaume 13
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
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Oct 30, 2005 Sylvain Jaume 14
Contributions
No region is left out
Fast (less than 2 min)
Open Source
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Oct 30, 2005 Sylvain Jaume 15
Algorithm Overview
Marching Cubes
Handle Detection
Handle Correction
3D Image Triangle Mesh
Corrected 3D Image
Contours
![Page 16: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/16.jpg)
Oct 30, 2005 Sylvain Jaume 16
Algorithm Overview
Marching Cubes
Handle Detection
Handle Correction
3D Image Triangle Mesh
Contours
Corrected 3D Image
![Page 17: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/17.jpg)
Oct 30, 2005 Sylvain Jaume 17
Algorithm Overview
Marching Cubes
Handle Detection
Handle Correction
3D Image Triangle Mesh
Contours
Corrected 3D Image
![Page 18: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/18.jpg)
Oct 30, 2005 Sylvain Jaume 18
Algorithm Overview
Marching Cubes
Handle Detection
Handle Correction
3D Image Triangle Mesh
Polylines
Corrected 3D Image
![Page 19: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/19.jpg)
Oct 30, 2005 Sylvain Jaume 19
Algorithm Overview
Marching Cubes
Handle Detection
Handle Correction
3D Image Triangle Mesh
Contours
Corrected 3D Image
![Page 20: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/20.jpg)
Oct 30, 2005 Sylvain Jaume 20
Algorithm Overview
Marching Cubes
Handle Detection
Handle Correction
3D Image Triangle Mesh
Contours
Corrected 3D Image
![Page 21: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/21.jpg)
Oct 30, 2005 Sylvain Jaume 21
Algorithm Overview
Marching Cubes
Handle Detection
Handle Correction
3D Image Triangle Mesh
Contours
Corrected 3D Image
![Page 22: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/22.jpg)
Oct 30, 2005 Sylvain Jaume 22
Algorithm Overview
Marching Cubes
Handle Detection
Handle Correction
3D Image Triangle Mesh
Contours
Marching Cubes Corrected Mesh
Corrected 3D Image
![Page 23: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/23.jpg)
Oct 30, 2005 Sylvain Jaume 23
Algorithm Overview
Marching Cubes
Handle Detection
Handle Correction
3D Image Triangle Mesh
Contours
Marching Cubes Corrected Mesh
Corrected 3D Image
![Page 24: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/24.jpg)
Oct 30, 2005 Sylvain Jaume 24
Key Points
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Oct 30, 2005 Sylvain Jaume 25
1. Embracing the Handle
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Oct 30, 2005 Sylvain Jaume 26
1. Embracing the Handle
• Init
![Page 27: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/27.jpg)
Oct 30, 2005 Sylvain Jaume 27
1. Embracing the Handle
• Init
![Page 28: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/28.jpg)
Oct 30, 2005 Sylvain Jaume 28
1. Embracing the Handle
• Init
![Page 29: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/29.jpg)
Oct 30, 2005 Sylvain Jaume 29
1. Embracing the Handle
• Init
![Page 30: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/30.jpg)
Oct 30, 2005 Sylvain Jaume 30
1. Embracing the Handle
• Split
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Oct 30, 2005 Sylvain Jaume 31
1. Embracing the Handle
• Split
![Page 32: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/32.jpg)
Oct 30, 2005 Sylvain Jaume 32
1. Embracing the Handle
• Split
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Oct 30, 2005 Sylvain Jaume 33
1. Embracing the Handle
• Merge
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Oct 30, 2005 Sylvain Jaume 34
1. Embracing the Handle
• Merge
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Oct 30, 2005 Sylvain Jaume 35
1. Embracing the Handle
• Merge
![Page 36: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/36.jpg)
Oct 30, 2005 Sylvain Jaume 36
1. Embracing the Handle
• Merge
![Page 37: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/37.jpg)
Oct 30, 2005 Sylvain Jaume 37
1. Embracing the Handle
• Merge
![Page 38: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/38.jpg)
Oct 30, 2005 Sylvain Jaume 38
1. Embracing the Handle
