Abstract

Quantifying collagen fiber architecture has clinical and scientific relevance across a variety of tissue types and adds functionality to otherwise largely qualitative imaging modalities. Optical coherence tomography (OCT) is uniquely suited for this task due to its ability to capture the collagen microstructure over larger fields of view than traditional microscopy. Existing image processing techniques for quantifying fiber architecture, while accurate and effective, are very slow for processing large datasets and tend to lack structural specificity. We describe here a computationally efficient method for quantifying and visualizing collagen fiber organization. The algorithm is demonstrated on swine atria, bovine anterior cruciate ligament, and human cervical tissue samples. Additionally, we show an improved performance for images with crimped fiber textures and low signal to noise when compared to similar methods.

© 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

Full Article  |  PDF Article
OSA Recommended Articles
Extracting three-dimensional orientation and tractography of myofibers using optical coherence tomography

Yu Gan and Christine P. Fleming
Biomed. Opt. Express 4(10) 2150-2165 (2013)

Imaging myocardial fiber orientation using polarization sensitive optical coherence tomography

Chuanmao Fan and Gang Yao
Biomed. Opt. Express 4(3) 460-465 (2013)

Rapid three-dimensional quantification of voxel-wise collagen fiber orientation

Zhiyi Liu, Kyle P. Quinn, Lucia Speroni, Lisa Arendt, Charlotte Kuperwasser, Carlos Sonnenschein, Ana M. Soto, and Irene Georgakoudi
Biomed. Opt. Express 6(7) 2294-2310 (2015)

References

  • View by:
  • |
  • |
  • |

  1. T. H. Lye, K. P. Vincent, A. D. McCulloch, and C. P. Hendon, “Tissue-specific optical mapping models of swine atria informed by Optical Coherence Tomography,” Biophys. J. 114, 1477–1489 (2018).
  2. R. Zareian, M. E. Susilo, J. A. Paten, J. P. McLean, J. Hollmann, D. Karamichos, C. S. Messer, D. T. Tambe, N. Saeidi, J. D. Zieske, and J. W. Ruberti, “Human corneal fibroblast pattern evolution and matrix synthesis on mechanically biased substrates,” Tissue Eng. Part A 22, 1204–1217 (2016).
  3. F. J. Avila and J. M. Bueno, “Analysis and quantification of collagen organization with the structure tensor in second harmonic microscopy images of ocular tissues,” Appl. Opt. 54, 9848–9854 (2015).
  4. M. Eggen, C. Swingen, and P. Iaizzo, “Analysis of fiber orientation in normal and failing human hearts using diffusion tensor MRI,” 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (IEEE, 2009), pp. 642–645.
  5. H. Yan, O. Carmichael, D. Paul, and J. Peng, “Estimating fiber orientation distribution from diffusion MRI with spherical needlets,” Med. Image Anal. 46, 57–72 (2018).
  6. W. N. Lee, M. Pernot, M. Couade, E. Messas, P. Bruneval, A. Bel, A. A. Hagège, M. Fink, and M. Tanter, “Mapping myocardial fiber orientation using echocardiography-based shear wave imaging,” IEEE Trans. Med. Imaging 31, 554–562 (2012).
  7. T. B. Leergaard, N. S. White, A. de Crespigny, I. Bolstad, H. D’Arceuil, J. G. Bjaalie, and A. M. Dale, “Quantitative histological validation of diffusion MRI fiber orientation distributions in the rat brain,” PLoS ONE 5, 1–8 (2010).
  8. K. G. Schilling, V. Janve, Y. Gao, I. Stepniewska, B. A. Landman, and A. W. Anderson, “Histological validation of diffusion MRI fiber orientation distributions and dispersion,” Neuroimage 165, 200–221 (2018).
  9. C. M. Ambrosi, V. V. Fedorov, R. B. Schuessler, A. M. Rollins, and I. R. Efimov, “Quantification of fiber orientation in the canine atrial pacemaker complex using optical coherence tomography,” J. Biomed. Opt. 17, 071309 (2012).
  10. C. Fan and G. Yao, “Imaging myocardial fiber orientation using polarization sensitive optical coherence tomography,” Biomed. Opt. Express 4, 460–465 (2013).
  11. K. M. Myers, C. P. Hendon, Y. Gan, W. Yao, K. Yoshida, M. Fernandez, J. Vink, and R. J. Wapner, “A continuous fiber distribution material model for human cervical tissue,” J. Biomech. 48, 1533–1540 (2015).
  12. D. Qu, P. J. Chuang, S. Prateepchinda, P. S. Balasubramanian, X. Yao, S. B. Doty, C. P. Hendon, and H. H. Lu, “Micro-and ultrastructural characterization of age-related changes at the anterior cruciate ligament-to-bone insertion,” ACS Biomater. Sci. Eng. 3, 2806–2814 (2017).
  13. E. Li, S. Makita, Y.-J. Hong, D. Kasaragod, and Y. Yasuno, “Three-dimensional multi-contrast imaging of in vivo human skin by Jones matrix optical coherence tomography,” Biomed. Opt. Express 8, 1290–1305 (2017).
  14. J. Walther, Q. Li, M. Villiger, C. S. Farah, E. Koch, K. Karnowski, and D. D. Sampson, “Depth-resolved birefringence imaging of collagen fiber organization in the human oral mucosa in vivo,” Biomed. Opt. Express 10, 1942–1956 (2019).
  15. N. Ugryumova, J. Jacobs, M. Bonesi, and S. J. Matcher, “Novel optical imaging technique to determine the 3-D orientation of collagen fibers in cartilage: variable-incidence angle polarization-sensitive optical coherence tomography,” Osteoarthr. Cartil. 17, 33–42 (2009).
  16. Y. Wang and G. Yao, “Optical tractography of the mouse heart using polarization-sensitive optical coherence tomography,” Biomed. Opt. Express 4, 2540–2545 (2013).
  17. L. Azinfar, M. Ravanfar, Y. Wang, K. Zhang, D. Duan, and G. Yao, “High resolution imaging of the fibrous microstructure in bovine common carotid artery using optical polarization tractography,” J. Biophotonics 10, 231–241 (2017).
  18. C. P. Fleming, C. M. Ripplinger, B. Webb, I. R. Efimov, and A. M. Rollins, “Quantification of cardiac fiber orientation using optical coherence tomography,” J. Biomed. Opt. 13, 030505 (2008).
  19. J. A. Germann, E. Martinez-Enriquez, and S. Marcos, “Quantization of collagen organization in the stroma with a new order coefficient,” Biomed. Opt. Express 9, 173–189 (2018).
  20. C. J. Goergen, H. Radhakrishnan, S. Sakadžic, E. T. Mandeville, E. H. Lo, D. E. Sosnovik, and V. J. Srinivasan, “Optical coherence tractography using intrinsic contrast,” Opt. Lett. 37, 3882–3884 (2012).
  21. Y. Mega, M. Robitaille, R. Zareian, J. McLean, J. Ruberti, and C. DiMarzio, “Quantification of lamellar orientation in corneal collagen using second harmonic generation images,” Opt. Lett. 37, 3312–3314 (2012).
  22. E. Z. Psarakis, V. G. Mertzios, and G. P. Alexiou, “Design of two-dimensional zero phase FIR fan filters via the McClellan transform,” IEEE Trans. Circuits Syst. 37, 10–16 (1990).
  23. Y. Gan, W. Yao, K. M. Myers, J. Y. Vink, R. J. Wapner, and C. P. Hendon, “Analyzing three-dimensional ultrastructure of human cervical tissue using optical coherence tomography,” Biomed. Opt. Express 6, 1090–1108 (2015).
  24. W. van Aarle, W. J. Palenstijn, J. Cant, E. Janssens, F. Bleichrodt, A. Dabravolski, J. De Beenhouwer, K. Joost Batenburg, and J. Sijbers, “Fast and flexible X-ray tomography using the ASTRA toolbox,” Opt. Express 24, 25129–25147 (2016).
  25. Y. Gan and C. P. Fleming, “Extracting three-dimensional orientation and tractography of myofibers using optical coherence tomography,” Biomed. Opt. Express 4, 2150–2165 (2013).
  26. K. P. Quinn and I. Georgakoudi, “Rapid quantification of pixel-wise fiber orientation data in micrographs,” J. Biomed. Opt. 18, 046003 (2013).
  27. W. Yao, Y. Gan, K. M. Myers, J. Y. Vink, R. J. Wapner, and C. P. Hendon, “Collagen fiber orientation and dispersion in the upper cervix of non-pregnant and pregnant women,” PLoS ONE 11, 1–20 (2016).
  28. F. H. Silver, J. W. Freeman, and G. P. Seehra, “Collagen self-assembly and the development of tendon mechanical properties,” J. Biomech. 36, 1529–1553 (2003).
  29. C. J. Stender, E. Rust, P. T. Martin, E. E. Neumann, R. J. Brown, and T. J. Lujan, “Modeling the effect of collagen fibril alignment on ligament mechanical behavior,” Biomech. Model. Mechanobiol. 17, 543–557 (2018).
  30. P. Whittaker and P. B. Canham, “Demonstration of quantitative fabric analysis of tendon collagen using two-dimensional polarized light microscopy,” Matrix 11, 56–62 (1991).
  31. T. Y. Lau, R. Ambekar, and K. C. Toussaint, “Quantification of collagen fiber organization using three-dimensional Fourier transform-second-harmonic generation imaging,” Opt. Express 20, 21821–21832 (2012).
  32. M. Franchi, V. Ottani, R. Stagni, and A. Ruggeri, “Tendon and ligament fibrillar crimps give rise to left-handed helices of collagen fibrils in both planar and helical crimps,” J. Anat. 216, 301–309 (2010).
  33. C. T. Laurencin and J. W. Freeman, “Ligament tissue engineering: An evolutionary materials science approach,” Biomaterials 26, 7530–7536 (2005).
  34. M. Franchi, M. Fini, M. Quaranta, V. De Pasquale, M. Raspanti, G. Giavaresi, V. Ottani, and A. Ruggeri, “Crimp morphology in relaxed and stretched rat Achilles tendon,” J. Anat. 210, 1–7 (2007).
  35. S. Pei and J. Shyu, “Design of 2D FIR digital filters by McClellan transformation and least squares eigencontour mapping,” IEEE Trans. Circuits Syst. II Analog. Digit. Signal Process. 40, 546–555 (1993).
  36. W. Zhu and S. Nakamura, “An efficient approach for the synthesis of 2-D recursive fan filters using 1-D prototypes,” IEEE Trans. Signal Process. 44, 979–983 (1996).
  37. T. Bindima, U. K. Shahanas, and E. Elias, “Low complexity fan filters using multiobjective artificial bee colony optimization aided McClellan Transformation for directional filtering,” IEEE Trans Circuits Syst II Express Briefs 65, 2057–2061 (2018).
  38. K. Dabov, A. Foi, V. Katkovnik, and K. Egiazarian, “Image denoising by sparse 3-D transform-domain collaborative filtering,” IEEE Trans. Image Process. 16, 2080–2095 (2007).
  39. C. Cuartas-Vélez, R. Restrepo, B. E. Bouma, and N. Uribe-Patarroyo, “Volumetric non-local-means based speckle reduction for optical coherence tomography,” Biomed. Opt. Express 9, 3354–3372 (2018).

