Abstract

We report a generic method for automatic segmentation of endoscopic optical coherence tomography (OCT) images. In this method, OCT images are first processed with L1-L0 norm minimization based de-noising and smoothing algorithms to increase the signal-to-noise ratio (SNR) and enhance the contrast between adjacent layers. The smoothed images are then formulated into cost graphs based on their vertical gradients. After that, tissue-layer segmentation is performed with the shortest path search algorithm. The efficacy and capability of this method are demonstrated by automatically and robustly identifying all five interested layers of guinea pig esophagus from in vivo endoscopic OCT images. Furthermore, thanks to the ultrahigh resolution, high SNR of endoscopic OCT images and the high segmentation accuracy, this method permits in vivo optical staining histology and facilitates quantitative analysis of tissue geometric properties, which can be very useful for studying tissue pathologies and potentially aiding clinical diagnosis in real time.

© 2017 Optical Society of America

Full Article  |  PDF Article
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  1. D. Huang, E. A. Swanson, C. P. Lin, J. S. Schuman, W. G. Stinson, W. Chang, M. R. Hee, T. Flotte, K. Gregory, C. A. Puliafito, and et, “Optical coherence tomography,” Science 254(5035), 1178–1181 (1991).
    [Crossref] [PubMed]
  2. G. J. Tearney, M. E. Brezinski, B. E. Bouma, S. A. Boppart, C. Pitris, J. F. Southern, and J. G. Fujimoto, “In vivo endoscopic optical biopsy with optical coherence tomography,” Science 276(5321), 2037–2039 (1997).
    [Crossref] [PubMed]
  3. D. C. Adler, C. Zhou, T.-H. Tsai, J. Schmitt, Q. Huang, H. Mashimo, and J. G. Fujimoto, “Three-dimensional endomicroscopy of the human colon using optical coherence tomography,” Opt. Express 17(2), 784–796 (2009).
    [Crossref] [PubMed]
  4. Y. Liang, W. Yuan, J. Mavadia-Shukla, and X. Li, “Optical clearing for luminal organ imaging with ultrahigh-resolution optical coherence tomography,” J. Biomed. Opt. 21(8), 081211 (2016).
    [Crossref] [PubMed]
  5. J. Xi, L. Huo, Y. Wu, M. J. Cobb, J. H. Hwang, and X. Li, “High-resolution OCT balloon imaging catheter with astigmatism correction,” Opt. Lett. 34(13), 1943–1945 (2009).
    [Crossref] [PubMed]
  6. J. Xi, A. Zhang, Z. Liu, W. Liang, L. Y. Lin, S. Yu, and X. Li, “Diffractive catheter for ultrahigh-resolution spectral-domain volumetric OCT imaging,” Opt. Lett. 39(7), 2016–2019 (2014).
    [Crossref] [PubMed]
  7. W. Yuan, J. Mavadia-Shukla, J. Xi, W. Liang, X. Yu, S. Yu, and X. Li, “Optimal operational conditions for supercontinuum-based ultrahigh-resolution endoscopic OCT imaging,” Opt. Lett. 41(2), 250–253 (2016).
    [Crossref] [PubMed]
  8. J. M. Wessel, F. K. Horn, R. P. Tornow, M. Schmid, C. Y. Mardin, F. E. Kruse, A. G. Juenemann, and R. Laemmer, “Longitudinal analysis of progression in glaucoma using spectral-domain optical coherence tomography,” Invest. Ophthalmol. Vis. Sci. 54(5), 3613–3620 (2013).
    [Crossref] [PubMed]
  9. Z. M. Dong, G. Wollstein, and J. S. Schuman, “Clinical utility of optical coherence tomography in glaucoma,” Invest. Ophthalmol. Vis. Sci. 57(9), OCT556 (2016).
    [Crossref] [PubMed]
  10. D. Cabrera Fernández, H. M. Salinas, and C. A. Puliafito, “Automated detection of retinal layer structures on optical coherence tomography images,” Opt. Express 13(25), 10200–10216 (2005).
    [Crossref] [PubMed]
  11. M. J. Cobb, Y. Chen, R. A. Underwood, M. L. Usui, J. Olerud, and X. Li, “Noninvasive assessment of cutaneous wound healing using ultrahigh-resolution optical coherence tomography,” J. Biomed. Opt. 11(6), 064002 (2006).
    [Crossref] [PubMed]
  12. A. M. Bagci, M. Shahidi, R. Ansari, M. Blair, N. P. Blair, and R. Zelkha, “Thickness profiles of retinal layers by optical coherence tomography image segmentation,” Am. J. Ophthalmol. 146(5), 679–687 (2008).
    [Crossref] [PubMed]
  13. R. J. Zawadzki, A. R. Fuller, D. F. Wiley, B. Hamann, S. S. Choi, and J. S. Werner, “Adaptation of a support vector machine algorithm for segmentation and visualization of retinal structures in volumetric optical coherence tomography data sets,” J. Biomed. Opt. 12(4), 041206 (2007).
    [Crossref] [PubMed]
  14. Y. Gan, D. Tsay, S. B. Amir, C. C. Marboe, and C. P. Hendon, “Automated classification of optical coherence tomography images of human atrial tissue,” J. Biomed. Opt. 21(10), 101407 (2016).
    [Crossref] [PubMed]
  15. T. Fabritius, S. Makita, M. Miura, R. Myllylä, and Y. Yasuno, “Automated segmentation of the macula by optical coherence tomography,” Opt. Express 17(18), 15659–15669 (2009).
    [Crossref] [PubMed]
  16. M. K. Garvin, M. D. Abràmoff, R. Kardon, S. R. Russell, X. Wu, and M. Sonka, “Intraretinal layer segmentation of macular optical coherence tomography images using optimal 3-D graph search,” IEEE Trans. Med. Imaging 27(10), 1495–1505 (2008).
    [Crossref] [PubMed]
  17. M. Haeker, M. Sonka, R. Kardon, V. A. Shah, X. Wu, and M. D. Abràmoff, “Automated segmentation of intraretinal layers from macular optical coherence tomography images,” in Medical Imaging, (International Society for Optics and Photonics, 2007), 651214.
  18. M. Mujat, R. Chan, B. Cense, B. Park, C. Joo, T. Akkin, T. Chen, and J. de Boer, “Retinal nerve fiber layer thickness map determined from optical coherence tomography images,” Opt. Express 13(23), 9480–9491 (2005).
    [Crossref] [PubMed]
  19. A. Mishra, A. Wong, K. Bizheva, and D. A. Clausi, “Intra-retinal layer segmentation in optical coherence tomography images,” Opt. Express 17(26), 23719–23728 (2009).
    [Crossref] [PubMed]
  20. Q. Yang, C. A. Reisman, K. Chan, R. Ramachandran, A. Raza, and D. C. Hood, “Automated segmentation of outer retinal layers in macular OCT images of patients with retinitis pigmentosa,” Biomed. Opt. Express 2(9), 2493–2503 (2011).
    [Crossref] [PubMed]
  21. S. J. Chiu, X. T. Li, P. Nicholas, C. A. Toth, J. A. Izatt, and S. Farsiu, “Automatic segmentation of seven retinal layers in SDOCT images congruent with expert manual segmentation,” Opt. Express 18(18), 19413–19428 (2010).
    [Crossref] [PubMed]
  22. S. J. Chiu, J. A. Izatt, R. V. O’Connell, K. P. Winter, C. A. Toth, and S. Farsiu, “Validated automatic segmentation of AMD pathology including drusen and geographic atrophy in SD-OCT images,” Invest. Ophthalmol. Vis. Sci. 53(1), 53–61 (2012).
    [Crossref] [PubMed]
  23. S. J. Chiu, M. J. Allingham, P. S. Mettu, S. W. Cousins, J. A. Izatt, and S. Farsiu, “Kernel regression based segmentation of optical coherence tomography images with diabetic macular edema,” Biomed. Opt. Express 6(4), 1172–1194 (2015).
    [Crossref] [PubMed]
  24. B. Keller, D. Cunefare, D. S. Grewal, T. H. Mahmoud, J. A. Izatt, and S. Farsiu, “Length-adaptive graph search for automatic segmentation of pathological features in optical coherence tomography images,” J. Biomed. Opt. 21(7), 076015 (2016).
    [Crossref] [PubMed]
  25. H. Yoo, D. Kang, A. J. Katz, G. Y. Lauwers, N. S. Nishioka, Y. Yagi, P. Tanpowpong, J. Namati, B. E. Bouma, and G. J. Tearney, “Reflectance confocal microscopy for the diagnosis of eosinophilic esophagitis: a pilot study conducted on biopsy specimens,” Gastrointest. Endosc. 74(5), 992–1000 (2011).
    [Crossref] [PubMed]
  26. P. R. Pfau, M. V. Sivak, A. Chak, M. Kinnard, R. C. Wong, G. A. Isenberg, J. A. Izatt, A. Rollins, and V. Westphal, “Criteria for the diagnosis of dysplasia by endoscopic optical coherence tomography,” Gastrointest. Endosc. 58(2), 196–202 (2003).
    [Crossref] [PubMed]
  27. M. J. Gora, J. S. Sauk, R. W. Carruth, K. A. Gallagher, M. J. Suter, N. S. Nishioka, L. E. Kava, M. Rosenberg, B. E. Bouma, and G. J. Tearney, “Tethered capsule endomicroscopy enables less invasive imaging of gastrointestinal tract microstructure,” Nat. Med. 19(2), 238–240 (2013).
    [Crossref] [PubMed]
  28. L. I. Rudin, S. Osher, and E. Fatemi, “Nonlinear total variation based noise removal algorithms,” Physica D 60(1-4), 259–268 (1992).
    [Crossref]
  29. L. Xu, C. Lu, Y. Xu, and J. Jia, “Image smoothing via L0 gradient minimization,” in ACM Transactions on Graphics (TOG), (ACM, 2011), 174.
  30. R. C. Gonzalez and R. E. Woods, “Digital Image Processing,” (Prentice Hall, 2002).
  31. L. A. Vese and S. J. Osher, “Modeling textures with total variation minimization and oscillating patterns in image processing,” J. Sci. Comput. 19(1/3), 553–572 (2003).
    [Crossref]
  32. E. DiBenedetto, Real Analysis (Springer Science & Business Media, 2012).
  33. S. Boyd and L. Vandenberghe, Convex Optimization (Cambridge University Press, 2004).
  34. A. Beck and M. Teboulle, “A fast iterative shrinkage-thresholding algorithm for linear inverse problems,” SIAM J. Imaging Sci. 2(1), 183–202 (2009).
    [Crossref]
  35. M. Sonka, V. Hlavac, and R. Boyle, Image Processing, Analysis, and Machine Vision (Cengage Learning, 2014).
  36. E. W. Dijkstra, “A note on two problems in connexion with graphs,” Numer. Math. 1(1), 269–271 (1959).
    [Crossref]
  37. R. Bellman, “On a routing problem,” Q. Appl. Math. 16(1), 87–90 (1958).
    [Crossref]
  38. L. R. Ford, Jr. and D. R. Fulkerson, Flows in Networks (Princeton University Press, 2015).
  39. Y. Boykov, O. Veksler, and R. Zabih, “Fast approximate energy minimization via graph cuts,” IEEE T. Pattern Anal. 23(11), 1222–1239 (2001).
    [Crossref]
  40. Z. Wang, D. Chamie, H. G. Bezerra, H. Yamamoto, J. Kanovsky, D. L. Wilson, M. A. Costa, and A. M. Rollins, “Volumetric quantification of fibrous caps using intravascular optical coherence tomography,” Biomed. Opt. Express 3(6), 1413–1426 (2012).
    [Crossref] [PubMed]
  41. L. Thrane, M. H. Frosz, T. M. Jørgensen, A. Tycho, H. T. Yura, and P. E. Andersen, “Extraction of optical scattering parameters and attenuation compensation in optical coherence tomography images of multilayered tissue structures,” Opt. Lett. 29(14), 1641–1643 (2004).
    [Crossref] [PubMed]
  42. Q. Yang, C. A. Reisman, Z. Wang, Y. Fukuma, M. Hangai, N. Yoshimura, A. Tomidokoro, M. Araie, A. S. Raza, D. C. Hood, and K. Chan, “Automated layer segmentation of macular OCT images using dual-scale gradient information,” Opt. Express 18(20), 21293–21307 (2010).
    [Crossref] [PubMed]
  43. Z. Liu, Y. Hu, X. Yu, J. Xi, X. Fan, C.-M. Tse, A. C. Myers, P. J. Pasricha, X. Li, and S. Yu, “Allergen challenge sensitizes TRPA1 in vagal sensory neurons and afferent C-fiber subtypes in guinea pig esophagus,” Am. J. Physiol. Gastrointest. Liver Physiol. 308(6), G482–G488 (2015).
    [Crossref] [PubMed]
  44. M. Baroni, P. Fortunato, and A. La Torre, “Towards quantitative analysis of retinal features in optical coherence tomography,” Med. Eng. Phys. 29(4), 432–441 (2007).
    [Crossref] [PubMed]
  45. Z. Liu, J. Xi, M. Tse, A. C. Myers, X. D. Li, P. J. Pasricha, and S. Yu, “Allergic inflammation-induced structural and functional changes in esophageal epithelium in a guinea pig model of eosinophilic esophagitis,” Gastroenterology 5(5), 92 (2014).
    [Crossref]

