1. 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

2. Desiree Abdurrachim2 Introduction Blobness measure: a blob predictor Algorithm Results Conclusions Future works Outline

3. Desiree Abdurrachim3 The thickness of collagen fiber determines the strength of the engineered tissue [Billiar et.al] Aim: To quantify the thickness of the fiber Introduction [1/2]

4. Desiree Abdurrachim4 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

5. Desiree Abdurrachim5 Introduction Blobness measure: a blob predictor Algorithm Results Conclusions Future works Outline

6. Desiree Abdurrachim6 Blobness measure [1/2] A good detector for a blob structure: Higher measure for a better-fit scale s=8 s=11 s=8 s=1 1 a66.3241.89 b61.2372.36 a b

7. Desiree Abdurrachim7 Blobness measure [2/2] Experiment: the relation between the real diameter and s: Linear relation! diameter = -0.11 + 2.84 s

8. Desiree Abdurrachim8 Introduction Blobness measure: a blob predictor Algorithm Results Conclusions Future works Outline

9. Desiree Abdurrachim9 Algorithm [1/3] Input: 3D CED image (256 x 256 x 81) Extracted fiber skeleton. Centre point Fiber extraction Skeleton extraction (thinning) Blobness measure in cross-sectional area Fiber indexing Diameter prediction in each fiber

10. Desiree Abdurrachim10 Algorithm [2/3] Extracted fiber Cross-sectional areas: blobness measure s=0.8 to 7, step =0.2 Fiber extraction Skeleton extraction (thinning) Blobness measure in cross-sectional area Fiber indexing Diameter prediction in each fiber

11. Desiree Abdurrachim11 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:

12. Desiree Abdurrachim12 Introduction Blobness measure: a blob predictor Algorithm Results Conclusions Future works Outline

13. Desiree Abdurrachim13 Results [1/2] Distribution of s in the calculated fibers What happens in s = 0.8? What happens in s = 7?

14. Desiree Abdurrachim14 Results [2/2] Calibration: scale  pixels (1 pixel = 0.78 m m) A set of diameters in one fiber Distribution: Diameter : 1.6 m m to 6 m m –heart leaflet diameter : 20 m m & depends on age [Baer et.al] –smaller value: due to the young tissue (4 weeks)

15. Desiree Abdurrachim15 Introduction Blobness measure: a blob predictor Algorithm Results Conclusions Future works Outline

16. Desiree Abdurrachim16 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)

17. Desiree Abdurrachim17 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)

18. Desiree Abdurrachim18 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.

19. Desiree Abdurrachim19 References Phantom validation dd Thank you!