2019 (1)

2018 (7)

J. A. Germann, E. Martinez-Enriquez, and S. Marcos, “Quantization of collagen organization in the stroma with a new order coefficient,” Biomed. Opt. Express 9, 173–189 (2018).

T. H. Lye, K. P. Vincent, A. D. McCulloch, and C. P. Hendon, “Tissue-specific optical mapping models of swine atria informed by Optical Coherence Tomography,” Biophys. J. 114, 1477–1489 (2018).

H. Yan, O. Carmichael, D. Paul, and J. Peng, “Estimating fiber orientation distribution from diffusion MRI with spherical needlets,” Med. Image Anal. 46, 57–72 (2018).

K. G. Schilling, V. Janve, Y. Gao, I. Stepniewska, B. A. Landman, and A. W. Anderson, “Histological validation of diffusion MRI fiber orientation distributions and dispersion,” Neuroimage 165, 200–221 (2018).

C. J. Stender, E. Rust, P. T. Martin, E. E. Neumann, R. J. Brown, and T. J. Lujan, “Modeling the effect of collagen fibril alignment on ligament mechanical behavior,” Biomech. Model. Mechanobiol. 17, 543–557 (2018).

T. Bindima, U. K. Shahanas, and E. Elias, “Low complexity fan filters using multiobjective artificial bee colony optimization aided McClellan Transformation for directional filtering,” IEEE Trans Circuits Syst II Express Briefs 65, 2057–2061 (2018).

C. Cuartas-Vélez, R. Restrepo, B. E. Bouma, and N. Uribe-Patarroyo, “Volumetric non-local-means based speckle reduction for optical coherence tomography,” Biomed. Opt. Express 9, 3354–3372 (2018).

2017 (3)

L. Azinfar, M. Ravanfar, Y. Wang, K. Zhang, D. Duan, and G. Yao, “High resolution imaging of the fibrous microstructure in bovine common carotid artery using optical polarization tractography,” J. Biophotonics 10, 231–241 (2017).

D. Qu, P. J. Chuang, S. Prateepchinda, P. S. Balasubramanian, X. Yao, S. B. Doty, C. P. Hendon, and H. H. Lu, “Micro-and ultrastructural characterization of age-related changes at the anterior cruciate ligament-to-bone insertion,” ACS Biomater. Sci. Eng. 3, 2806–2814 (2017).

E. Li, S. Makita, Y.-J. Hong, D. Kasaragod, and Y. Yasuno, “Three-dimensional multi-contrast imaging of in vivo human skin by Jones matrix optical coherence tomography,” Biomed. Opt. Express 8, 1290–1305 (2017).

2016 (3)

R. Zareian, M. E. Susilo, J. A. Paten, J. P. McLean, J. Hollmann, D. Karamichos, C. S. Messer, D. T. Tambe, N. Saeidi, J. D. Zieske, and J. W. Ruberti, “Human corneal fibroblast pattern evolution and matrix synthesis on mechanically biased substrates,” Tissue Eng. Part A 22, 1204–1217 (2016).

W. van Aarle, W. J. Palenstijn, J. Cant, E. Janssens, F. Bleichrodt, A. Dabravolski, J. De Beenhouwer, K. Joost Batenburg, and J. Sijbers, “Fast and flexible X-ray tomography using the ASTRA toolbox,” Opt. Express 24, 25129–25147 (2016).

W. Yao, Y. Gan, K. M. Myers, J. Y. Vink, R. J. Wapner, and C. P. Hendon, “Collagen fiber orientation and dispersion in the upper cervix of non-pregnant and pregnant women,” PLoS ONE 11, 1–20 (2016).

2015 (3)

2013 (4)

2012 (5)

T. Y. Lau, R. Ambekar, and K. C. Toussaint, “Quantification of collagen fiber organization using three-dimensional Fourier transform-second-harmonic generation imaging,” Opt. Express 20, 21821–21832 (2012).

C. M. Ambrosi, V. V. Fedorov, R. B. Schuessler, A. M. Rollins, and I. R. Efimov, “Quantification of fiber orientation in the canine atrial pacemaker complex using optical coherence tomography,” J. Biomed. Opt. 17, 071309 (2012).

W. N. Lee, M. Pernot, M. Couade, E. Messas, P. Bruneval, A. Bel, A. A. Hagège, M. Fink, and M. Tanter, “Mapping myocardial fiber orientation using echocardiography-based shear wave imaging,” IEEE Trans. Med. Imaging 31, 554–562 (2012).

C. J. Goergen, H. Radhakrishnan, S. Sakadžic, E. T. Mandeville, E. H. Lo, D. E. Sosnovik, and V. J. Srinivasan, “Optical coherence tractography using intrinsic contrast,” Opt. Lett. 37, 3882–3884 (2012).

Y. Mega, M. Robitaille, R. Zareian, J. McLean, J. Ruberti, and C. DiMarzio, “Quantification of lamellar orientation in corneal collagen using second harmonic generation images,” Opt. Lett. 37, 3312–3314 (2012).

2010 (2)

T. B. Leergaard, N. S. White, A. de Crespigny, I. Bolstad, H. D’Arceuil, J. G. Bjaalie, and A. M. Dale, “Quantitative histological validation of diffusion MRI fiber orientation distributions in the rat brain,” PLoS ONE 5, 1–8 (2010).

M. Franchi, V. Ottani, R. Stagni, and A. Ruggeri, “Tendon and ligament fibrillar crimps give rise to left-handed helices of collagen fibrils in both planar and helical crimps,” J. Anat. 216, 301–309 (2010).

2009 (1)

N. Ugryumova, J. Jacobs, M. Bonesi, and S. J. Matcher, “Novel optical imaging technique to determine the 3-D orientation of collagen fibers in cartilage: variable-incidence angle polarization-sensitive optical coherence tomography,” Osteoarthr. Cartil. 17, 33–42 (2009).

2008 (1)

C. P. Fleming, C. M. Ripplinger, B. Webb, I. R. Efimov, and A. M. Rollins, “Quantification of cardiac fiber orientation using optical coherence tomography,” J. Biomed. Opt. 13, 030505 (2008).

2007 (2)

K. Dabov, A. Foi, V. Katkovnik, and K. Egiazarian, “Image denoising by sparse 3-D transform-domain collaborative filtering,” IEEE Trans. Image Process. 16, 2080–2095 (2007).

M. Franchi, M. Fini, M. Quaranta, V. De Pasquale, M. Raspanti, G. Giavaresi, V. Ottani, and A. Ruggeri, “Crimp morphology in relaxed and stretched rat Achilles tendon,” J. Anat. 210, 1–7 (2007).

2005 (1)

C. T. Laurencin and J. W. Freeman, “Ligament tissue engineering: An evolutionary materials science approach,” Biomaterials 26, 7530–7536 (2005).

2003 (1)

F. H. Silver, J. W. Freeman, and G. P. Seehra, “Collagen self-assembly and the development of tendon mechanical properties,” J. Biomech. 36, 1529–1553 (2003).