2016 (5)

Y. Liang, W. Yuan, J. Mavadia-Shukla, and X. Li, “Optical clearing for luminal organ imaging with ultrahigh-resolution optical coherence tomography,” J. Biomed. Opt. 21(8), 081211 (2016).
[Crossref] [PubMed]

W. Yuan, J. Mavadia-Shukla, J. Xi, W. Liang, X. Yu, S. Yu, and X. Li, “Optimal operational conditions for supercontinuum-based ultrahigh-resolution endoscopic OCT imaging,” Opt. Lett. 41(2), 250–253 (2016).
[Crossref] [PubMed]

Z. M. Dong, G. Wollstein, and J. S. Schuman, “Clinical utility of optical coherence tomography in glaucoma,” Invest. Ophthalmol. Vis. Sci. 57(9), OCT556 (2016).
[Crossref] [PubMed]

Y. Gan, D. Tsay, S. B. Amir, C. C. Marboe, and C. P. Hendon, “Automated classification of optical coherence tomography images of human atrial tissue,” J. Biomed. Opt. 21(10), 101407 (2016).
[Crossref] [PubMed]

B. Keller, D. Cunefare, D. S. Grewal, T. H. Mahmoud, J. A. Izatt, and S. Farsiu, “Length-adaptive graph search for automatic segmentation of pathological features in optical coherence tomography images,” J. Biomed. Opt. 21(7), 076015 (2016).
[Crossref] [PubMed]

2015 (2)

S. J. Chiu, M. J. Allingham, P. S. Mettu, S. W. Cousins, J. A. Izatt, and S. Farsiu, “Kernel regression based segmentation of optical coherence tomography images with diabetic macular edema,” Biomed. Opt. Express 6(4), 1172–1194 (2015).
[Crossref] [PubMed]

Z. Liu, Y. Hu, X. Yu, J. Xi, X. Fan, C.-M. Tse, A. C. Myers, P. J. Pasricha, X. Li, and S. Yu, “Allergen challenge sensitizes TRPA1 in vagal sensory neurons and afferent C-fiber subtypes in guinea pig esophagus,” Am. J. Physiol. Gastrointest. Liver Physiol. 308(6), G482–G488 (2015).
[Crossref] [PubMed]

2014 (2)

Z. Liu, J. Xi, M. Tse, A. C. Myers, X. D. Li, P. J. Pasricha, and S. Yu, “Allergic inflammation-induced structural and functional changes in esophageal epithelium in a guinea pig model of eosinophilic esophagitis,” Gastroenterology 5(5), 92 (2014).
[Crossref]

J. Xi, A. Zhang, Z. Liu, W. Liang, L. Y. Lin, S. Yu, and X. Li, “Diffractive catheter for ultrahigh-resolution spectral-domain volumetric OCT imaging,” Opt. Lett. 39(7), 2016–2019 (2014).
[Crossref] [PubMed]

2013 (2)

J. M. Wessel, F. K. Horn, R. P. Tornow, M. Schmid, C. Y. Mardin, F. E. Kruse, A. G. Juenemann, and R. Laemmer, “Longitudinal analysis of progression in glaucoma using spectral-domain optical coherence tomography,” Invest. Ophthalmol. Vis. Sci. 54(5), 3613–3620 (2013).
[Crossref] [PubMed]

M. J. Gora, J. S. Sauk, R. W. Carruth, K. A. Gallagher, M. J. Suter, N. S. Nishioka, L. E. Kava, M. Rosenberg, B. E. Bouma, and G. J. Tearney, “Tethered capsule endomicroscopy enables less invasive imaging of gastrointestinal tract microstructure,” Nat. Med. 19(2), 238–240 (2013).
[Crossref] [PubMed]

2012 (2)

Z. Wang, D. Chamie, H. G. Bezerra, H. Yamamoto, J. Kanovsky, D. L. Wilson, M. A. Costa, and A. M. Rollins, “Volumetric quantification of fibrous caps using intravascular optical coherence tomography,” Biomed. Opt. Express 3(6), 1413–1426 (2012).
[Crossref] [PubMed]

S. J. Chiu, J. A. Izatt, R. V. O’Connell, K. P. Winter, C. A. Toth, and S. Farsiu, “Validated automatic segmentation of AMD pathology including drusen and geographic atrophy in SD-OCT images,” Invest. Ophthalmol. Vis. Sci. 53(1), 53–61 (2012).
[Crossref] [PubMed]

2011 (2)

H. Yoo, D. Kang, A. J. Katz, G. Y. Lauwers, N. S. Nishioka, Y. Yagi, P. Tanpowpong, J. Namati, B. E. Bouma, and G. J. Tearney, “Reflectance confocal microscopy for the diagnosis of eosinophilic esophagitis: a pilot study conducted on biopsy specimens,” Gastrointest. Endosc. 74(5), 992–1000 (2011).
[Crossref] [PubMed]

Q. Yang, C. A. Reisman, K. Chan, R. Ramachandran, A. Raza, and D. C. Hood, “Automated segmentation of outer retinal layers in macular OCT images of patients with retinitis pigmentosa,” Biomed. Opt. Express 2(9), 2493–2503 (2011).
[Crossref] [PubMed]

2010 (2)

2009 (5)

2008 (2)

M. K. Garvin, M. D. Abràmoff, R. Kardon, S. R. Russell, X. Wu, and M. Sonka, “Intraretinal layer segmentation of macular optical coherence tomography images using optimal 3-D graph search,” IEEE Trans. Med. Imaging 27(10), 1495–1505 (2008).
[Crossref] [PubMed]

A. M. Bagci, M. Shahidi, R. Ansari, M. Blair, N. P. Blair, and R. Zelkha, “Thickness profiles of retinal layers by optical coherence tomography image segmentation,” Am. J. Ophthalmol. 146(5), 679–687 (2008).
[Crossref] [PubMed]

