segmentation of tree like structures as minimisation problem applied to lung vasculature pieter...
TRANSCRIPT
![Page 1: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/1.jpg)
Segmentation of Tree like Structures as Minimisation Problem applied to Lung
Vasculature
Pieter Bruyninckx
![Page 2: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/2.jpg)
•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Overview
• Introduction– What is vessel segmentation– Lung anatomy and pathology
• State of the Art• Minimisation Approach• Discussion
![Page 3: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/3.jpg)
•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Introduction
• Vessel segmentation– Extracting vessels from an image (3D)– Multiple representations possible
• Hard: Centerline, border
• Soft: Probability
• Use general properties– Intensity range– Tubular shape– Tree like structure
• Connectedness
• Bifurcations
Pathological cases?
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•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Lung anatomy and pathology
• General Structure– Vessels
– Bronchi
• Common pathology– Mosaic Perfusion
• Pulmonary embolism
• Small airways disease
• Emphysema
![Page 5: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/5.jpg)
•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Overview
• Introduction• State of the Art
– Top-down (initialisation)• Single Vessel
• Tracking
– Bottom-up (no initialisation)• Vessel Enhancement Filter
• Tschirren
• Minimisation Approach• Discussion
![Page 6: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/6.jpg)
•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Top-down: Single Vessel
• Initialisation– Start and end-point
• Iteration– Optimal path
– Minimal energy
– Intensity, smoothness
• Challenges– Whole vessel tree?
[Wink2002]
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•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Top-down: Tracking
• Initialisation– Start point (tree root)
• Iteration– Centerline tracking
– More advanced• Region growing• Wave front propagation• Level sets
• Challenges– Handling bifurcations
– Mathematical framework
[Wink2000]
![Page 8: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/8.jpg)
•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Bottom-up: Vessel Enhancement Filters
• Soft segmentation =vessel enhancement:
– Improve hard segmentation– Improve visualization
• No initialisation• Single iteration
– Eigenvalues/vectors Hessian• Vesselness and orientation
– Multiresolution approach– Anisotropic filtering
• Challenges– Physical units?– Sensitive to noise (second
derivatives)[Frangi1998]
![Page 9: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/9.jpg)
•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Bottom-up: Tschirren
• Initialisation– Detection of probably-
vessel voxels (intensity)
– Compute orientation
– Classify: • vessel, junction, nodule
• Iteration– Join points into a tree
• Challenge– Rather ad hoc method
[Tschirren2005]
![Page 10: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/10.jpg)
•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Overview
• Introduction• State of the Art• Minimisation Approach
– Pre-processing– Initialisation– Iteration– Results
• Discussion
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•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Minimisation Approach
Initial vesselness
(intensity only)
Patient scan
Initial vessel orientation
(with uncertainty)
Final vesselness and orientation through energy optimization
Energy: function ofneighbourhood and
local vessel orientation and vesselness
Lung Segmentation
![Page 12: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/12.jpg)
•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Lung Segmentation
• Goal– Separate lung from other tissue
– Allow for intensity-based vessel segmentation
– Increased efficiency
• Implementation– Simple ad hoc algorithm
![Page 13: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/13.jpg)
•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Minimisation Approach
Initial vesselness
(intensity only)
Patient scan
Initial vessel orientation
(with uncertainty)
Final vesselness and orientation through energy optimization
Energy: function ofneighbourhood and
local vessel orientation and vesselness
Lung Segmentation
![Page 14: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/14.jpg)
•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Vesselness Initialisation
• Based on intensities only• First step
– Determine average and standard deviationof local background(10x10x10 mm³)
• Second step– Express vesselness as a ‘probability’ [0,1]
(function of background , and intensity)
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•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Vesselness Initalisation
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•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Vesselness Initialisation
![Page 17: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/17.jpg)
•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Minimisation Approach
Initial vesselness
(intensity only)
Patient scan
Initial vessel orientation
(with uncertainty)
Final vesselness and orientation through energy optimization
Energy: function ofneighbourhood and
local vessel orientation and vesselness
Lung Segmentation
![Page 18: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/18.jpg)
•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Initial Vessel Orientation