• Merge
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Oct 30, 2005 Sylvain Jaume 39
1. Embracing the Handle
• Finalize
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Oct 30, 2005 Sylvain Jaume 40
1. Embracing the Handle
• Finalize
![Page 41: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/41.jpg)
Oct 30, 2005 Sylvain Jaume 41
1. Embracing the Handle
• Finalize
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Oct 30, 2005 Sylvain Jaume 42
2. Holding it Tight
• Distance
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Oct 30, 2005 Sylvain Jaume 43
2. Holding it Tight
• Distance
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Oct 30, 2005 Sylvain Jaume 44
2. Holding it Tight
• Distance
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Oct 30, 2005 Sylvain Jaume 45
2. Holding it Tight
• Distance
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Oct 30, 2005 Sylvain Jaume 46
2. Holding it Tight
• Distance
![Page 47: Open Topology: A Toolkit for Brain Isosurface Correction-776](https://reader035.vdocument.in/reader035/viewer/2022062514/558e45111a28ab88668b47be/html5/thumbnails/47.jpg)
Oct 30, 2005 Sylvain Jaume 47
2. Holding it Tight
• Distance
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Oct 30, 2005 Sylvain Jaume 48
2. Holding it Tight
• Distance
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Oct 30, 2005 Sylvain Jaume 49
2. Holding it Tight
• Distance
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Oct 30, 2005 Sylvain Jaume 50
2. Holding it Tight
• Distance
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Oct 30, 2005 Sylvain Jaume 51
3. Filling the Handle
• New pixel intensity inside the loop
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Oct 30, 2005 Sylvain Jaume 52
Putting it Together
1. Handle Detection– Embracing the handle
2. Handle Localization– Holding it tight
3. Handle Correction– Filling the handle
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Oct 30, 2005 Sylvain Jaume 53
Performance
• g: genus, i.e. number of handles• V: number of vertices• E: number of edges• F: number of faces• C: number of connected components
Euler Characteristic
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Oct 30, 2005 Sylvain Jaume 54
Data Structures
vtkCellLinks
vtkPoints vtkCellArray
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Oct 30, 2005 Sylvain Jaume 55
Data Structures
• Edge to Start Point• Edge to End Point
• Edge to Polygon
vtkPoints vtkCellArray Half-Edge
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Oct 30, 2005 Sylvain Jaume 56
Data Structures
• Edge to Reverse Edge• Edge to Parent Edge
vtkPoints vtkCellArray Half-Edge
Detection
Localization
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Oct 30, 2005 Sylvain Jaume 57
Data Structures
• Edge to Contour• Edge to Distance
vtkPoints vtkCellArray Half-Edge
Detection
Localization
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Oct 30, 2005 Sylvain Jaume 58
Data Structures
Extended Half-Edge Structure:• Edge to Polygon• Edge to Start Point• Edge to End Point• Edge to Reverse Edge• Edge to Parent Edge• Edge to Contour• Edge to Distance
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Oct 30, 2005 Sylvain Jaume 59
Code
• vtkHandleDetection– Half-edge structure– Area growing– Shortest loop
• vtkHandleCorrection– Loop to image– Water-tight region
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Oct 30, 2005 Sylvain Jaume 60
Goal
Correct EVERY handle FAST!
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Oct 30, 2005 Sylvain Jaume 61
Perspectives
Visualization, measurements, source localization
Benchmarking with other methods
Half-Edge algorithms
Integration into CARET Software
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Oct 30, 2005 Sylvain Jaume 62
MICCAI Open Source Workshop
• "Open Topology: A Toolkit for Brain Isosurface Correction", Jaume, Rondao, Macq, MICCAI WS 2005.
• Article• Code• Data• Demo
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Oct 30, 2005 Sylvain Jaume 63
www.OpenTopology.org
• Algorithm
• Source code
• Documentation
• Data
• Updates