2007 (2)

R. J. Zawadzki, A. R. Fuller, D. F. Wiley, B. Hamann, S. S. Choi, and J. S. Werner, “Adaptation of a support vector machine algorithm for segmentation and visualization of retinal structures in volumetric optical coherence tomography data sets,” J. Biomed. Opt. 12(4), 041206 (2007).
[Crossref] [PubMed]

M. Baroni, P. Fortunato, and A. La Torre, “Towards quantitative analysis of retinal features in optical coherence tomography,” Med. Eng. Phys. 29(4), 432–441 (2007).
[Crossref] [PubMed]

2006 (1)

M. J. Cobb, Y. Chen, R. A. Underwood, M. L. Usui, J. Olerud, and X. Li, “Noninvasive assessment of cutaneous wound healing using ultrahigh-resolution optical coherence tomography,” J. Biomed. Opt. 11(6), 064002 (2006).
[Crossref] [PubMed]

2005 (2)

2004 (1)

2003 (2)

L. A. Vese and S. J. Osher, “Modeling textures with total variation minimization and oscillating patterns in image processing,” J. Sci. Comput. 19(1/3), 553–572 (2003).
[Crossref]

P. R. Pfau, M. V. Sivak, A. Chak, M. Kinnard, R. C. Wong, G. A. Isenberg, J. A. Izatt, A. Rollins, and V. Westphal, “Criteria for the diagnosis of dysplasia by endoscopic optical coherence tomography,” Gastrointest. Endosc. 58(2), 196–202 (2003).
[Crossref] [PubMed]

2001 (1)

Y. Boykov, O. Veksler, and R. Zabih, “Fast approximate energy minimization via graph cuts,” IEEE T. Pattern Anal. 23(11), 1222–1239 (2001).
[Crossref]

1997 (1)

G. J. Tearney, M. E. Brezinski, B. E. Bouma, S. A. Boppart, C. Pitris, J. F. Southern, and J. G. Fujimoto, “In vivo endoscopic optical biopsy with optical coherence tomography,” Science 276(5321), 2037–2039 (1997).
[Crossref] [PubMed]

1992 (1)

L. I. Rudin, S. Osher, and E. Fatemi, “Nonlinear total variation based noise removal algorithms,” Physica D 60(1-4), 259–268 (1992).
[Crossref]

1991 (1)

D. Huang, E. A. Swanson, C. P. Lin, J. S. Schuman, W. G. Stinson, W. Chang, M. R. Hee, T. Flotte, K. Gregory, C. A. Puliafito, and et, “Optical coherence tomography,” Science 254(5035), 1178–1181 (1991).
[Crossref] [PubMed]

1959 (1)

E. W. Dijkstra, “A note on two problems in connexion with graphs,” Numer. Math. 1(1), 269–271 (1959).
[Crossref]

1958 (1)

R. Bellman, “On a routing problem,” Q. Appl. Math. 16(1), 87–90 (1958).
[Crossref]

Abràmoff, M. D.

M. K. Garvin, M. D. Abràmoff, R. Kardon, S. R. Russell, X. Wu, and M. Sonka, “Intraretinal layer segmentation of macular optical coherence tomography images using optimal 3-D graph search,” IEEE Trans. Med. Imaging 27(10), 1495–1505 (2008).
[Crossref] [PubMed]

Adler, D. C.

Akkin, T.

Allingham, M. J.

Amir, S. B.

Y. Gan, D. Tsay, S. B. Amir, C. C. Marboe, and C. P. Hendon, “Automated classification of optical coherence tomography images of human atrial tissue,” J. Biomed. Opt. 21(10), 101407 (2016).
[Crossref] [PubMed]

Andersen, P. E.

Ansari, R.

A. M. Bagci, M. Shahidi, R. Ansari, M. Blair, N. P. Blair, and R. Zelkha, “Thickness profiles of retinal layers by optical coherence tomography image segmentation,” Am. J. Ophthalmol. 146(5), 679–687 (2008).
[Crossref] [PubMed]

Araie, M.

Bagci, A. M.

A. M. Bagci, M. Shahidi, R. Ansari, M. Blair, N. P. Blair, and R. Zelkha, “Thickness profiles of retinal layers by optical coherence tomography image segmentation,” Am. J. Ophthalmol. 146(5), 679–687 (2008).
[Crossref] [PubMed]

Baroni, M.

M. Baroni, P. Fortunato, and A. La Torre, “Towards quantitative analysis of retinal features in optical coherence tomography,” Med. Eng. Phys. 29(4), 432–441 (2007).
[Crossref] [PubMed]

Beck, A.

A. Beck and M. Teboulle, “A fast iterative shrinkage-thresholding algorithm for linear inverse problems,” SIAM J. Imaging Sci. 2(1), 183–202 (2009).
[Crossref]

Bellman, R.

R. Bellman, “On a routing problem,” Q. Appl. Math. 16(1), 87–90 (1958).
[Crossref]

Bezerra, H. G.

Bizheva, K.

Blair, M.

A. M. Bagci, M. Shahidi, R. Ansari, M. Blair, N. P. Blair, and R. Zelkha, “Thickness profiles of retinal layers by optical coherence tomography image segmentation,” Am. J. Ophthalmol. 146(5), 679–687 (2008).
[Crossref] [PubMed]

Blair, N. P.

A. M. Bagci, M. Shahidi, R. Ansari, M. Blair, N. P. Blair, and R. Zelkha, “Thickness profiles of retinal layers by optical coherence tomography image segmentation,” Am. J. Ophthalmol. 146(5), 679–687 (2008).
[Crossref] [PubMed]

Boppart, S. A.

G. J. Tearney, M. E. Brezinski, B. E. Bouma, S. A. Boppart, C. Pitris, J. F. Southern, and J. G. Fujimoto, “In vivo endoscopic optical biopsy with optical coherence tomography,” Science 276(5321), 2037–2039 (1997).
[Crossref] [PubMed]

Bouma, B. E.

M. J. Gora, J. S. Sauk, R. W. Carruth, K. A. Gallagher, M. J. Suter, N. S. Nishioka, L. E. Kava, M. Rosenberg, B. E. Bouma, and G. J. Tearney, “Tethered capsule endomicroscopy enables less invasive imaging of gastrointestinal tract microstructure,” Nat. Med. 19(2), 238–240 (2013).
[Crossref] [PubMed]

H. Yoo, D. Kang, A. J. Katz, G. Y. Lauwers, N. S. Nishioka, Y. Yagi, P. Tanpowpong, J. Namati, B. E. Bouma, and G. J. Tearney, “Reflectance confocal microscopy for the diagnosis of eosinophilic esophagitis: a pilot study conducted on biopsy specimens,” Gastrointest. Endosc. 74(5), 992–1000 (2011).
[Crossref] [PubMed]

G. J. Tearney, M. E. Brezinski, B. E. Bouma, S. A. Boppart, C. Pitris, J. F. Southern, and J. G. Fujimoto, “In vivo endoscopic optical biopsy with optical coherence tomography,” Science 276(5321), 2037–2039 (1997).
[Crossref] [PubMed]

Boykov, Y.

Y. Boykov, O. Veksler, and R. Zabih, “Fast approximate energy minimization via graph cuts,” IEEE T. Pattern Anal. 23(11), 1222–1239 (2001).
[Crossref]

Brezinski, M. E.

G. J. Tearney, M. E. Brezinski, B. E. Bouma, S. A. Boppart, C. Pitris, J. F. Southern, and J. G. Fujimoto, “In vivo endoscopic optical biopsy with optical coherence tomography,” Science 276(5321), 2037–2039 (1997).
[Crossref] [PubMed]

Cabrera Fernández, D.

Carruth, R. W.

M. J. Gora, J. S. Sauk, R. W. Carruth, K. A. Gallagher, M. J. Suter, N. S. Nishioka, L. E. Kava, M. Rosenberg, B. E. Bouma, and G. J. Tearney, “Tethered capsule endomicroscopy enables less invasive imaging of gastrointestinal tract microstructure,” Nat. Med. 19(2), 238–240 (2013).
[Crossref] [PubMed]

Cense, B.

Chak, A.

P. R. Pfau, M. V. Sivak, A. Chak, M. Kinnard, R. C. Wong, G. A. Isenberg, J. A. Izatt, A. Rollins, and V. Westphal, “Criteria for the diagnosis of dysplasia by endoscopic optical coherence tomography,” Gastrointest. Endosc. 58(2), 196–202 (2003).
[Crossref] [PubMed]

Chamie, D.

Chan, K.

Chan, R.

Chang, W.

D. Huang, E. A. Swanson, C. P. Lin, J. S. Schuman, W. G. Stinson, W. Chang, M. R. Hee, T. Flotte, K. Gregory, C. A. Puliafito, and et, “Optical coherence tomography,” Science 254(5035), 1178–1181 (1991).
[Crossref] [PubMed]

Chen, T.

Chen, Y.

M. J. Cobb, Y. Chen, R. A. Underwood, M. L. Usui, J. Olerud, and X. Li, “Noninvasive assessment of cutaneous wound healing using ultrahigh-resolution optical coherence tomography,” J. Biomed. Opt. 11(6), 064002 (2006).
[Crossref] [PubMed]

Chiu, S. J.

Choi, S. S.

R. J. Zawadzki, A. R. Fuller, D. F. Wiley, B. Hamann, S. S. Choi, and J. S. Werner, “Adaptation of a support vector machine algorithm for segmentation and visualization of retinal structures in volumetric optical coherence tomography data sets,” J. Biomed. Opt. 12(4), 041206 (2007).
[Crossref] [PubMed]

Clausi, D. A.