1996 (1)

W. Zhu and S. Nakamura, “An efficient approach for the synthesis of 2-D recursive fan filters using 1-D prototypes,” IEEE Trans. Signal Process. 44, 979–983 (1996).

1993 (1)

S. Pei and J. Shyu, “Design of 2D FIR digital filters by McClellan transformation and least squares eigencontour mapping,” IEEE Trans. Circuits Syst. II Analog. Digit. Signal Process. 40, 546–555 (1993).

1991 (1)

P. Whittaker and P. B. Canham, “Demonstration of quantitative fabric analysis of tendon collagen using two-dimensional polarized light microscopy,” Matrix 11, 56–62 (1991).

1990 (1)

E. Z. Psarakis, V. G. Mertzios, and G. P. Alexiou, “Design of two-dimensional zero phase FIR fan filters via the McClellan transform,” IEEE Trans. Circuits Syst. 37, 10–16 (1990).

Alexiou, G. P.

E. Z. Psarakis, V. G. Mertzios, and G. P. Alexiou, “Design of two-dimensional zero phase FIR fan filters via the McClellan transform,” IEEE Trans. Circuits Syst. 37, 10–16 (1990).

Ambekar, R.

Ambrosi, C. M.

C. M. Ambrosi, V. V. Fedorov, R. B. Schuessler, A. M. Rollins, and I. R. Efimov, “Quantification of fiber orientation in the canine atrial pacemaker complex using optical coherence tomography,” J. Biomed. Opt. 17, 071309 (2012).

Anderson, A. W.

K. G. Schilling, V. Janve, Y. Gao, I. Stepniewska, B. A. Landman, and A. W. Anderson, “Histological validation of diffusion MRI fiber orientation distributions and dispersion,” Neuroimage 165, 200–221 (2018).

Avila, F. J.

Azinfar, L.

L. Azinfar, M. Ravanfar, Y. Wang, K. Zhang, D. Duan, and G. Yao, “High resolution imaging of the fibrous microstructure in bovine common carotid artery using optical polarization tractography,” J. Biophotonics 10, 231–241 (2017).

Balasubramanian, P. S.

D. Qu, P. J. Chuang, S. Prateepchinda, P. S. Balasubramanian, X. Yao, S. B. Doty, C. P. Hendon, and H. H. Lu, “Micro-and ultrastructural characterization of age-related changes at the anterior cruciate ligament-to-bone insertion,” ACS Biomater. Sci. Eng. 3, 2806–2814 (2017).

Beenhouwer, J. De

Bel, A.

W. N. Lee, M. Pernot, M. Couade, E. Messas, P. Bruneval, A. Bel, A. A. Hagège, M. Fink, and M. Tanter, “Mapping myocardial fiber orientation using echocardiography-based shear wave imaging,” IEEE Trans. Med. Imaging 31, 554–562 (2012).

Bindima, T.

T. Bindima, U. K. Shahanas, and E. Elias, “Low complexity fan filters using multiobjective artificial bee colony optimization aided McClellan Transformation for directional filtering,” IEEE Trans Circuits Syst II Express Briefs 65, 2057–2061 (2018).

Bjaalie, J. G.

T. B. Leergaard, N. S. White, A. de Crespigny, I. Bolstad, H. D’Arceuil, J. G. Bjaalie, and A. M. Dale, “Quantitative histological validation of diffusion MRI fiber orientation distributions in the rat brain,” PLoS ONE 5, 1–8 (2010).

Bleichrodt, F.

Bolstad, I.

T. B. Leergaard, N. S. White, A. de Crespigny, I. Bolstad, H. D’Arceuil, J. G. Bjaalie, and A. M. Dale, “Quantitative histological validation of diffusion MRI fiber orientation distributions in the rat brain,” PLoS ONE 5, 1–8 (2010).

Bonesi, M.

N. Ugryumova, J. Jacobs, M. Bonesi, and S. J. Matcher, “Novel optical imaging technique to determine the 3-D orientation of collagen fibers in cartilage: variable-incidence angle polarization-sensitive optical coherence tomography,” Osteoarthr. Cartil. 17, 33–42 (2009).

Bouma, B. E.

Brown, R. J.

C. J. Stender, E. Rust, P. T. Martin, E. E. Neumann, R. J. Brown, and T. J. Lujan, “Modeling the effect of collagen fibril alignment on ligament mechanical behavior,” Biomech. Model. Mechanobiol. 17, 543–557 (2018).

Bruneval, P.

W. N. Lee, M. Pernot, M. Couade, E. Messas, P. Bruneval, A. Bel, A. A. Hagège, M. Fink, and M. Tanter, “Mapping myocardial fiber orientation using echocardiography-based shear wave imaging,” IEEE Trans. Med. Imaging 31, 554–562 (2012).

Bueno, J. M.

Canham, P. B.

P. Whittaker and P. B. Canham, “Demonstration of quantitative fabric analysis of tendon collagen using two-dimensional polarized light microscopy,” Matrix 11, 56–62 (1991).

Cant, J.

Carmichael, O.

H. Yan, O. Carmichael, D. Paul, and J. Peng, “Estimating fiber orientation distribution from diffusion MRI with spherical needlets,” Med. Image Anal. 46, 57–72 (2018).

Chuang, P. J.

D. Qu, P. J. Chuang, S. Prateepchinda, P. S. Balasubramanian, X. Yao, S. B. Doty, C. P. Hendon, and H. H. Lu, “Micro-and ultrastructural characterization of age-related changes at the anterior cruciate ligament-to-bone insertion,” ACS Biomater. Sci. Eng. 3, 2806–2814 (2017).

Couade, M.

W. N. Lee, M. Pernot, M. Couade, E. Messas, P. Bruneval, A. Bel, A. A. Hagège, M. Fink, and M. Tanter, “Mapping myocardial fiber orientation using echocardiography-based shear wave imaging,” IEEE Trans. Med. Imaging 31, 554–562 (2012).

Cuartas-Vélez, C.

D’Arceuil, H.

T. B. Leergaard, N. S. White, A. de Crespigny, I. Bolstad, H. D’Arceuil, J. G. Bjaalie, and A. M. Dale, “Quantitative histological validation of diffusion MRI fiber orientation distributions in the rat brain,” PLoS ONE 5, 1–8 (2010).

Dabov, K.

K. Dabov, A. Foi, V. Katkovnik, and K. Egiazarian, “Image denoising by sparse 3-D transform-domain collaborative filtering,” IEEE Trans. Image Process. 16, 2080–2095 (2007).

Dabravolski, A.

Dale, A. M.

T. B. Leergaard, N. S. White, A. de Crespigny, I. Bolstad, H. D’Arceuil, J. G. Bjaalie, and A. M. Dale, “Quantitative histological validation of diffusion MRI fiber orientation distributions in the rat brain,” PLoS ONE 5, 1–8 (2010).

de Crespigny, A.

T. B. Leergaard, N. S. White, A. de Crespigny, I. Bolstad, H. D’Arceuil, J. G. Bjaalie, and A. M. Dale, “Quantitative histological validation of diffusion MRI fiber orientation distributions in the rat brain,” PLoS ONE 5, 1–8 (2010).

De Pasquale, V.

M. Franchi, M. Fini, M. Quaranta, V. De Pasquale, M. Raspanti, G. Giavaresi, V. Ottani, and A. Ruggeri, “Crimp morphology in relaxed and stretched rat Achilles tendon,” J. Anat. 210, 1–7 (2007).

DiMarzio, C.

Doty, S. B.

D. Qu, P. J. Chuang, S. Prateepchinda, P. S. Balasubramanian, X. Yao, S. B. Doty, C. P. Hendon, and H. H. Lu, “Micro-and ultrastructural characterization of age-related changes at the anterior cruciate ligament-to-bone insertion,” ACS Biomater. Sci. Eng. 3, 2806–2814 (2017).

Duan, D.

L. Azinfar, M. Ravanfar, Y. Wang, K. Zhang, D. Duan, and G. Yao, “High resolution imaging of the fibrous microstructure in bovine common carotid artery using optical polarization tractography,” J. Biophotonics 10, 231–241 (2017).

Efimov, I. R.

C. M. Ambrosi, V. V. Fedorov, R. B. Schuessler, A. M. Rollins, and I. R. Efimov, “Quantification of fiber orientation in the canine atrial pacemaker complex using optical coherence tomography,” J. Biomed. Opt. 17, 071309 (2012).

C. P. Fleming, C. M. Ripplinger, B. Webb, I. R. Efimov, and A. M. Rollins, “Quantification of cardiac fiber orientation using optical coherence tomography,” J. Biomed. Opt. 13, 030505 (2008).

Eggen, M.

M. Eggen, C. Swingen, and P. Iaizzo, “Analysis of fiber orientation in normal and failing human hearts using diffusion tensor MRI,” 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (IEEE, 2009), pp. 642–645.

Egiazarian, K.

K. Dabov, A. Foi, V. Katkovnik, and K. Egiazarian, “Image denoising by sparse 3-D transform-domain collaborative filtering,” IEEE Trans. Image Process. 16, 2080–2095 (2007).

Elias, E.