• Estimate– Orientation
– Uncertainty
• Method– Compute gradients
perpendicular orientation
– Hessian approach also possible
![Page 19: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/19.jpg)
•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Minimisation Approach
Initial vesselness
(intensity only)
Patient scan
Initial vessel orientation
(with uncertainty)
Final vesselness and orientation through energy optimization
Energy: function ofneighbourhood and
local vessel orientation and vesselness
Lung Segmentation
![Page 20: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/20.jpg)
•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Iteration: Energy Function
• Energy Function f– Energy ~ Vessel-likeness
internal energy EE( ) < E( )
– Energy ~ ‘distance’ to original distance DD( , ) < D( , )
1,0,1 DEf
![Page 21: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/21.jpg)
•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Iteration: Energy Function
Vv i
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•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Iteration: Energy Function
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![Page 23: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/23.jpg)
•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Iteration: Energy Function
• Distance function D– Extension of d
– gn: main directions (orthogonal) ( )
1,0,1 DEf
TTTv ggggggG 332211
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![Page 24: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/24.jpg)
•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Iteration: Energy Function
Vv
vTjj GvvD
2
2
1,0,1 DEf
No uncertainty
No certainty
Some uncertainty
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•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Optimisation: Method
• Possible approaches– Simulated annealing (SA)
• Slow
– Local alignment• Fast
• Global optimum?
• Proposed solution– Local everywhere– SA at ‘difficult’ locations
Best of both worldsIf difficult locations can be found
(high local energy)
![Page 26: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/26.jpg)
•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Results: 2D
original α = 0.1α = 0.4α = 0.6α = 0.8α = 0.9α = 0.95α = 0.99
1,0,1 DEf
![Page 27: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/27.jpg)
•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Results: 2D (detail)
original α = 0.99
![Page 28: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/28.jpg)
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Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Visualisation: 3D
• Result: soft segmentation• Visualisation
– Volume rendering (Voxar3D)– Intensity = vesselness– (no orientation information)– Window/level
(can't see the wood for the trees)
![Page 29: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/29.jpg)
•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Results: 3D (Overview)
![Page 30: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/30.jpg)
•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Results: 3D (Detail)
![Page 31: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/31.jpg)
•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Overview
• Introduction• State of the Art• Minimisation Approach• Discussion
– Current challenges– Future Work
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Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Current Problems
• Bronchi– Tubular structures– Walls are likely
to be enhanced– Multiresolution needed?
• Speed– Processing time > 24 h
• Rewrite code partially in C• More efficient optimisation
![Page 33: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/33.jpg)
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Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Current Problem: Discrete weights
• Current weights
– Influence of all neighbours Vessels get wider
• Discrete weights– Look at two neighbors– Smaller vessels possible– Better delineation– Efficient local alignment?
2
vn
vnw
i
Ti
i
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Vv i
ii uvdwE 2,
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Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Future Work: Liver and Bronchi
• Liver vasculature– Complex tree like structure
• Arterial and venous
– More ‘noisy’ background
• Bronchi– Complex tree like structure– Intensity based classification difficult
• Low intense centre surrounded by high intense wall (partial volume artefacts)
– Multiresolution?
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•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Future work
• Multiresolution– Separation:
• Vessel wall Vessel
– Improve speed?
• Model extensions– Synchronous segmentation:
• Vessels and Bronchi
– Bifurcation detection
![Page 36: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/36.jpg)
•
Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Future Work
• Post processing– Multitude of information
• Vesselness
• Orientation
• (3 degrees of freedom / voxel)
– Advanced visualisation– Improved hard segmentation algorithms
• Validation
![Page 37: Segmentation of Tree like Structures as Minimisation Problem applied to Lung Vasculature Pieter Bruyninckx](https://reader035.vdocuments.net/reader035/viewer/2022070413/5697bfc91a28abf838ca9321/html5/thumbnails/37.jpg)
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Minimisation Approach
State of the Art
Introduction
Discussion
Vessel segmentation Thank you for your attention
Questions ?