Cobb, M. J.

J. Xi, L. Huo, Y. Wu, M. J. Cobb, J. H. Hwang, and X. Li, “High-resolution OCT balloon imaging catheter with astigmatism correction,” Opt. Lett. 34(13), 1943–1945 (2009).
[Crossref] [PubMed]

M. J. Cobb, Y. Chen, R. A. Underwood, M. L. Usui, J. Olerud, and X. Li, “Noninvasive assessment of cutaneous wound healing using ultrahigh-resolution optical coherence tomography,” J. Biomed. Opt. 11(6), 064002 (2006).
[Crossref] [PubMed]

Costa, M. A.

Cousins, S. W.

Cunefare, D.

B. Keller, D. Cunefare, D. S. Grewal, T. H. Mahmoud, J. A. Izatt, and S. Farsiu, “Length-adaptive graph search for automatic segmentation of pathological features in optical coherence tomography images,” J. Biomed. Opt. 21(7), 076015 (2016).
[Crossref] [PubMed]

de Boer, J.

Dijkstra, E. W.

E. W. Dijkstra, “A note on two problems in connexion with graphs,” Numer. Math. 1(1), 269–271 (1959).
[Crossref]

Dong, Z. M.

Z. M. Dong, G. Wollstein, and J. S. Schuman, “Clinical utility of optical coherence tomography in glaucoma,” Invest. Ophthalmol. Vis. Sci. 57(9), OCT556 (2016).
[Crossref] [PubMed]

et,

D. Huang, E. A. Swanson, C. P. Lin, J. S. Schuman, W. G. Stinson, W. Chang, M. R. Hee, T. Flotte, K. Gregory, C. A. Puliafito, and et, “Optical coherence tomography,” Science 254(5035), 1178–1181 (1991).
[Crossref] [PubMed]

Fabritius, T.

Fan, X.

Z. Liu, Y. Hu, X. Yu, J. Xi, X. Fan, C.-M. Tse, A. C. Myers, P. J. Pasricha, X. Li, and S. Yu, “Allergen challenge sensitizes TRPA1 in vagal sensory neurons and afferent C-fiber subtypes in guinea pig esophagus,” Am. J. Physiol. Gastrointest. Liver Physiol. 308(6), G482–G488 (2015).
[Crossref] [PubMed]

Farsiu, S.

B. Keller, D. Cunefare, D. S. Grewal, T. H. Mahmoud, J. A. Izatt, and S. Farsiu, “Length-adaptive graph search for automatic segmentation of pathological features in optical coherence tomography images,” J. Biomed. Opt. 21(7), 076015 (2016).
[Crossref] [PubMed]

S. J. Chiu, M. J. Allingham, P. S. Mettu, S. W. Cousins, J. A. Izatt, and S. Farsiu, “Kernel regression based segmentation of optical coherence tomography images with diabetic macular edema,” Biomed. Opt. Express 6(4), 1172–1194 (2015).
[Crossref] [PubMed]

S. J. Chiu, J. A. Izatt, R. V. O’Connell, K. P. Winter, C. A. Toth, and S. Farsiu, “Validated automatic segmentation of AMD pathology including drusen and geographic atrophy in SD-OCT images,” Invest. Ophthalmol. Vis. Sci. 53(1), 53–61 (2012).
[Crossref] [PubMed]

S. J. Chiu, X. T. Li, P. Nicholas, C. A. Toth, J. A. Izatt, and S. Farsiu, “Automatic segmentation of seven retinal layers in SDOCT images congruent with expert manual segmentation,” Opt. Express 18(18), 19413–19428 (2010).
[Crossref] [PubMed]

Fatemi, E.

L. I. Rudin, S. Osher, and E. Fatemi, “Nonlinear total variation based noise removal algorithms,” Physica D 60(1-4), 259–268 (1992).
[Crossref]

Flotte, T.

D. Huang, E. A. Swanson, C. P. Lin, J. S. Schuman, W. G. Stinson, W. Chang, M. R. Hee, T. Flotte, K. Gregory, C. A. Puliafito, and et, “Optical coherence tomography,” Science 254(5035), 1178–1181 (1991).
[Crossref] [PubMed]

Fortunato, P.

M. Baroni, P. Fortunato, and A. La Torre, “Towards quantitative analysis of retinal features in optical coherence tomography,” Med. Eng. Phys. 29(4), 432–441 (2007).
[Crossref] [PubMed]

Frosz, M. H.

Fujimoto, J. G.

D. C. Adler, C. Zhou, T.-H. Tsai, J. Schmitt, Q. Huang, H. Mashimo, and J. G. Fujimoto, “Three-dimensional endomicroscopy of the human colon using optical coherence tomography,” Opt. Express 17(2), 784–796 (2009).
[Crossref] [PubMed]

G. J. Tearney, M. E. Brezinski, B. E. Bouma, S. A. Boppart, C. Pitris, J. F. Southern, and J. G. Fujimoto, “In vivo endoscopic optical biopsy with optical coherence tomography,” Science 276(5321), 2037–2039 (1997).
[Crossref] [PubMed]

Fukuma, Y.

Fuller, A. R.

R. J. Zawadzki, A. R. Fuller, D. F. Wiley, B. Hamann, S. S. Choi, and J. S. Werner, “Adaptation of a support vector machine algorithm for segmentation and visualization of retinal structures in volumetric optical coherence tomography data sets,” J. Biomed. Opt. 12(4), 041206 (2007).
[Crossref] [PubMed]

Gallagher, K. A.

M. J. Gora, J. S. Sauk, R. W. Carruth, K. A. Gallagher, M. J. Suter, N. S. Nishioka, L. E. Kava, M. Rosenberg, B. E. Bouma, and G. J. Tearney, “Tethered capsule endomicroscopy enables less invasive imaging of gastrointestinal tract microstructure,” Nat. Med. 19(2), 238–240 (2013).
[Crossref] [PubMed]

Gan, Y.

Y. Gan, D. Tsay, S. B. Amir, C. C. Marboe, and C. P. Hendon, “Automated classification of optical coherence tomography images of human atrial tissue,” J. Biomed. Opt. 21(10), 101407 (2016).
[Crossref] [PubMed]

Garvin, M. K.

M. K. Garvin, M. D. Abràmoff, R. Kardon, S. R. Russell, X. Wu, and M. Sonka, “Intraretinal layer segmentation of macular optical coherence tomography images using optimal 3-D graph search,” IEEE Trans. Med. Imaging 27(10), 1495–1505 (2008).
[Crossref] [PubMed]

Gora, M. J.

M. J. Gora, J. S. Sauk, R. W. Carruth, K. A. Gallagher, M. J. Suter, N. S. Nishioka, L. E. Kava, M. Rosenberg, B. E. Bouma, and G. J. Tearney, “Tethered capsule endomicroscopy enables less invasive imaging of gastrointestinal tract microstructure,” Nat. Med. 19(2), 238–240 (2013).
[Crossref] [PubMed]

Gregory, K.

D. Huang, E. A. Swanson, C. P. Lin, J. S. Schuman, W. G. Stinson, W. Chang, M. R. Hee, T. Flotte, K. Gregory, C. A. Puliafito, and et, “Optical coherence tomography,” Science 254(5035), 1178–1181 (1991).
[Crossref] [PubMed]

Grewal, D. S.

B. Keller, D. Cunefare, D. S. Grewal, T. H. Mahmoud, J. A. Izatt, and S. Farsiu, “Length-adaptive graph search for automatic segmentation of pathological features in optical coherence tomography images,” J. Biomed. Opt. 21(7), 076015 (2016).
[Crossref] [PubMed]

Hamann, B.

R. J. Zawadzki, A. R. Fuller, D. F. Wiley, B. Hamann, S. S. Choi, and J. S. Werner, “Adaptation of a support vector machine algorithm for segmentation and visualization of retinal structures in volumetric optical coherence tomography data sets,” J. Biomed. Opt. 12(4), 041206 (2007).
[Crossref] [PubMed]

Hangai, M.

Hee, M. R.

D. Huang, E. A. Swanson, C. P. Lin, J. S. Schuman, W. G. Stinson, W. Chang, M. R. Hee, T. Flotte, K. Gregory, C. A. Puliafito, and et, “Optical coherence tomography,” Science 254(5035), 1178–1181 (1991).
[Crossref] [PubMed]

Hendon, C. P.

Y. Gan, D. Tsay, S. B. Amir, C. C. Marboe, and C. P. Hendon, “Automated classification of optical coherence tomography images of human atrial tissue,” J. Biomed. Opt. 21(10), 101407 (2016).
[Crossref] [PubMed]

Hood, D. C.

Horn, F. K.

J. M. Wessel, F. K. Horn, R. P. Tornow, M. Schmid, C. Y. Mardin, F. E. Kruse, A. G. Juenemann, and R. Laemmer, “Longitudinal analysis of progression in glaucoma using spectral-domain optical coherence tomography,” Invest. Ophthalmol. Vis. Sci. 54(5), 3613–3620 (2013).
[Crossref] [PubMed]

Hu, Y.

Z. Liu, Y. Hu, X. Yu, J. Xi, X. Fan, C.-M. Tse, A. C. Myers, P. J. Pasricha, X. Li, and S. Yu, “Allergen challenge sensitizes TRPA1 in vagal sensory neurons and afferent C-fiber subtypes in guinea pig esophagus,” Am. J. Physiol. Gastrointest. Liver Physiol. 308(6), G482–G488 (2015).
[Crossref] [PubMed]

Huang, D.