T. Bindima, U. K. Shahanas, and E. Elias, “Low complexity fan filters using multiobjective artificial bee colony optimization aided McClellan Transformation for directional filtering,” IEEE Trans Circuits Syst II Express Briefs 65, 2057–2061 (2018).

Fan, C.

Farah, C. S.

Fedorov, V. V.

C. M. Ambrosi, V. V. Fedorov, R. B. Schuessler, A. M. Rollins, and I. R. Efimov, “Quantification of fiber orientation in the canine atrial pacemaker complex using optical coherence tomography,” J. Biomed. Opt. 17, 071309 (2012).

Fernandez, M.

K. M. Myers, C. P. Hendon, Y. Gan, W. Yao, K. Yoshida, M. Fernandez, J. Vink, and R. J. Wapner, “A continuous fiber distribution material model for human cervical tissue,” J. Biomech. 48, 1533–1540 (2015).

Fini, M.

M. Franchi, M. Fini, M. Quaranta, V. De Pasquale, M. Raspanti, G. Giavaresi, V. Ottani, and A. Ruggeri, “Crimp morphology in relaxed and stretched rat Achilles tendon,” J. Anat. 210, 1–7 (2007).

Fink, M.

W. N. Lee, M. Pernot, M. Couade, E. Messas, P. Bruneval, A. Bel, A. A. Hagège, M. Fink, and M. Tanter, “Mapping myocardial fiber orientation using echocardiography-based shear wave imaging,” IEEE Trans. Med. Imaging 31, 554–562 (2012).

Fleming, C. P.

Y. Gan and C. P. Fleming, “Extracting three-dimensional orientation and tractography of myofibers using optical coherence tomography,” Biomed. Opt. Express 4, 2150–2165 (2013).

C. P. Fleming, C. M. Ripplinger, B. Webb, I. R. Efimov, and A. M. Rollins, “Quantification of cardiac fiber orientation using optical coherence tomography,” J. Biomed. Opt. 13, 030505 (2008).

Foi, A.

K. Dabov, A. Foi, V. Katkovnik, and K. Egiazarian, “Image denoising by sparse 3-D transform-domain collaborative filtering,” IEEE Trans. Image Process. 16, 2080–2095 (2007).

Franchi, M.

M. Franchi, V. Ottani, R. Stagni, and A. Ruggeri, “Tendon and ligament fibrillar crimps give rise to left-handed helices of collagen fibrils in both planar and helical crimps,” J. Anat. 216, 301–309 (2010).

M. Franchi, M. Fini, M. Quaranta, V. De Pasquale, M. Raspanti, G. Giavaresi, V. Ottani, and A. Ruggeri, “Crimp morphology in relaxed and stretched rat Achilles tendon,” J. Anat. 210, 1–7 (2007).

Freeman, J. W.

C. T. Laurencin and J. W. Freeman, “Ligament tissue engineering: An evolutionary materials science approach,” Biomaterials 26, 7530–7536 (2005).

F. H. Silver, J. W. Freeman, and G. P. Seehra, “Collagen self-assembly and the development of tendon mechanical properties,” J. Biomech. 36, 1529–1553 (2003).

Gan, Y.

W. Yao, Y. Gan, K. M. Myers, J. Y. Vink, R. J. Wapner, and C. P. Hendon, “Collagen fiber orientation and dispersion in the upper cervix of non-pregnant and pregnant women,” PLoS ONE 11, 1–20 (2016).

K. M. Myers, C. P. Hendon, Y. Gan, W. Yao, K. Yoshida, M. Fernandez, J. Vink, and R. J. Wapner, “A continuous fiber distribution material model for human cervical tissue,” J. Biomech. 48, 1533–1540 (2015).

Y. Gan, W. Yao, K. M. Myers, J. Y. Vink, R. J. Wapner, and C. P. Hendon, “Analyzing three-dimensional ultrastructure of human cervical tissue using optical coherence tomography,” Biomed. Opt. Express 6, 1090–1108 (2015).

Y. Gan and C. P. Fleming, “Extracting three-dimensional orientation and tractography of myofibers using optical coherence tomography,” Biomed. Opt. Express 4, 2150–2165 (2013).

Gao, Y.

K. G. Schilling, V. Janve, Y. Gao, I. Stepniewska, B. A. Landman, and A. W. Anderson, “Histological validation of diffusion MRI fiber orientation distributions and dispersion,” Neuroimage 165, 200–221 (2018).

Georgakoudi, I.

K. P. Quinn and I. Georgakoudi, “Rapid quantification of pixel-wise fiber orientation data in micrographs,” J. Biomed. Opt. 18, 046003 (2013).

Germann, J. A.

Giavaresi, G.

M. Franchi, M. Fini, M. Quaranta, V. De Pasquale, M. Raspanti, G. Giavaresi, V. Ottani, and A. Ruggeri, “Crimp morphology in relaxed and stretched rat Achilles tendon,” J. Anat. 210, 1–7 (2007).

Goergen, C. J.

Hagège, A. A.

W. N. Lee, M. Pernot, M. Couade, E. Messas, P. Bruneval, A. Bel, A. A. Hagège, M. Fink, and M. Tanter, “Mapping myocardial fiber orientation using echocardiography-based shear wave imaging,” IEEE Trans. Med. Imaging 31, 554–562 (2012).

Hendon, C. P.

T. H. Lye, K. P. Vincent, A. D. McCulloch, and C. P. Hendon, “Tissue-specific optical mapping models of swine atria informed by Optical Coherence Tomography,” Biophys. J. 114, 1477–1489 (2018).

D. Qu, P. J. Chuang, S. Prateepchinda, P. S. Balasubramanian, X. Yao, S. B. Doty, C. P. Hendon, and H. H. Lu, “Micro-and ultrastructural characterization of age-related changes at the anterior cruciate ligament-to-bone insertion,” ACS Biomater. Sci. Eng. 3, 2806–2814 (2017).

W. Yao, Y. Gan, K. M. Myers, J. Y. Vink, R. J. Wapner, and C. P. Hendon, “Collagen fiber orientation and dispersion in the upper cervix of non-pregnant and pregnant women,” PLoS ONE 11, 1–20 (2016).

K. M. Myers, C. P. Hendon, Y. Gan, W. Yao, K. Yoshida, M. Fernandez, J. Vink, and R. J. Wapner, “A continuous fiber distribution material model for human cervical tissue,” J. Biomech. 48, 1533–1540 (2015).

Y. Gan, W. Yao, K. M. Myers, J. Y. Vink, R. J. Wapner, and C. P. Hendon, “Analyzing three-dimensional ultrastructure of human cervical tissue using optical coherence tomography,” Biomed. Opt. Express 6, 1090–1108 (2015).

Hollmann, J.

R. Zareian, M. E. Susilo, J. A. Paten, J. P. McLean, J. Hollmann, D. Karamichos, C. S. Messer, D. T. Tambe, N. Saeidi, J. D. Zieske, and J. W. Ruberti, “Human corneal fibroblast pattern evolution and matrix synthesis on mechanically biased substrates,” Tissue Eng. Part A 22, 1204–1217 (2016).

Hong, Y.-J.

Iaizzo, P.

M. Eggen, C. Swingen, and P. Iaizzo, “Analysis of fiber orientation in normal and failing human hearts using diffusion tensor MRI,” 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (IEEE, 2009), pp. 642–645.

Jacobs, J.

N. Ugryumova, J. Jacobs, M. Bonesi, and S. J. Matcher, “Novel optical imaging technique to determine the 3-D orientation of collagen fibers in cartilage: variable-incidence angle polarization-sensitive optical coherence tomography,” Osteoarthr. Cartil. 17, 33–42 (2009).

Janssens, E.

Janve, V.

K. G. Schilling, V. Janve, Y. Gao, I. Stepniewska, B. A. Landman, and A. W. Anderson, “Histological validation of diffusion MRI fiber orientation distributions and dispersion,” Neuroimage 165, 200–221 (2018).

Joost Batenburg, K.

Karamichos, D.

R. Zareian, M. E. Susilo, J. A. Paten, J. P. McLean, J. Hollmann, D. Karamichos, C. S. Messer, D. T. Tambe, N. Saeidi, J. D. Zieske, and J. W. Ruberti, “Human corneal fibroblast pattern evolution and matrix synthesis on mechanically biased substrates,” Tissue Eng. Part A 22, 1204–1217 (2016).

Karnowski, K.

Kasaragod, D.

Katkovnik, V.

K. Dabov, A. Foi, V. Katkovnik, and K. Egiazarian, “Image denoising by sparse 3-D transform-domain collaborative filtering,” IEEE Trans. Image Process. 16, 2080–2095 (2007).

Koch, E.

Landman, B. A.

K. G. Schilling, V. Janve, Y. Gao, I. Stepniewska, B. A. Landman, and A. W. Anderson, “Histological validation of diffusion MRI fiber orientation distributions and dispersion,” Neuroimage 165, 200–221 (2018).

Lau, T. Y.

Laurencin, C. T.

C. T. Laurencin and J. W. Freeman, “Ligament tissue engineering: An evolutionary materials science approach,” Biomaterials 26, 7530–7536 (2005).

Lee, W. N.

