Quantification of collagen architecture 3D thickness structure by ert554898

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									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




                     Desiree Abdurrachim   2
             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

                      Desiree Abdurrachim             3
              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

                       Desiree Abdurrachim                   4
                    Outline
• Introduction
• Blobness measure: a blob predictor
• Algorithm
• Results
• Conclusions
• Future works




                     Desiree Abdurrachim   5
          Blobness measure [1/2]
              A good detector for a blob structure:




• Higher measure for a better-fit scale

a
                                               s=8   s=1
                                                     1
                                             a 66.32 41.89
    s=8
     b                                      s=11
                      Desiree Abdurrachim    b 61.23 72.36   6
       Blobness measure [2/2]
• Experiment:
  the relation between the real diameter and s:




• Linear relation!
   diameter = -0.11 + 2.84 s

                      Desiree Abdurrachim         7
                    Outline
• Introduction
• Blobness measure: a blob predictor
• Algorithm
• Results
• Conclusions
• Future works




                     Desiree Abdurrachim   8
                 Algorithm [1/3]
   Fiber extraction


 Skeleton extraction
     (thinning)


  Blobness measure         Input: 3D CED image
                                                     Extracted fiber
in cross-sectional area    (256 x 256 x 81)



                                    skeleton
    Fiber indexing
                                                 .
 Diameter prediction                                 Centre point
    in each fiber
                          Desiree Abdurrachim                          9
                 Algorithm [2/3]
   Fiber extraction


 Skeleton extraction
     (thinning)

                                                Extracted fiber
  Blobness measure
in cross-sectional area


    Fiber indexing


 Diameter prediction                   Cross-sectional areas:
    in each fiber                      blobness measure s=0.8 to 7, step =0.2
                          Desiree Abdurrachim                           10
         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:


                         Desiree Abdurrachim                11
                    Outline
• Introduction
• Blobness measure: a blob predictor
• Algorithm
• Results
• Conclusions
• Future works




                     Desiree Abdurrachim   12
                  Results [1/2]
• Distribution of s in the calculated fibers




• What happens in s = 0.8?
• What happens in s = 7?
                       Desiree Abdurrachim     13
                  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)
                        Desiree Abdurrachim                  14
                    Outline
• Introduction
• Blobness measure: a blob predictor
• Algorithm
• Results
• Conclusions
• Future works




                     Desiree Abdurrachim   15
                   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)

                        Desiree Abdurrachim              16
                 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)

                      Desiree Abdurrachim             17
                       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.




                             Desiree Abdurrachim                        18
                References
• Phantom validation




                           Thank you!




• dd
                       Desiree Abdurrachim   19

								
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