Transcript Quantification of collagen architecture 3D thickness structure

Quantification of collagen architecture:
3D thickness structure
Internship project
Biomedical Image Analysis & Tissue Engineering
October 2006 – January 2007
Desiree Abdurrachim
Supervisor: Bart terHaar Romeny & Mirjam Rubbens
Outline
• Introduction
• Blobness measure: a blob predictor
• Algorithm
• Results
• Conclusions
• Future works
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Introduction [1/2]
The thickness of collagen fiber determines the strength
of the engineered tissue [Billiar et.al]
Aim:
To quantify the thickness of the fiber
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Introduction [2/2]
• the cross-sectional area of the fiber is assumed to be a
circle
• Implemented in Mathematica
• Tested to the real data: 4 week-old strained B2_63_loc1
• Limited for the fiber parallel to x-axis
x-axis
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Outline
• Introduction
• Blobness measure: a blob predictor
• Algorithm
• Results
• Conclusions
• Future works
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Blobness measure [1/2]
A good detector for a blob structure:
• Higher measure for a better-fit scale
a
s=8
b
s=8
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s=1
1
a 66.32 41.89
s=11
b 61.23 72.36
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Blobness measure [2/2]
• Experiment:
the relation between the real diameter and s:
• Linear relation!
diameter = -0.11 + 2.84 s
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Outline
• Introduction
• Blobness measure: a blob predictor
• Algorithm
• Results
• Conclusions
• Future works
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Algorithm [1/3]
Fiber extraction
Skeleton extraction
(thinning)
Blobness measure
in cross-sectional area
Fiber indexing
Input: 3D CED image
(256 x 256 x 81)
skeleton
Diameter prediction
in each fiber
Extracted fiber
.
Centre point
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Algorithm [2/3]
Fiber extraction
Skeleton extraction
(thinning)
Extracted fiber
Blobness measure
in cross-sectional area
Fiber indexing
Diameter prediction
in each fiber
Cross-sectional areas:
blobness measure s=0.8 to 7, step =0.2
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Algorithm [3/3] – check!
Follow this fiber:
• Consists of 6 cross-sectional area (parallel to x-axis)
• Observe three slices:
• By observation : 6 – 8 pixels
• By blobness measure:
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Outline
• Introduction
• Blobness measure: a blob predictor
• Algorithm
• Results
• Conclusions
• Future works
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Results [1/2]
• Distribution of s in the calculated fibers
• What happens in s = 0.8?
• What happens in s = 7?
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Results [2/2]
• Calibration: scale  pixels (1 pixel = 0.78 mm)
• A set of diameters in one fiber
• Distribution:
• Diameter : 1.6 mm to 6 mm
– heart leaflet diameter : 20 mm & depends on age [Baer
et.al]
– smaller value: due to the young tissue (4 weeks)
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Outline
• Introduction
• Blobness measure: a blob predictor
• Algorithm
• Results
• Conclusions
• Future works
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Conclusions
• A framework to quantify the thickness of the fibers has
been successfully developed
• Circular assumption  blobness measure
• Implemented in Mathematica
• Tested to the real data
• The experiment has shown promising results
• Limitations:
– No phantom validation
– Quantification only for fibers parallel to x-axis
– Not able to measure < 2 pixels (=1.6 mm)
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Future work
• Phantom validation
• Inclusion of the fibers with other orientations
- gauge coordinate (v and w are eigenvectors)
- modification of the blobness measure:
• Experiments on various data (strained-unstrained,
young-mature)
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References
• [Billiar et. al]
Billiar K.L. Sacks M.S., Biaxial mechanical properties of the native and
glutaraldehyde-treated aortic valve cusp: Part II-A Structural constitutive
model. Journal of Biomedical Engineering., 122:137-335, 2000
• [Baer et. al]
Baer E., Cassidy James J., and Hiltner A. Hierarchical structure of
collagen composite systems: lesson from biology. Pure & Appl. Chem.,
Vol. 63, No.7, pp. 961-973, 1991.
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References
• Phantom validation
Thank you!
• dd
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