W. N. Lee, M. Pernot, M. Couade, E. Messas, P. Bruneval, A. Bel, A. A. Hagège, M. Fink, and M. Tanter, “Mapping myocardial fiber orientation using echocardiography-based shear wave imaging,” IEEE Trans. Med. Imaging 31, 554–562 (2012).

Leergaard, T. B.

T. B. Leergaard, N. S. White, A. de Crespigny, I. Bolstad, H. D’Arceuil, J. G. Bjaalie, and A. M. Dale, “Quantitative histological validation of diffusion MRI fiber orientation distributions in the rat brain,” PLoS ONE 5, 1–8 (2010).

Li, E.

Li, Q.

Lo, E. H.

Lu, H. H.

D. Qu, P. J. Chuang, S. Prateepchinda, P. S. Balasubramanian, X. Yao, S. B. Doty, C. P. Hendon, and H. H. Lu, “Micro-and ultrastructural characterization of age-related changes at the anterior cruciate ligament-to-bone insertion,” ACS Biomater. Sci. Eng. 3, 2806–2814 (2017).

Lujan, T. J.

C. J. Stender, E. Rust, P. T. Martin, E. E. Neumann, R. J. Brown, and T. J. Lujan, “Modeling the effect of collagen fibril alignment on ligament mechanical behavior,” Biomech. Model. Mechanobiol. 17, 543–557 (2018).

Lye, T. H.

T. H. Lye, K. P. Vincent, A. D. McCulloch, and C. P. Hendon, “Tissue-specific optical mapping models of swine atria informed by Optical Coherence Tomography,” Biophys. J. 114, 1477–1489 (2018).

Makita, S.

Mandeville, E. T.

Marcos, S.

Martin, P. T.

C. J. Stender, E. Rust, P. T. Martin, E. E. Neumann, R. J. Brown, and T. J. Lujan, “Modeling the effect of collagen fibril alignment on ligament mechanical behavior,” Biomech. Model. Mechanobiol. 17, 543–557 (2018).

Martinez-Enriquez, E.

Matcher, S. J.

N. Ugryumova, J. Jacobs, M. Bonesi, and S. J. Matcher, “Novel optical imaging technique to determine the 3-D orientation of collagen fibers in cartilage: variable-incidence angle polarization-sensitive optical coherence tomography,” Osteoarthr. Cartil. 17, 33–42 (2009).

McCulloch, A. D.

T. H. Lye, K. P. Vincent, A. D. McCulloch, and C. P. Hendon, “Tissue-specific optical mapping models of swine atria informed by Optical Coherence Tomography,” Biophys. J. 114, 1477–1489 (2018).

McLean, J.

McLean, J. P.

R. Zareian, M. E. Susilo, J. A. Paten, J. P. McLean, J. Hollmann, D. Karamichos, C. S. Messer, D. T. Tambe, N. Saeidi, J. D. Zieske, and J. W. Ruberti, “Human corneal fibroblast pattern evolution and matrix synthesis on mechanically biased substrates,” Tissue Eng. Part A 22, 1204–1217 (2016).

Mega, Y.

Mertzios, V. G.

E. Z. Psarakis, V. G. Mertzios, and G. P. Alexiou, “Design of two-dimensional zero phase FIR fan filters via the McClellan transform,” IEEE Trans. Circuits Syst. 37, 10–16 (1990).

Messas, E.

W. N. Lee, M. Pernot, M. Couade, E. Messas, P. Bruneval, A. Bel, A. A. Hagège, M. Fink, and M. Tanter, “Mapping myocardial fiber orientation using echocardiography-based shear wave imaging,” IEEE Trans. Med. Imaging 31, 554–562 (2012).

Messer, C. S.

R. Zareian, M. E. Susilo, J. A. Paten, J. P. McLean, J. Hollmann, D. Karamichos, C. S. Messer, D. T. Tambe, N. Saeidi, J. D. Zieske, and J. W. Ruberti, “Human corneal fibroblast pattern evolution and matrix synthesis on mechanically biased substrates,” Tissue Eng. Part A 22, 1204–1217 (2016).

Myers, K. M.

W. Yao, Y. Gan, K. M. Myers, J. Y. Vink, R. J. Wapner, and C. P. Hendon, “Collagen fiber orientation and dispersion in the upper cervix of non-pregnant and pregnant women,” PLoS ONE 11, 1–20 (2016).

K. M. Myers, C. P. Hendon, Y. Gan, W. Yao, K. Yoshida, M. Fernandez, J. Vink, and R. J. Wapner, “A continuous fiber distribution material model for human cervical tissue,” J. Biomech. 48, 1533–1540 (2015).

Y. Gan, W. Yao, K. M. Myers, J. Y. Vink, R. J. Wapner, and C. P. Hendon, “Analyzing three-dimensional ultrastructure of human cervical tissue using optical coherence tomography,” Biomed. Opt. Express 6, 1090–1108 (2015).

Nakamura, S.

W. Zhu and S. Nakamura, “An efficient approach for the synthesis of 2-D recursive fan filters using 1-D prototypes,” IEEE Trans. Signal Process. 44, 979–983 (1996).

Neumann, E. E.

C. J. Stender, E. Rust, P. T. Martin, E. E. Neumann, R. J. Brown, and T. J. Lujan, “Modeling the effect of collagen fibril alignment on ligament mechanical behavior,” Biomech. Model. Mechanobiol. 17, 543–557 (2018).

Ottani, V.

M. Franchi, V. Ottani, R. Stagni, and A. Ruggeri, “Tendon and ligament fibrillar crimps give rise to left-handed helices of collagen fibrils in both planar and helical crimps,” J. Anat. 216, 301–309 (2010).

M. Franchi, M. Fini, M. Quaranta, V. De Pasquale, M. Raspanti, G. Giavaresi, V. Ottani, and A. Ruggeri, “Crimp morphology in relaxed and stretched rat Achilles tendon,” J. Anat. 210, 1–7 (2007).

Palenstijn, W. J.

Paten, J. A.

R. Zareian, M. E. Susilo, J. A. Paten, J. P. McLean, J. Hollmann, D. Karamichos, C. S. Messer, D. T. Tambe, N. Saeidi, J. D. Zieske, and J. W. Ruberti, “Human corneal fibroblast pattern evolution and matrix synthesis on mechanically biased substrates,” Tissue Eng. Part A 22, 1204–1217 (2016).

Paul, D.

H. Yan, O. Carmichael, D. Paul, and J. Peng, “Estimating fiber orientation distribution from diffusion MRI with spherical needlets,” Med. Image Anal. 46, 57–72 (2018).

Pei, S.

S. Pei and J. Shyu, “Design of 2D FIR digital filters by McClellan transformation and least squares eigencontour mapping,” IEEE Trans. Circuits Syst. II Analog. Digit. Signal Process. 40, 546–555 (1993).

Peng, J.

H. Yan, O. Carmichael, D. Paul, and J. Peng, “Estimating fiber orientation distribution from diffusion MRI with spherical needlets,” Med. Image Anal. 46, 57–72 (2018).

Pernot, M.

W. N. Lee, M. Pernot, M. Couade, E. Messas, P. Bruneval, A. Bel, A. A. Hagège, M. Fink, and M. Tanter, “Mapping myocardial fiber orientation using echocardiography-based shear wave imaging,” IEEE Trans. Med. Imaging 31, 554–562 (2012).

Prateepchinda, S.

D. Qu, P. J. Chuang, S. Prateepchinda, P. S. Balasubramanian, X. Yao, S. B. Doty, C. P. Hendon, and H. H. Lu, “Micro-and ultrastructural characterization of age-related changes at the anterior cruciate ligament-to-bone insertion,” ACS Biomater. Sci. Eng. 3, 2806–2814 (2017).

Psarakis, E. Z.

E. Z. Psarakis, V. G. Mertzios, and G. P. Alexiou, “Design of two-dimensional zero phase FIR fan filters via the McClellan transform,” IEEE Trans. Circuits Syst. 37, 10–16 (1990).

Qu, D.

D. Qu, P. J. Chuang, S. Prateepchinda, P. S. Balasubramanian, X. Yao, S. B. Doty, C. P. Hendon, and H. H. Lu, “Micro-and ultrastructural characterization of age-related changes at the anterior cruciate ligament-to-bone insertion,” ACS Biomater. Sci. Eng. 3, 2806–2814 (2017).

Quaranta, M.

M. Franchi, M. Fini, M. Quaranta, V. De Pasquale, M. Raspanti, G. Giavaresi, V. Ottani, and A. Ruggeri, “Crimp morphology in relaxed and stretched rat Achilles tendon,” J. Anat. 210, 1–7 (2007).

Quinn, K. P.

K. P. Quinn and I. Georgakoudi, “Rapid quantification of pixel-wise fiber orientation data in micrographs,” J. Biomed. Opt. 18, 046003 (2013).

Radhakrishnan, H.

Raspanti, M.

M. Franchi, M. Fini, M. Quaranta, V. De Pasquale, M. Raspanti, G. Giavaresi, V. Ottani, and A. Ruggeri, “Crimp morphology in relaxed and stretched rat Achilles tendon,” J. Anat. 210, 1–7 (2007).

Ravanfar, M.