D. Huang, E. A. Swanson, C. P. Lin, J. S. Schuman, W. G. Stinson, W. Chang, M. R. Hee, T. Flotte, K. Gregory, C. A. Puliafito, and et, “Optical coherence tomography,” Science 254(5035), 1178–1181 (1991).
[Crossref] [PubMed]

Huang, Q.

Huo, L.

Hwang, J. H.

Isenberg, G. A.

P. R. Pfau, M. V. Sivak, A. Chak, M. Kinnard, R. C. Wong, G. A. Isenberg, J. A. Izatt, A. Rollins, and V. Westphal, “Criteria for the diagnosis of dysplasia by endoscopic optical coherence tomography,” Gastrointest. Endosc. 58(2), 196–202 (2003).
[Crossref] [PubMed]

Izatt, J. A.

B. Keller, D. Cunefare, D. S. Grewal, T. H. Mahmoud, J. A. Izatt, and S. Farsiu, “Length-adaptive graph search for automatic segmentation of pathological features in optical coherence tomography images,” J. Biomed. Opt. 21(7), 076015 (2016).
[Crossref] [PubMed]

S. J. Chiu, M. J. Allingham, P. S. Mettu, S. W. Cousins, J. A. Izatt, and S. Farsiu, “Kernel regression based segmentation of optical coherence tomography images with diabetic macular edema,” Biomed. Opt. Express 6(4), 1172–1194 (2015).
[Crossref] [PubMed]

S. J. Chiu, J. A. Izatt, R. V. O’Connell, K. P. Winter, C. A. Toth, and S. Farsiu, “Validated automatic segmentation of AMD pathology including drusen and geographic atrophy in SD-OCT images,” Invest. Ophthalmol. Vis. Sci. 53(1), 53–61 (2012).
[Crossref] [PubMed]

S. J. Chiu, X. T. Li, P. Nicholas, C. A. Toth, J. A. Izatt, and S. Farsiu, “Automatic segmentation of seven retinal layers in SDOCT images congruent with expert manual segmentation,” Opt. Express 18(18), 19413–19428 (2010).
[Crossref] [PubMed]

P. R. Pfau, M. V. Sivak, A. Chak, M. Kinnard, R. C. Wong, G. A. Isenberg, J. A. Izatt, A. Rollins, and V. Westphal, “Criteria for the diagnosis of dysplasia by endoscopic optical coherence tomography,” Gastrointest. Endosc. 58(2), 196–202 (2003).
[Crossref] [PubMed]

Joo, C.

Jørgensen, T. M.

Juenemann, A. G.

J. M. Wessel, F. K. Horn, R. P. Tornow, M. Schmid, C. Y. Mardin, F. E. Kruse, A. G. Juenemann, and R. Laemmer, “Longitudinal analysis of progression in glaucoma using spectral-domain optical coherence tomography,” Invest. Ophthalmol. Vis. Sci. 54(5), 3613–3620 (2013).
[Crossref] [PubMed]

Kang, D.

H. Yoo, D. Kang, A. J. Katz, G. Y. Lauwers, N. S. Nishioka, Y. Yagi, P. Tanpowpong, J. Namati, B. E. Bouma, and G. J. Tearney, “Reflectance confocal microscopy for the diagnosis of eosinophilic esophagitis: a pilot study conducted on biopsy specimens,” Gastrointest. Endosc. 74(5), 992–1000 (2011).
[Crossref] [PubMed]

Kanovsky, J.

Kardon, R.

M. K. Garvin, M. D. Abràmoff, R. Kardon, S. R. Russell, X. Wu, and M. Sonka, “Intraretinal layer segmentation of macular optical coherence tomography images using optimal 3-D graph search,” IEEE Trans. Med. Imaging 27(10), 1495–1505 (2008).
[Crossref] [PubMed]

Katz, A. J.

H. Yoo, D. Kang, A. J. Katz, G. Y. Lauwers, N. S. Nishioka, Y. Yagi, P. Tanpowpong, J. Namati, B. E. Bouma, and G. J. Tearney, “Reflectance confocal microscopy for the diagnosis of eosinophilic esophagitis: a pilot study conducted on biopsy specimens,” Gastrointest. Endosc. 74(5), 992–1000 (2011).
[Crossref] [PubMed]

Kava, L. E.

M. J. Gora, J. S. Sauk, R. W. Carruth, K. A. Gallagher, M. J. Suter, N. S. Nishioka, L. E. Kava, M. Rosenberg, B. E. Bouma, and G. J. Tearney, “Tethered capsule endomicroscopy enables less invasive imaging of gastrointestinal tract microstructure,” Nat. Med. 19(2), 238–240 (2013).
[Crossref] [PubMed]

Keller, B.

B. Keller, D. Cunefare, D. S. Grewal, T. H. Mahmoud, J. A. Izatt, and S. Farsiu, “Length-adaptive graph search for automatic segmentation of pathological features in optical coherence tomography images,” J. Biomed. Opt. 21(7), 076015 (2016).
[Crossref] [PubMed]

Kinnard, M.

P. R. Pfau, M. V. Sivak, A. Chak, M. Kinnard, R. C. Wong, G. A. Isenberg, J. A. Izatt, A. Rollins, and V. Westphal, “Criteria for the diagnosis of dysplasia by endoscopic optical coherence tomography,” Gastrointest. Endosc. 58(2), 196–202 (2003).
[Crossref] [PubMed]

Kruse, F. E.

J. M. Wessel, F. K. Horn, R. P. Tornow, M. Schmid, C. Y. Mardin, F. E. Kruse, A. G. Juenemann, and R. Laemmer, “Longitudinal analysis of progression in glaucoma using spectral-domain optical coherence tomography,” Invest. Ophthalmol. Vis. Sci. 54(5), 3613–3620 (2013).
[Crossref] [PubMed]

La Torre, A.

M. Baroni, P. Fortunato, and A. La Torre, “Towards quantitative analysis of retinal features in optical coherence tomography,” Med. Eng. Phys. 29(4), 432–441 (2007).
[Crossref] [PubMed]

Laemmer, R.

J. M. Wessel, F. K. Horn, R. P. Tornow, M. Schmid, C. Y. Mardin, F. E. Kruse, A. G. Juenemann, and R. Laemmer, “Longitudinal analysis of progression in glaucoma using spectral-domain optical coherence tomography,” Invest. Ophthalmol. Vis. Sci. 54(5), 3613–3620 (2013).
[Crossref] [PubMed]

Lauwers, G. Y.

H. Yoo, D. Kang, A. J. Katz, G. Y. Lauwers, N. S. Nishioka, Y. Yagi, P. Tanpowpong, J. Namati, B. E. Bouma, and G. J. Tearney, “Reflectance confocal microscopy for the diagnosis of eosinophilic esophagitis: a pilot study conducted on biopsy specimens,” Gastrointest. Endosc. 74(5), 992–1000 (2011).
[Crossref] [PubMed]

Li, X.

W. Yuan, J. Mavadia-Shukla, J. Xi, W. Liang, X. Yu, S. Yu, and X. Li, “Optimal operational conditions for supercontinuum-based ultrahigh-resolution endoscopic OCT imaging,” Opt. Lett. 41(2), 250–253 (2016).
[Crossref] [PubMed]

Y. Liang, W. Yuan, J. Mavadia-Shukla, and X. Li, “Optical clearing for luminal organ imaging with ultrahigh-resolution optical coherence tomography,” J. Biomed. Opt. 21(8), 081211 (2016).
[Crossref] [PubMed]

Z. Liu, Y. Hu, X. Yu, J. Xi, X. Fan, C.-M. Tse, A. C. Myers, P. J. Pasricha, X. Li, and S. Yu, “Allergen challenge sensitizes TRPA1 in vagal sensory neurons and afferent C-fiber subtypes in guinea pig esophagus,” Am. J. Physiol. Gastrointest. Liver Physiol. 308(6), G482–G488 (2015).
[Crossref] [PubMed]

J. Xi, A. Zhang, Z. Liu, W. Liang, L. Y. Lin, S. Yu, and X. Li, “Diffractive catheter for ultrahigh-resolution spectral-domain volumetric OCT imaging,” Opt. Lett. 39(7), 2016–2019 (2014).
[Crossref] [PubMed]

J. Xi, L. Huo, Y. Wu, M. J. Cobb, J. H. Hwang, and X. Li, “High-resolution OCT balloon imaging catheter with astigmatism correction,” Opt. Lett. 34(13), 1943–1945 (2009).
[Crossref] [PubMed]

M. J. Cobb, Y. Chen, R. A. Underwood, M. L. Usui, J. Olerud, and X. Li, “Noninvasive assessment of cutaneous wound healing using ultrahigh-resolution optical coherence tomography,” J. Biomed. Opt. 11(6), 064002 (2006).
[Crossref] [PubMed]

Li, X. D.

Z. Liu, J. Xi, M. Tse, A. C. Myers, X. D. Li, P. J. Pasricha, and S. Yu, “Allergic inflammation-induced structural and functional changes in esophageal epithelium in a guinea pig model of eosinophilic esophagitis,” Gastroenterology 5(5), 92 (2014).
[Crossref]

Li, X. T.

Liang, W.

Liang, Y.

Y. Liang, W. Yuan, J. Mavadia-Shukla, and X. Li, “Optical clearing for luminal organ imaging with ultrahigh-resolution optical coherence tomography,” J. Biomed. Opt. 21(8), 081211 (2016).
[Crossref] [PubMed]

Lin, C. P.

D. Huang, E. A. Swanson, C. P. Lin, J. S. Schuman, W. G. Stinson, W. Chang, M. R. Hee, T. Flotte, K. Gregory, C. A. Puliafito, and et, “Optical coherence tomography,” Science 254(5035), 1178–1181 (1991).
[Crossref] [PubMed]

Lin, L. Y.

