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technische universiteit eindhoven
/department of biomedical engineering
Segmentation Techniques for the Visible mouse
By Virjanand Panday
Supervisor: B.M. ter Haar Romeny
Date: 4 June 2003
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technische universiteit eindhoven
/department of biomedical engineering
The Visible Mouse Project
• Magnetic Resonance Lab
• 3D database of the mouse
• Develop non-invasive diagnostic routines for humans
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technische universiteit eindhoven
/department of biomedical engineering
Comparable to The Visible Human
• Fast overview of organs and possible anomalies
• For 3D rendering organs must first be detected from surrounding tissue
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technische universiteit eindhoven
/department of biomedical engineering
Example: Detection Kidney
• Weak edge
• Structures inside
• Strong edges surrounding
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technische universiteit eindhoven
/department of biomedical engineering
Definition of Problem
Investigate segmentation techniques for the visible mouse
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technische universiteit eindhoven
/department of biomedical engineering
Overview of Presentation
• Introduction
• Overview Segmentation Techniques
• Watershed Segmentation
•Active Contours Segmentation
• Levelset
• Snake
• Some Results
• Discussion
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technische universiteit eindhoven
/department of biomedical engineering
Classification Segmentation Techniques
Region Based:
• Homogeneities
• Region Growing
Edge Based
• Inhomogeneities
• LoG, Sobel operators
• Graph Searching or dynamic programming
Classification:
• Multiple values
• Clusters
•Minimum distance to means or artificial neural networks
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technische universiteit eindhoven
/department of biomedical engineering
Used Segmentation Techniques
• Watershed (uses region and edge based techniques)
• Active Contours (geometric reasoning)
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technische universiteit eindhoven
/department of biomedical engineering
Watershed: Theory
Image as landscape
Dam construction
Plaatje van landscape plaatje van sinus dam
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technische universiteit eindhoven
/department of biomedical engineering
Watershed: Nabla Vision
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technische universiteit eindhoven
/department of biomedical engineering
Active Contours
• Forces derived from the curve itself (Curvature, Size surface enclosed, etc.)
• Forces derived from image (Gradient, Texture, etc.)
• Other Forces (Balloon force)
Plaatje van random contour op muis beeld
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technische universiteit eindhoven
/department of biomedical engineering
Levelset: Evolution Function
Fnt
x
0))(( tx
n
Fn
F
t
x
00
F
F
t
x
xtdt
dtt
Plaatje van cone distance function
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technische universiteit eindhoven
/department of biomedical engineering
Levelset: Flow Function F
Constant: F= Curvature: F=-
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technische universiteit eindhoven
/department of biomedical engineering
Levelset: Stopping Terms
IGeg
Filmpje curve met stop term
Plaatje stopping term
IGc
0)( ce IGt
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technische universiteit eindhoven
/department of biomedical engineering
Snake: Evolution Equation
nIGs
sV
ss
sV
st
sV
)()()( 2
2
2
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technische universiteit eindhoven
/department of biomedical engineering
Comparing Results
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technische universiteit eindhoven
/department of biomedical engineering
Results Visualized in 3D
• Multiple slices
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technische universiteit eindhoven
/department of biomedical engineering
Discussion and Future Work
• Watershed needs postprocessing, but automatic
• Levelset requires strong edges (Stronger attraction towards edges), but addapts very well to topology of image
• Snake stays one contour, but spans gaps in edges well
• 3D looks smoother if methods applied directly on 3D: for levelset easy with 4D function, for snake a lot of bookkeeping of the surface points
• Better testing of correctness segmentation
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technische universiteit eindhoven
/department of biomedical engineering
Acknowledgements
• Bart ter Haar Romeny
• Aurelie Bugeau
• Markus van Almsick
• Anna Vilanova Bartroli
• Arnold Schilham
• Gustav Strijker and Willem Mulder
• Paul van den Bosch