L. Azinfar, M. Ravanfar, Y. Wang, K. Zhang, D. Duan, and G. Yao, “High resolution imaging of the fibrous microstructure in bovine common carotid artery using optical polarization tractography,” J. Biophotonics 10, 231–241 (2017).

Restrepo, R.

Ripplinger, C. M.

C. P. Fleming, C. M. Ripplinger, B. Webb, I. R. Efimov, and A. M. Rollins, “Quantification of cardiac fiber orientation using optical coherence tomography,” J. Biomed. Opt. 13, 030505 (2008).

Robitaille, M.

Rollins, A. M.

C. M. Ambrosi, V. V. Fedorov, R. B. Schuessler, A. M. Rollins, and I. R. Efimov, “Quantification of fiber orientation in the canine atrial pacemaker complex using optical coherence tomography,” J. Biomed. Opt. 17, 071309 (2012).

C. P. Fleming, C. M. Ripplinger, B. Webb, I. R. Efimov, and A. M. Rollins, “Quantification of cardiac fiber orientation using optical coherence tomography,” J. Biomed. Opt. 13, 030505 (2008).

Ruberti, J.

Ruberti, J. W.

R. Zareian, M. E. Susilo, J. A. Paten, J. P. McLean, J. Hollmann, D. Karamichos, C. S. Messer, D. T. Tambe, N. Saeidi, J. D. Zieske, and J. W. Ruberti, “Human corneal fibroblast pattern evolution and matrix synthesis on mechanically biased substrates,” Tissue Eng. Part A 22, 1204–1217 (2016).

Ruggeri, A.

M. Franchi, V. Ottani, R. Stagni, and A. Ruggeri, “Tendon and ligament fibrillar crimps give rise to left-handed helices of collagen fibrils in both planar and helical crimps,” J. Anat. 216, 301–309 (2010).

M. Franchi, M. Fini, M. Quaranta, V. De Pasquale, M. Raspanti, G. Giavaresi, V. Ottani, and A. Ruggeri, “Crimp morphology in relaxed and stretched rat Achilles tendon,” J. Anat. 210, 1–7 (2007).

Rust, E.

C. J. Stender, E. Rust, P. T. Martin, E. E. Neumann, R. J. Brown, and T. J. Lujan, “Modeling the effect of collagen fibril alignment on ligament mechanical behavior,” Biomech. Model. Mechanobiol. 17, 543–557 (2018).

Saeidi, N.

R. Zareian, M. E. Susilo, J. A. Paten, J. P. McLean, J. Hollmann, D. Karamichos, C. S. Messer, D. T. Tambe, N. Saeidi, J. D. Zieske, and J. W. Ruberti, “Human corneal fibroblast pattern evolution and matrix synthesis on mechanically biased substrates,” Tissue Eng. Part A 22, 1204–1217 (2016).

Sakadžic, S.

Sampson, D. D.

Schilling, K. G.

K. G. Schilling, V. Janve, Y. Gao, I. Stepniewska, B. A. Landman, and A. W. Anderson, “Histological validation of diffusion MRI fiber orientation distributions and dispersion,” Neuroimage 165, 200–221 (2018).

Schuessler, R. B.

C. M. Ambrosi, V. V. Fedorov, R. B. Schuessler, A. M. Rollins, and I. R. Efimov, “Quantification of fiber orientation in the canine atrial pacemaker complex using optical coherence tomography,” J. Biomed. Opt. 17, 071309 (2012).

Seehra, G. P.

F. H. Silver, J. W. Freeman, and G. P. Seehra, “Collagen self-assembly and the development of tendon mechanical properties,” J. Biomech. 36, 1529–1553 (2003).

Shahanas, U. K.

T. Bindima, U. K. Shahanas, and E. Elias, “Low complexity fan filters using multiobjective artificial bee colony optimization aided McClellan Transformation for directional filtering,” IEEE Trans Circuits Syst II Express Briefs 65, 2057–2061 (2018).

Shyu, J.

S. Pei and J. Shyu, “Design of 2D FIR digital filters by McClellan transformation and least squares eigencontour mapping,” IEEE Trans. Circuits Syst. II Analog. Digit. Signal Process. 40, 546–555 (1993).

Sijbers, J.

Silver, F. H.

F. H. Silver, J. W. Freeman, and G. P. Seehra, “Collagen self-assembly and the development of tendon mechanical properties,” J. Biomech. 36, 1529–1553 (2003).

Sosnovik, D. E.

Srinivasan, V. J.

Stagni, R.

M. Franchi, V. Ottani, R. Stagni, and A. Ruggeri, “Tendon and ligament fibrillar crimps give rise to left-handed helices of collagen fibrils in both planar and helical crimps,” J. Anat. 216, 301–309 (2010).

Stender, C. J.

C. J. Stender, E. Rust, P. T. Martin, E. E. Neumann, R. J. Brown, and T. J. Lujan, “Modeling the effect of collagen fibril alignment on ligament mechanical behavior,” Biomech. Model. Mechanobiol. 17, 543–557 (2018).

Stepniewska, I.

K. G. Schilling, V. Janve, Y. Gao, I. Stepniewska, B. A. Landman, and A. W. Anderson, “Histological validation of diffusion MRI fiber orientation distributions and dispersion,” Neuroimage 165, 200–221 (2018).

Susilo, M. E.

R. Zareian, M. E. Susilo, J. A. Paten, J. P. McLean, J. Hollmann, D. Karamichos, C. S. Messer, D. T. Tambe, N. Saeidi, J. D. Zieske, and J. W. Ruberti, “Human corneal fibroblast pattern evolution and matrix synthesis on mechanically biased substrates,” Tissue Eng. Part A 22, 1204–1217 (2016).

Swingen, C.

M. Eggen, C. Swingen, and P. Iaizzo, “Analysis of fiber orientation in normal and failing human hearts using diffusion tensor MRI,” 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (IEEE, 2009), pp. 642–645.

Tambe, D. T.

R. Zareian, M. E. Susilo, J. A. Paten, J. P. McLean, J. Hollmann, D. Karamichos, C. S. Messer, D. T. Tambe, N. Saeidi, J. D. Zieske, and J. W. Ruberti, “Human corneal fibroblast pattern evolution and matrix synthesis on mechanically biased substrates,” Tissue Eng. Part A 22, 1204–1217 (2016).

Tanter, M.

W. N. Lee, M. Pernot, M. Couade, E. Messas, P. Bruneval, A. Bel, A. A. Hagège, M. Fink, and M. Tanter, “Mapping myocardial fiber orientation using echocardiography-based shear wave imaging,” IEEE Trans. Med. Imaging 31, 554–562 (2012).

Toussaint, K. C.

Ugryumova, N.

N. Ugryumova, J. Jacobs, M. Bonesi, and S. J. Matcher, “Novel optical imaging technique to determine the 3-D orientation of collagen fibers in cartilage: variable-incidence angle polarization-sensitive optical coherence tomography,” Osteoarthr. Cartil. 17, 33–42 (2009).

Uribe-Patarroyo, N.

van Aarle, W.

Villiger, M.

Vincent, K. P.

T. H. Lye, K. P. Vincent, A. D. McCulloch, and C. P. Hendon, “Tissue-specific optical mapping models of swine atria informed by Optical Coherence Tomography,” Biophys. J. 114, 1477–1489 (2018).

Vink, J.

K. M. Myers, C. P. Hendon, Y. Gan, W. Yao, K. Yoshida, M. Fernandez, J. Vink, and R. J. Wapner, “A continuous fiber distribution material model for human cervical tissue,” J. Biomech. 48, 1533–1540 (2015).

Vink, J. Y.

W. Yao, Y. Gan, K. M. Myers, J. Y. Vink, R. J. Wapner, and C. P. Hendon, “Collagen fiber orientation and dispersion in the upper cervix of non-pregnant and pregnant women,” PLoS ONE 11, 1–20 (2016).

Y. Gan, W. Yao, K. M. Myers, J. Y. Vink, R. J. Wapner, and C. P. Hendon, “Analyzing three-dimensional ultrastructure of human cervical tissue using optical coherence tomography,” Biomed. Opt. Express 6, 1090–1108 (2015).

Walther, J.

Wang, Y.

L. Azinfar, M. Ravanfar, Y. Wang, K. Zhang, D. Duan, and G. Yao, “High resolution imaging of the fibrous microstructure in bovine common carotid artery using optical polarization tractography,” J. Biophotonics 10, 231–241 (2017).

Y. Wang and G. Yao, “Optical tractography of the mouse heart using polarization-sensitive optical coherence tomography,” Biomed. Opt. Express 4, 2540–2545 (2013).

Wapner, R. J.

W. Yao, Y. Gan, K. M. Myers, J. Y. Vink, R. J. Wapner, and C. P. Hendon, “Collagen fiber orientation and dispersion in the upper cervix of non-pregnant and pregnant women,” PLoS ONE 11, 1–20 (2016).

K. M. Myers, C. P. Hendon, Y. Gan, W. Yao, K. Yoshida, M. Fernandez, J. Vink, and R. J. Wapner, “A continuous fiber distribution material model for human cervical tissue,” J. Biomech. 48, 1533–1540 (2015).