Liu, Z.

Z. Liu, Y. Hu, X. Yu, J. Xi, X. Fan, C.-M. Tse, A. C. Myers, P. J. Pasricha, X. Li, and S. Yu, “Allergen challenge sensitizes TRPA1 in vagal sensory neurons and afferent C-fiber subtypes in guinea pig esophagus,” Am. J. Physiol. Gastrointest. Liver Physiol. 308(6), G482–G488 (2015).
[Crossref] [PubMed]

Z. Liu, J. Xi, M. Tse, A. C. Myers, X. D. Li, P. J. Pasricha, and S. Yu, “Allergic inflammation-induced structural and functional changes in esophageal epithelium in a guinea pig model of eosinophilic esophagitis,” Gastroenterology 5(5), 92 (2014).
[Crossref]

J. Xi, A. Zhang, Z. Liu, W. Liang, L. Y. Lin, S. Yu, and X. Li, “Diffractive catheter for ultrahigh-resolution spectral-domain volumetric OCT imaging,” Opt. Lett. 39(7), 2016–2019 (2014).
[Crossref] [PubMed]

Mahmoud, T. H.

B. Keller, D. Cunefare, D. S. Grewal, T. H. Mahmoud, J. A. Izatt, and S. Farsiu, “Length-adaptive graph search for automatic segmentation of pathological features in optical coherence tomography images,” J. Biomed. Opt. 21(7), 076015 (2016).
[Crossref] [PubMed]

Makita, S.

Marboe, C. C.

Y. Gan, D. Tsay, S. B. Amir, C. C. Marboe, and C. P. Hendon, “Automated classification of optical coherence tomography images of human atrial tissue,” J. Biomed. Opt. 21(10), 101407 (2016).
[Crossref] [PubMed]

Mardin, C. Y.

J. M. Wessel, F. K. Horn, R. P. Tornow, M. Schmid, C. Y. Mardin, F. E. Kruse, A. G. Juenemann, and R. Laemmer, “Longitudinal analysis of progression in glaucoma using spectral-domain optical coherence tomography,” Invest. Ophthalmol. Vis. Sci. 54(5), 3613–3620 (2013).
[Crossref] [PubMed]

Mashimo, H.

Mavadia-Shukla, J.

Y. Liang, W. Yuan, J. Mavadia-Shukla, and X. Li, “Optical clearing for luminal organ imaging with ultrahigh-resolution optical coherence tomography,” J. Biomed. Opt. 21(8), 081211 (2016).
[Crossref] [PubMed]

W. Yuan, J. Mavadia-Shukla, J. Xi, W. Liang, X. Yu, S. Yu, and X. Li, “Optimal operational conditions for supercontinuum-based ultrahigh-resolution endoscopic OCT imaging,” Opt. Lett. 41(2), 250–253 (2016).
[Crossref] [PubMed]

Mettu, P. S.

Mishra, A.

Miura, M.

Mujat, M.

Myers, A. C.

Z. Liu, Y. Hu, X. Yu, J. Xi, X. Fan, C.-M. Tse, A. C. Myers, P. J. Pasricha, X. Li, and S. Yu, “Allergen challenge sensitizes TRPA1 in vagal sensory neurons and afferent C-fiber subtypes in guinea pig esophagus,” Am. J. Physiol. Gastrointest. Liver Physiol. 308(6), G482–G488 (2015).
[Crossref] [PubMed]

Z. Liu, J. Xi, M. Tse, A. C. Myers, X. D. Li, P. J. Pasricha, and S. Yu, “Allergic inflammation-induced structural and functional changes in esophageal epithelium in a guinea pig model of eosinophilic esophagitis,” Gastroenterology 5(5), 92 (2014).
[Crossref]

Myllylä, R.

Namati, J.

H. Yoo, D. Kang, A. J. Katz, G. Y. Lauwers, N. S. Nishioka, Y. Yagi, P. Tanpowpong, J. Namati, B. E. Bouma, and G. J. Tearney, “Reflectance confocal microscopy for the diagnosis of eosinophilic esophagitis: a pilot study conducted on biopsy specimens,” Gastrointest. Endosc. 74(5), 992–1000 (2011).
[Crossref] [PubMed]

Nicholas, P.

Nishioka, N. S.

M. J. Gora, J. S. Sauk, R. W. Carruth, K. A. Gallagher, M. J. Suter, N. S. Nishioka, L. E. Kava, M. Rosenberg, B. E. Bouma, and G. J. Tearney, “Tethered capsule endomicroscopy enables less invasive imaging of gastrointestinal tract microstructure,” Nat. Med. 19(2), 238–240 (2013).
[Crossref] [PubMed]

H. Yoo, D. Kang, A. J. Katz, G. Y. Lauwers, N. S. Nishioka, Y. Yagi, P. Tanpowpong, J. Namati, B. E. Bouma, and G. J. Tearney, “Reflectance confocal microscopy for the diagnosis of eosinophilic esophagitis: a pilot study conducted on biopsy specimens,” Gastrointest. Endosc. 74(5), 992–1000 (2011).
[Crossref] [PubMed]

O’Connell, R. V.

S. J. Chiu, J. A. Izatt, R. V. O’Connell, K. P. Winter, C. A. Toth, and S. Farsiu, “Validated automatic segmentation of AMD pathology including drusen and geographic atrophy in SD-OCT images,” Invest. Ophthalmol. Vis. Sci. 53(1), 53–61 (2012).
[Crossref] [PubMed]

Olerud, J.

M. J. Cobb, Y. Chen, R. A. Underwood, M. L. Usui, J. Olerud, and X. Li, “Noninvasive assessment of cutaneous wound healing using ultrahigh-resolution optical coherence tomography,” J. Biomed. Opt. 11(6), 064002 (2006).
[Crossref] [PubMed]

Osher, S.

L. I. Rudin, S. Osher, and E. Fatemi, “Nonlinear total variation based noise removal algorithms,” Physica D 60(1-4), 259–268 (1992).
[Crossref]

Osher, S. J.

L. A. Vese and S. J. Osher, “Modeling textures with total variation minimization and oscillating patterns in image processing,” J. Sci. Comput. 19(1/3), 553–572 (2003).
[Crossref]

Park, B.

Pasricha, P. J.

Z. Liu, Y. Hu, X. Yu, J. Xi, X. Fan, C.-M. Tse, A. C. Myers, P. J. Pasricha, X. Li, and S. Yu, “Allergen challenge sensitizes TRPA1 in vagal sensory neurons and afferent C-fiber subtypes in guinea pig esophagus,” Am. J. Physiol. Gastrointest. Liver Physiol. 308(6), G482–G488 (2015).
[Crossref] [PubMed]

Z. Liu, J. Xi, M. Tse, A. C. Myers, X. D. Li, P. J. Pasricha, and S. Yu, “Allergic inflammation-induced structural and functional changes in esophageal epithelium in a guinea pig model of eosinophilic esophagitis,” Gastroenterology 5(5), 92 (2014).
[Crossref]

Pfau, P. R.

P. R. Pfau, M. V. Sivak, A. Chak, M. Kinnard, R. C. Wong, G. A. Isenberg, J. A. Izatt, A. Rollins, and V. Westphal, “Criteria for the diagnosis of dysplasia by endoscopic optical coherence tomography,” Gastrointest. Endosc. 58(2), 196–202 (2003).
[Crossref] [PubMed]

Pitris, C.

G. J. Tearney, M. E. Brezinski, B. E. Bouma, S. A. Boppart, C. Pitris, J. F. Southern, and J. G. Fujimoto, “In vivo endoscopic optical biopsy with optical coherence tomography,” Science 276(5321), 2037–2039 (1997).
[Crossref] [PubMed]

Puliafito, C. A.

D. Cabrera Fernández, H. M. Salinas, and C. A. Puliafito, “Automated detection of retinal layer structures on optical coherence tomography images,” Opt. Express 13(25), 10200–10216 (2005).
[Crossref] [PubMed]

D. Huang, E. A. Swanson, C. P. Lin, J. S. Schuman, W. G. Stinson, W. Chang, M. R. Hee, T. Flotte, K. Gregory, C. A. Puliafito, and et, “Optical coherence tomography,” Science 254(5035), 1178–1181 (1991).
[Crossref] [PubMed]

Ramachandran, R.

Raza, A.

Raza, A. S.

Reisman, C. A.

Rollins, A.

P. R. Pfau, M. V. Sivak, A. Chak, M. Kinnard, R. C. Wong, G. A. Isenberg, J. A. Izatt, A. Rollins, and V. Westphal, “Criteria for the diagnosis of dysplasia by endoscopic optical coherence tomography,” Gastrointest. Endosc. 58(2), 196–202 (2003).
[Crossref] [PubMed]

Rollins, A. M.

Rosenberg, M.

M. J. Gora, J. S. Sauk, R. W. Carruth, K. A. Gallagher, M. J. Suter, N. S. Nishioka, L. E. Kava, M. Rosenberg, B. E. Bouma, and G. J. Tearney, “Tethered capsule endomicroscopy enables less invasive imaging of gastrointestinal tract microstructure,” Nat. Med. 19(2), 238–240 (2013).
[Crossref] [PubMed]

Rudin, L. I.

L. I. Rudin, S. Osher, and E. Fatemi, “Nonlinear total variation based noise removal algorithms,” Physica D 60(1-4), 259–268 (1992).
[Crossref]

Russell, S. R.