Y. Gan, W. Yao, K. M. Myers, J. Y. Vink, R. J. Wapner, and C. P. Hendon, “Analyzing three-dimensional ultrastructure of human cervical tissue using optical coherence tomography,” Biomed. Opt. Express 6, 1090–1108 (2015).

Webb, B.

C. P. Fleming, C. M. Ripplinger, B. Webb, I. R. Efimov, and A. M. Rollins, “Quantification of cardiac fiber orientation using optical coherence tomography,” J. Biomed. Opt. 13, 030505 (2008).

White, N. S.

T. B. Leergaard, N. S. White, A. de Crespigny, I. Bolstad, H. D’Arceuil, J. G. Bjaalie, and A. M. Dale, “Quantitative histological validation of diffusion MRI fiber orientation distributions in the rat brain,” PLoS ONE 5, 1–8 (2010).

Whittaker, P.

P. Whittaker and P. B. Canham, “Demonstration of quantitative fabric analysis of tendon collagen using two-dimensional polarized light microscopy,” Matrix 11, 56–62 (1991).

Yan, H.

H. Yan, O. Carmichael, D. Paul, and J. Peng, “Estimating fiber orientation distribution from diffusion MRI with spherical needlets,” Med. Image Anal. 46, 57–72 (2018).

Yao, G.

L. Azinfar, M. Ravanfar, Y. Wang, K. Zhang, D. Duan, and G. Yao, “High resolution imaging of the fibrous microstructure in bovine common carotid artery using optical polarization tractography,” J. Biophotonics 10, 231–241 (2017).

C. Fan and G. Yao, “Imaging myocardial fiber orientation using polarization sensitive optical coherence tomography,” Biomed. Opt. Express 4, 460–465 (2013).

Y. Wang and G. Yao, “Optical tractography of the mouse heart using polarization-sensitive optical coherence tomography,” Biomed. Opt. Express 4, 2540–2545 (2013).

Yao, W.

W. Yao, Y. Gan, K. M. Myers, J. Y. Vink, R. J. Wapner, and C. P. Hendon, “Collagen fiber orientation and dispersion in the upper cervix of non-pregnant and pregnant women,” PLoS ONE 11, 1–20 (2016).

K. M. Myers, C. P. Hendon, Y. Gan, W. Yao, K. Yoshida, M. Fernandez, J. Vink, and R. J. Wapner, “A continuous fiber distribution material model for human cervical tissue,” J. Biomech. 48, 1533–1540 (2015).

Y. Gan, W. Yao, K. M. Myers, J. Y. Vink, R. J. Wapner, and C. P. Hendon, “Analyzing three-dimensional ultrastructure of human cervical tissue using optical coherence tomography,” Biomed. Opt. Express 6, 1090–1108 (2015).

Yao, X.

D. Qu, P. J. Chuang, S. Prateepchinda, P. S. Balasubramanian, X. Yao, S. B. Doty, C. P. Hendon, and H. H. Lu, “Micro-and ultrastructural characterization of age-related changes at the anterior cruciate ligament-to-bone insertion,” ACS Biomater. Sci. Eng. 3, 2806–2814 (2017).

Yasuno, Y.

Yoshida, K.

K. M. Myers, C. P. Hendon, Y. Gan, W. Yao, K. Yoshida, M. Fernandez, J. Vink, and R. J. Wapner, “A continuous fiber distribution material model for human cervical tissue,” J. Biomech. 48, 1533–1540 (2015).

Zareian, R.

R. Zareian, M. E. Susilo, J. A. Paten, J. P. McLean, J. Hollmann, D. Karamichos, C. S. Messer, D. T. Tambe, N. Saeidi, J. D. Zieske, and J. W. Ruberti, “Human corneal fibroblast pattern evolution and matrix synthesis on mechanically biased substrates,” Tissue Eng. Part A 22, 1204–1217 (2016).

Y. Mega, M. Robitaille, R. Zareian, J. McLean, J. Ruberti, and C. DiMarzio, “Quantification of lamellar orientation in corneal collagen using second harmonic generation images,” Opt. Lett. 37, 3312–3314 (2012).

Zhang, K.

L. Azinfar, M. Ravanfar, Y. Wang, K. Zhang, D. Duan, and G. Yao, “High resolution imaging of the fibrous microstructure in bovine common carotid artery using optical polarization tractography,” J. Biophotonics 10, 231–241 (2017).

Zhu, W.

W. Zhu and S. Nakamura, “An efficient approach for the synthesis of 2-D recursive fan filters using 1-D prototypes,” IEEE Trans. Signal Process. 44, 979–983 (1996).

Zieske, J. D.

R. Zareian, M. E. Susilo, J. A. Paten, J. P. McLean, J. Hollmann, D. Karamichos, C. S. Messer, D. T. Tambe, N. Saeidi, J. D. Zieske, and J. W. Ruberti, “Human corneal fibroblast pattern evolution and matrix synthesis on mechanically biased substrates,” Tissue Eng. Part A 22, 1204–1217 (2016).

ACS Biomater. Sci. Eng. (1)

D. Qu, P. J. Chuang, S. Prateepchinda, P. S. Balasubramanian, X. Yao, S. B. Doty, C. P. Hendon, and H. H. Lu, “Micro-and ultrastructural characterization of age-related changes at the anterior cruciate ligament-to-bone insertion,” ACS Biomater. Sci. Eng. 3, 2806–2814 (2017).

Appl. Opt. (1)

Biomaterials (1)

C. T. Laurencin and J. W. Freeman, “Ligament tissue engineering: An evolutionary materials science approach,” Biomaterials 26, 7530–7536 (2005).

Biomech. Model. Mechanobiol. (1)

C. J. Stender, E. Rust, P. T. Martin, E. E. Neumann, R. J. Brown, and T. J. Lujan, “Modeling the effect of collagen fibril alignment on ligament mechanical behavior,” Biomech. Model. Mechanobiol. 17, 543–557 (2018).

Biomed. Opt. Express (8)

J. A. Germann, E. Martinez-Enriquez, and S. Marcos, “Quantization of collagen organization in the stroma with a new order coefficient,” Biomed. Opt. Express 9, 173–189 (2018).

Y. Gan, W. Yao, K. M. Myers, J. Y. Vink, R. J. Wapner, and C. P. Hendon, “Analyzing three-dimensional ultrastructure of human cervical tissue using optical coherence tomography,” Biomed. Opt. Express 6, 1090–1108 (2015).

Y. Gan and C. P. Fleming, “Extracting three-dimensional orientation and tractography of myofibers using optical coherence tomography,” Biomed. Opt. Express 4, 2150–2165 (2013).

E. Li, S. Makita, Y.-J. Hong, D. Kasaragod, and Y. Yasuno, “Three-dimensional multi-contrast imaging of in vivo human skin by Jones matrix optical coherence tomography,” Biomed. Opt. Express 8, 1290–1305 (2017).

J. Walther, Q. Li, M. Villiger, C. S. Farah, E. Koch, K. Karnowski, and D. D. Sampson, “Depth-resolved birefringence imaging of collagen fiber organization in the human oral mucosa in vivo,” Biomed. Opt. Express 10, 1942–1956 (2019).

C. Fan and G. Yao, “Imaging myocardial fiber orientation using polarization sensitive optical coherence tomography,” Biomed. Opt. Express 4, 460–465 (2013).

Y. Wang and G. Yao, “Optical tractography of the mouse heart using polarization-sensitive optical coherence tomography,” Biomed. Opt. Express 4, 2540–2545 (2013).

C. Cuartas-Vélez, R. Restrepo, B. E. Bouma, and N. Uribe-Patarroyo, “Volumetric non-local-means based speckle reduction for optical coherence tomography,” Biomed. Opt. Express 9, 3354–3372 (2018).

Biophys. J. (1)

T. H. Lye, K. P. Vincent, A. D. McCulloch, and C. P. Hendon, “Tissue-specific optical mapping models of swine atria informed by Optical Coherence Tomography,” Biophys. J. 114, 1477–1489 (2018).

IEEE Trans Circuits Syst II Express Briefs (1)

T. Bindima, U. K. Shahanas, and E. Elias, “Low complexity fan filters using multiobjective artificial bee colony optimization aided McClellan Transformation for directional filtering,” IEEE Trans Circuits Syst II Express Briefs 65, 2057–2061 (2018).

IEEE Trans. Circuits Syst. (1)

E. Z. Psarakis, V. G. Mertzios, and G. P. Alexiou, “Design of two-dimensional zero phase FIR fan filters via the McClellan transform,” IEEE Trans. Circuits Syst. 37, 10–16 (1990).

IEEE Trans. Circuits Syst. II Analog. Digit. Signal Process. (1)

S. Pei and J. Shyu, “Design of 2D FIR digital filters by McClellan transformation and least squares eigencontour mapping,” IEEE Trans. Circuits Syst. II Analog. Digit. Signal Process. 40, 546–555 (1993).

IEEE Trans. Image Process. (1)

K. Dabov, A. Foi, V. Katkovnik, and K. Egiazarian, “Image denoising by sparse 3-D transform-domain collaborative filtering,” IEEE Trans. Image Process. 16, 2080–2095 (2007).

IEEE Trans. Med. Imaging (1)

W. N. Lee, M. Pernot, M. Couade, E. Messas, P. Bruneval, A. Bel, A. A. Hagège, M. Fink, and M. Tanter, “Mapping myocardial fiber orientation using echocardiography-based shear wave imaging,” IEEE Trans. Med. Imaging 31, 554–562 (2012).

IEEE Trans. Signal Process. (1)

W. Zhu and S. Nakamura, “An efficient approach for the synthesis of 2-D recursive fan filters using 1-D prototypes,” IEEE Trans. Signal Process. 44, 979–983 (1996).

J. Anat. (2)

M. Franchi, M. Fini, M. Quaranta, V. De Pasquale, M. Raspanti, G. Giavaresi, V. Ottani, and A. Ruggeri, “Crimp morphology in relaxed and stretched rat Achilles tendon,” J. Anat. 210, 1–7 (2007).

M. Franchi, V. Ottani, R. Stagni, and A. Ruggeri, “Tendon and ligament fibrillar crimps give rise to left-handed helices of collagen fibrils in both planar and helical crimps,” J. Anat. 216, 301–309 (2010).

J. Biomech. (2)

F. H. Silver, J. W. Freeman, and G. P. Seehra, “Collagen self-assembly and the development of tendon mechanical properties,” J. Biomech. 36, 1529–1553 (2003).

K. M. Myers, C. P. Hendon, Y. Gan, W. Yao, K. Yoshida, M. Fernandez, J. Vink, and R. J. Wapner, “A continuous fiber distribution material model for human cervical tissue,” J. Biomech. 48, 1533–1540 (2015).

J. Biomed. Opt. (3)

K. P. Quinn and I. Georgakoudi, “Rapid quantification of pixel-wise fiber orientation data in micrographs,” J. Biomed. Opt. 18, 046003 (2013).

C. M. Ambrosi, V. V. Fedorov, R. B. Schuessler, A. M. Rollins, and I. R. Efimov, “Quantification of fiber orientation in the canine atrial pacemaker complex using optical coherence tomography,” J. Biomed. Opt. 17, 071309 (2012).

C. P. Fleming, C. M. Ripplinger, B. Webb, I. R. Efimov, and A. M. Rollins, “Quantification of cardiac fiber orientation using optical coherence tomography,” J. Biomed. Opt. 13, 030505 (2008).

J. Biophotonics (1)

L. Azinfar, M. Ravanfar, Y. Wang, K. Zhang, D. Duan, and G. Yao, “High resolution imaging of the fibrous microstructure in bovine common carotid artery using optical polarization tractography,” J. Biophotonics 10, 231–241 (2017).

Matrix (1)

P. Whittaker and P. B. Canham, “Demonstration of quantitative fabric analysis of tendon collagen using two-dimensional polarized light microscopy,” Matrix 11, 56–62 (1991).

Med. Image Anal. (1)

H. Yan, O. Carmichael, D. Paul, and J. Peng, “Estimating fiber orientation distribution from diffusion MRI with spherical needlets,” Med. Image Anal. 46, 57–72 (2018).

Neuroimage (1)

K. G. Schilling, V. Janve, Y. Gao, I. Stepniewska, B. A. Landman, and A. W. Anderson, “Histological validation of diffusion MRI fiber orientation distributions and dispersion,” Neuroimage 165, 200–221 (2018).

Opt. Express (2)

Opt. Lett. (2)

Osteoarthr. Cartil. (1)

N. Ugryumova, J. Jacobs, M. Bonesi, and S. J. Matcher, “Novel optical imaging technique to determine the 3-D orientation of collagen fibers in cartilage: variable-incidence angle polarization-sensitive optical coherence tomography,” Osteoarthr. Cartil. 17, 33–42 (2009).

PLoS ONE (2)

T. B. Leergaard, N. S. White, A. de Crespigny, I. Bolstad, H. D’Arceuil, J. G. Bjaalie, and A. M. Dale, “Quantitative histological validation of diffusion MRI fiber orientation distributions in the rat brain,” PLoS ONE 5, 1–8 (2010).

W. Yao, Y. Gan, K. M. Myers, J. Y. Vink, R. J. Wapner, and C. P. Hendon, “Collagen fiber orientation and dispersion in the upper cervix of non-pregnant and pregnant women,” PLoS ONE 11, 1–20 (2016).

Tissue Eng. Part A (1)

R. Zareian, M. E. Susilo, J. A. Paten, J. P. McLean, J. Hollmann, D. Karamichos, C. S. Messer, D. T. Tambe, N. Saeidi, J. D. Zieske, and J. W. Ruberti, “Human corneal fibroblast pattern evolution and matrix synthesis on mechanically biased substrates,” Tissue Eng. Part A 22, 1204–1217 (2016).

Other (1)

M. Eggen, C. Swingen, and P. Iaizzo, “Analysis of fiber orientation in normal and failing human hearts using diffusion tensor MRI,” 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro (IEEE, 2009), pp. 642–645.

Supplementary Material (2)

NameDescription
» Visualization 1       Fiber visualization in swine atria
» Visualization 2       fiber visualization in bovine ACL

Cited By

OSA participates in Crossref's Cited-By Linking service. Citing articles from OSA journals and other participating publishers are listed here.

Alert me when this article is cited.


Figures (6)

Fig. 1
Fig. 1 Flow diagram for fiber orientation quantification and visualization methods. The “Orientation Quantification” method analyzes an en-face OCT image’s spectrum to obtain a distribution of the angles of aligned fiber structures in the image. Peaks in the distribution correspond with the dominant fiber angles in the image. The peak angle from the orientation distribution is used to create the “Fiber Visualization”. A fan-filter spanning +/−10° from the dominant angle is used to filter the OCT image. The result is visualized by applying adaptive thresholding to the fan-filtered image and overlaying the resulting binary image back onto the original OCT image.
Fig. 2
Fig. 2 (a) Synthetic image for validation. (b) Fan-filter visualization of synthetic image. (c) Angular distribution of synthetic image. Dashed red lines mark the true orientation of the overlapping shapes (45° and 135°). (c) En-face OCT image of collagen fiber bundles in a bovine ACL sample. (d) Fiber visualization of the OCT image using a 17° to 37° fan-filter. (e) Angular distribution of the OCT image. Dashed red line marks the average fiber orientation determined by manual measurement (26.5°).
Fig. 3
Fig. 3 Fiber visualization results are compared using three different approaches. (a) OCT en-face image of collagen fibers in the ligament portion of the ACL. The collagen fibers are horizontally oriented, but have a crimped feature with vertical orientation. (b) Normalized distribution of fiber orientations in (a) using the Radon method, regional method, and pixel-wise algorithm. Fiber visualization results using the Radon/Fan-Filter method (c), the pixel-wise algorithm (d), and regional algorithm (e).
Fig. 4
Fig. 4 (a) OCT en-face mosaic of human cervix cross-section completely spanning the edges of the outer canal. (b) Collagen fiber visualization created through iterative application of the fan-filter visualization algorithm on 200 × 200 pixel patches and overlaying the result on the original mosaics. (c,d) OCT en-face mosaics of a swine left atria cross-section at two different depths separated by 100µm. (e,f) 3-D views of collagen fiber visualization. The visualization method is applied to a stack of en-face images to create a 3-D fiber model. Refer to Visualization 1 for a video representation of the 3-D fiber model. Color bars correspond to dominant fiber orientation in the en-face plane [0° –180°]. Scale bars represent 2 mm.
Fig. 5
Fig. 5 (a) Computational speed test results for the proposed method, its GPU implementation and two similar methods. Total algorithm computation time was measured for each method and image sizes ranging from 0.01 to 3.61 megapixels. The slowest method was the pixel-wise algorithm, followed by the region-based gradient method. (b) Comparison between Radon method alone, Radon with the fan-filter visualization, and their GPU implementations. The GPU implementation of the Radon method proved to be the fastest at 0.39 seconds for a 3.61 megapixel (1900 × 1900 pixel) image. This is a nearly three orders of magnitude speed-up from the pixel-wise method and an order of magnitude speed-up from the CPU implementation.
Fig. 6
Fig. 6 Noise sensitivity was evaluated by measuring the fiber orientation distribution and dominant fiber angle for a single image with artificially added speckle (multiplicative) noise. (a,b) OCT en-face swine left atrium with 0 and 0.7 noise variance, respectively. (c) Dominant angle was measured as a function of noise variance, calculated as the angle corresponding to the max value of the fiber orientation histogram for the regional method (d), pixel-wise method (e), and the radon method (f), was compared against hand-measured ground truth. Sensitivity to depth was analyzed for an ACL image volume spanning a tissue depth of 0.275 mm (g) to 1.775 mm (g). (i) Dominant fiber orientation detected by each algorithm as a function of depth. Fiber orientation histograms were obtained using the regional method (j), pixel-wise method (k), and the radon method (l). In (c) and (i), the dominant angle was manually measured for the images at noise and depth equal to 0, respectively, and is plotted as a visual reference.

Equations (2)

Equations on this page are rendered with MathJax. Learn more.

R { F ( α , s ) } = F ( x ( z ) , y ( z ) ) d z
f a n ( l , k ) = { 1 r = l cos θ + k sin θ 0 o t h e r w i s e