M. K. Garvin, M. D. Abràmoff, R. Kardon, S. R. Russell, X. Wu, and M. Sonka, “Intraretinal layer segmentation of macular optical coherence tomography images using optimal 3-D graph search,” IEEE Trans. Med. Imaging 27(10), 1495–1505 (2008).
[Crossref] [PubMed]

Salinas, H. M.

Sauk, J. S.

M. J. Gora, J. S. Sauk, R. W. Carruth, K. A. Gallagher, M. J. Suter, N. S. Nishioka, L. E. Kava, M. Rosenberg, B. E. Bouma, and G. J. Tearney, “Tethered capsule endomicroscopy enables less invasive imaging of gastrointestinal tract microstructure,” Nat. Med. 19(2), 238–240 (2013).
[Crossref] [PubMed]

Schmid, M.

J. M. Wessel, F. K. Horn, R. P. Tornow, M. Schmid, C. Y. Mardin, F. E. Kruse, A. G. Juenemann, and R. Laemmer, “Longitudinal analysis of progression in glaucoma using spectral-domain optical coherence tomography,” Invest. Ophthalmol. Vis. Sci. 54(5), 3613–3620 (2013).
[Crossref] [PubMed]

Schmitt, J.

Schuman, J. S.

Z. M. Dong, G. Wollstein, and J. S. Schuman, “Clinical utility of optical coherence tomography in glaucoma,” Invest. Ophthalmol. Vis. Sci. 57(9), OCT556 (2016).
[Crossref] [PubMed]

D. Huang, E. A. Swanson, C. P. Lin, J. S. Schuman, W. G. Stinson, W. Chang, M. R. Hee, T. Flotte, K. Gregory, C. A. Puliafito, and et, “Optical coherence tomography,” Science 254(5035), 1178–1181 (1991).
[Crossref] [PubMed]

Shahidi, M.

A. M. Bagci, M. Shahidi, R. Ansari, M. Blair, N. P. Blair, and R. Zelkha, “Thickness profiles of retinal layers by optical coherence tomography image segmentation,” Am. J. Ophthalmol. 146(5), 679–687 (2008).
[Crossref] [PubMed]

Sivak, M. V.

P. R. Pfau, M. V. Sivak, A. Chak, M. Kinnard, R. C. Wong, G. A. Isenberg, J. A. Izatt, A. Rollins, and V. Westphal, “Criteria for the diagnosis of dysplasia by endoscopic optical coherence tomography,” Gastrointest. Endosc. 58(2), 196–202 (2003).
[Crossref] [PubMed]

Sonka, M.

M. K. Garvin, M. D. Abràmoff, R. Kardon, S. R. Russell, X. Wu, and M. Sonka, “Intraretinal layer segmentation of macular optical coherence tomography images using optimal 3-D graph search,” IEEE Trans. Med. Imaging 27(10), 1495–1505 (2008).
[Crossref] [PubMed]

Southern, J. F.

G. J. Tearney, M. E. Brezinski, B. E. Bouma, S. A. Boppart, C. Pitris, J. F. Southern, and J. G. Fujimoto, “In vivo endoscopic optical biopsy with optical coherence tomography,” Science 276(5321), 2037–2039 (1997).
[Crossref] [PubMed]

Stinson, W. G.

D. Huang, E. A. Swanson, C. P. Lin, J. S. Schuman, W. G. Stinson, W. Chang, M. R. Hee, T. Flotte, K. Gregory, C. A. Puliafito, and et, “Optical coherence tomography,” Science 254(5035), 1178–1181 (1991).
[Crossref] [PubMed]

Suter, M. J.

M. J. Gora, J. S. Sauk, R. W. Carruth, K. A. Gallagher, M. J. Suter, N. S. Nishioka, L. E. Kava, M. Rosenberg, B. E. Bouma, and G. J. Tearney, “Tethered capsule endomicroscopy enables less invasive imaging of gastrointestinal tract microstructure,” Nat. Med. 19(2), 238–240 (2013).
[Crossref] [PubMed]

Swanson, E. A.

D. Huang, E. A. Swanson, C. P. Lin, J. S. Schuman, W. G. Stinson, W. Chang, M. R. Hee, T. Flotte, K. Gregory, C. A. Puliafito, and et, “Optical coherence tomography,” Science 254(5035), 1178–1181 (1991).
[Crossref] [PubMed]

Tanpowpong, P.

H. Yoo, D. Kang, A. J. Katz, G. Y. Lauwers, N. S. Nishioka, Y. Yagi, P. Tanpowpong, J. Namati, B. E. Bouma, and G. J. Tearney, “Reflectance confocal microscopy for the diagnosis of eosinophilic esophagitis: a pilot study conducted on biopsy specimens,” Gastrointest. Endosc. 74(5), 992–1000 (2011).
[Crossref] [PubMed]

Tearney, G. J.

M. J. Gora, J. S. Sauk, R. W. Carruth, K. A. Gallagher, M. J. Suter, N. S. Nishioka, L. E. Kava, M. Rosenberg, B. E. Bouma, and G. J. Tearney, “Tethered capsule endomicroscopy enables less invasive imaging of gastrointestinal tract microstructure,” Nat. Med. 19(2), 238–240 (2013).
[Crossref] [PubMed]

H. Yoo, D. Kang, A. J. Katz, G. Y. Lauwers, N. S. Nishioka, Y. Yagi, P. Tanpowpong, J. Namati, B. E. Bouma, and G. J. Tearney, “Reflectance confocal microscopy for the diagnosis of eosinophilic esophagitis: a pilot study conducted on biopsy specimens,” Gastrointest. Endosc. 74(5), 992–1000 (2011).
[Crossref] [PubMed]

G. J. Tearney, M. E. Brezinski, B. E. Bouma, S. A. Boppart, C. Pitris, J. F. Southern, and J. G. Fujimoto, “In vivo endoscopic optical biopsy with optical coherence tomography,” Science 276(5321), 2037–2039 (1997).
[Crossref] [PubMed]

Teboulle, M.

A. Beck and M. Teboulle, “A fast iterative shrinkage-thresholding algorithm for linear inverse problems,” SIAM J. Imaging Sci. 2(1), 183–202 (2009).
[Crossref]

Thrane, L.

Tomidokoro, A.

Tornow, R. P.

J. M. Wessel, F. K. Horn, R. P. Tornow, M. Schmid, C. Y. Mardin, F. E. Kruse, A. G. Juenemann, and R. Laemmer, “Longitudinal analysis of progression in glaucoma using spectral-domain optical coherence tomography,” Invest. Ophthalmol. Vis. Sci. 54(5), 3613–3620 (2013).
[Crossref] [PubMed]

Toth, C. A.

S. J. Chiu, J. A. Izatt, R. V. O’Connell, K. P. Winter, C. A. Toth, and S. Farsiu, “Validated automatic segmentation of AMD pathology including drusen and geographic atrophy in SD-OCT images,” Invest. Ophthalmol. Vis. Sci. 53(1), 53–61 (2012).
[Crossref] [PubMed]

S. J. Chiu, X. T. Li, P. Nicholas, C. A. Toth, J. A. Izatt, and S. Farsiu, “Automatic segmentation of seven retinal layers in SDOCT images congruent with expert manual segmentation,” Opt. Express 18(18), 19413–19428 (2010).
[Crossref] [PubMed]

Tsai, T.-H.

Tsay, D.

Y. Gan, D. Tsay, S. B. Amir, C. C. Marboe, and C. P. Hendon, “Automated classification of optical coherence tomography images of human atrial tissue,” J. Biomed. Opt. 21(10), 101407 (2016).
[Crossref] [PubMed]

Tse, C.-M.

Z. Liu, Y. Hu, X. Yu, J. Xi, X. Fan, C.-M. Tse, A. C. Myers, P. J. Pasricha, X. Li, and S. Yu, “Allergen challenge sensitizes TRPA1 in vagal sensory neurons and afferent C-fiber subtypes in guinea pig esophagus,” Am. J. Physiol. Gastrointest. Liver Physiol. 308(6), G482–G488 (2015).
[Crossref] [PubMed]

Tse, M.

Z. Liu, J. Xi, M. Tse, A. C. Myers, X. D. Li, P. J. Pasricha, and S. Yu, “Allergic inflammation-induced structural and functional changes in esophageal epithelium in a guinea pig model of eosinophilic esophagitis,” Gastroenterology 5(5), 92 (2014).
[Crossref]

Tycho, A.

Underwood, R. A.

M. J. Cobb, Y. Chen, R. A. Underwood, M. L. Usui, J. Olerud, and X. Li, “Noninvasive assessment of cutaneous wound healing using ultrahigh-resolution optical coherence tomography,” J. Biomed. Opt. 11(6), 064002 (2006).
[Crossref] [PubMed]

Usui, M. L.

M. J. Cobb, Y. Chen, R. A. Underwood, M. L. Usui, J. Olerud, and X. Li, “Noninvasive assessment of cutaneous wound healing using ultrahigh-resolution optical coherence tomography,” J. Biomed. Opt. 11(6), 064002 (2006).
[Crossref] [PubMed]

Veksler, O.

Y. Boykov, O. Veksler, and R. Zabih, “Fast approximate energy minimization via graph cuts,” IEEE T. Pattern Anal. 23(11), 1222–1239 (2001).
[Crossref]

Vese, L. A.

L. A. Vese and S. J. Osher, “Modeling textures with total variation minimization and oscillating patterns in image processing,” J. Sci. Comput. 19(1/3), 553–572 (2003).
[Crossref]

Wang, Z.

Werner, J. S.

R. J. Zawadzki, A. R. Fuller, D. F. Wiley, B. Hamann, S. S. Choi, and J. S. Werner, “Adaptation of a support vector machine algorithm for segmentation and visualization of retinal structures in volumetric optical coherence tomography data sets,” J. Biomed. Opt. 12(4), 041206 (2007).
[Crossref] [PubMed]

Wessel, J. M.

J. M. Wessel, F. K. Horn, R. P. Tornow, M. Schmid, C. Y. Mardin, F. E. Kruse, A. G. Juenemann, and R. Laemmer, “Longitudinal analysis of progression in glaucoma using spectral-domain optical coherence tomography,” Invest. Ophthalmol. Vis. Sci. 54(5), 3613–3620 (2013).
[Crossref] [PubMed]

Westphal, V.

P. R. Pfau, M. V. Sivak, A. Chak, M. Kinnard, R. C. Wong, G. A. Isenberg, J. A. Izatt, A. Rollins, and V. Westphal, “Criteria for the diagnosis of dysplasia by endoscopic optical coherence tomography,” Gastrointest. Endosc. 58(2), 196–202 (2003).
[Crossref] [PubMed]

Wiley, D. F.

R. J. Zawadzki, A. R. Fuller, D. F. Wiley, B. Hamann, S. S. Choi, and J. S. Werner, “Adaptation of a support vector machine algorithm for segmentation and visualization of retinal structures in volumetric optical coherence tomography data sets,” J. Biomed. Opt. 12(4), 041206 (2007).
[Crossref] [PubMed]

Wilson, D. L.

Winter, K. P.

S. J. Chiu, J. A. Izatt, R. V. O’Connell, K. P. Winter, C. A. Toth, and S. Farsiu, “Validated automatic segmentation of AMD pathology including drusen and geographic atrophy in SD-OCT images,” Invest. Ophthalmol. Vis. Sci. 53(1), 53–61 (2012).
[Crossref] [PubMed]

Wollstein, G.

Z. M. Dong, G. Wollstein, and J. S. Schuman, “Clinical utility of optical coherence tomography in glaucoma,” Invest. Ophthalmol. Vis. Sci. 57(9), OCT556 (2016).
[Crossref] [PubMed]

Wong, A.

Wong, R. C.

P. R. Pfau, M. V. Sivak, A. Chak, M. Kinnard, R. C. Wong, G. A. Isenberg, J. A. Izatt, A. Rollins, and V. Westphal, “Criteria for the diagnosis of dysplasia by endoscopic optical coherence tomography,” Gastrointest. Endosc. 58(2), 196–202 (2003).
[Crossref] [PubMed]

Wu, X.

M. K. Garvin, M. D. Abràmoff, R. Kardon, S. R. Russell, X. Wu, and M. Sonka, “Intraretinal layer segmentation of macular optical coherence tomography images using optimal 3-D graph search,” IEEE Trans. Med. Imaging 27(10), 1495–1505 (2008).
[Crossref] [PubMed]

Wu, Y.

Xi, J.

W. Yuan, J. Mavadia-Shukla, J. Xi, W. Liang, X. Yu, S. Yu, and X. Li, “Optimal operational conditions for supercontinuum-based ultrahigh-resolution endoscopic OCT imaging,” Opt. Lett. 41(2), 250–253 (2016).
[Crossref] [PubMed]

Z. Liu, Y. Hu, X. Yu, J. Xi, X. Fan, C.-M. Tse, A. C. Myers, P. J. Pasricha, X. Li, and S. Yu, “Allergen challenge sensitizes TRPA1 in vagal sensory neurons and afferent C-fiber subtypes in guinea pig esophagus,” Am. J. Physiol. Gastrointest. Liver Physiol. 308(6), G482–G488 (2015).
[Crossref] [PubMed]

Z. Liu, J. Xi, M. Tse, A. C. Myers, X. D. Li, P. J. Pasricha, and S. Yu, “Allergic inflammation-induced structural and functional changes in esophageal epithelium in a guinea pig model of eosinophilic esophagitis,” Gastroenterology 5(5), 92 (2014).
[Crossref]

J. Xi, A. Zhang, Z. Liu, W. Liang, L. Y. Lin, S. Yu, and X. Li, “Diffractive catheter for ultrahigh-resolution spectral-domain volumetric OCT imaging,” Opt. Lett. 39(7), 2016–2019 (2014).
[Crossref] [PubMed]

J. Xi, L. Huo, Y. Wu, M. J. Cobb, J. H. Hwang, and X. Li, “High-resolution OCT balloon imaging catheter with astigmatism correction,” Opt. Lett. 34(13), 1943–1945 (2009).
[Crossref] [PubMed]

Yagi, Y.

H. Yoo, D. Kang, A. J. Katz, G. Y. Lauwers, N. S. Nishioka, Y. Yagi, P. Tanpowpong, J. Namati, B. E. Bouma, and G. J. Tearney, “Reflectance confocal microscopy for the diagnosis of eosinophilic esophagitis: a pilot study conducted on biopsy specimens,” Gastrointest. Endosc. 74(5), 992–1000 (2011).
[Crossref] [PubMed]

Yamamoto, H.

Yang, Q.

Yasuno, Y.

Yoo, H.

H. Yoo, D. Kang, A. J. Katz, G. Y. Lauwers, N. S. Nishioka, Y. Yagi, P. Tanpowpong, J. Namati, B. E. Bouma, and G. J. Tearney, “Reflectance confocal microscopy for the diagnosis of eosinophilic esophagitis: a pilot study conducted on biopsy specimens,” Gastrointest. Endosc. 74(5), 992–1000 (2011).
[Crossref] [PubMed]

Yoshimura, N.

Yu, S.

W. Yuan, J. Mavadia-Shukla, J. Xi, W. Liang, X. Yu, S. Yu, and X. Li, “Optimal operational conditions for supercontinuum-based ultrahigh-resolution endoscopic OCT imaging,” Opt. Lett. 41(2), 250–253 (2016).
[Crossref] [PubMed]

Z. Liu, Y. Hu, X. Yu, J. Xi, X. Fan, C.-M. Tse, A. C. Myers, P. J. Pasricha, X. Li, and S. Yu, “Allergen challenge sensitizes TRPA1 in vagal sensory neurons and afferent C-fiber subtypes in guinea pig esophagus,” Am. J. Physiol. Gastrointest. Liver Physiol. 308(6), G482–G488 (2015).
[Crossref] [PubMed]

Z. Liu, J. Xi, M. Tse, A. C. Myers, X. D. Li, P. J. Pasricha, and S. Yu, “Allergic inflammation-induced structural and functional changes in esophageal epithelium in a guinea pig model of eosinophilic esophagitis,” Gastroenterology 5(5), 92 (2014).
[Crossref]

J. Xi, A. Zhang, Z. Liu, W. Liang, L. Y. Lin, S. Yu, and X. Li, “Diffractive catheter for ultrahigh-resolution spectral-domain volumetric OCT imaging,” Opt. Lett. 39(7), 2016–2019 (2014).
[Crossref] [PubMed]

Yu, X.

W. Yuan, J. Mavadia-Shukla, J. Xi, W. Liang, X. Yu, S. Yu, and X. Li, “Optimal operational conditions for supercontinuum-based ultrahigh-resolution endoscopic OCT imaging,” Opt. Lett. 41(2), 250–253 (2016).
[Crossref] [PubMed]

Z. Liu, Y. Hu, X. Yu, J. Xi, X. Fan, C.-M. Tse, A. C. Myers, P. J. Pasricha, X. Li, and S. Yu, “Allergen challenge sensitizes TRPA1 in vagal sensory neurons and afferent C-fiber subtypes in guinea pig esophagus,” Am. J. Physiol. Gastrointest. Liver Physiol. 308(6), G482–G488 (2015).
[Crossref] [PubMed]

Yuan, W.

W. Yuan, J. Mavadia-Shukla, J. Xi, W. Liang, X. Yu, S. Yu, and X. Li, “Optimal operational conditions for supercontinuum-based ultrahigh-resolution endoscopic OCT imaging,” Opt. Lett. 41(2), 250–253 (2016).
[Crossref] [PubMed]

Y. Liang, W. Yuan, J. Mavadia-Shukla, and X. Li, “Optical clearing for luminal organ imaging with ultrahigh-resolution optical coherence tomography,” J. Biomed. Opt. 21(8), 081211 (2016).
[Crossref] [PubMed]

Yura, H. T.

Zabih, R.

Y. Boykov, O. Veksler, and R. Zabih, “Fast approximate energy minimization via graph cuts,” IEEE T. Pattern Anal. 23(11), 1222–1239 (2001).
[Crossref]

Zawadzki, R. J.

R. J. Zawadzki, A. R. Fuller, D. F. Wiley, B. Hamann, S. S. Choi, and J. S. Werner, “Adaptation of a support vector machine algorithm for segmentation and visualization of retinal structures in volumetric optical coherence tomography data sets,” J. Biomed. Opt. 12(4), 041206 (2007).
[Crossref] [PubMed]

Zelkha, R.

A. M. Bagci, M. Shahidi, R. Ansari, M. Blair, N. P. Blair, and R. Zelkha, “Thickness profiles of retinal layers by optical coherence tomography image segmentation,” Am. J. Ophthalmol. 146(5), 679–687 (2008).
[Crossref] [PubMed]

Zhang, A.

Zhou, C.

Am. J. Ophthalmol. (1)

A. M. Bagci, M. Shahidi, R. Ansari, M. Blair, N. P. Blair, and R. Zelkha, “Thickness profiles of retinal layers by optical coherence tomography image segmentation,” Am. J. Ophthalmol. 146(5), 679–687 (2008).
[Crossref] [PubMed]

Am. J. Physiol. Gastrointest. Liver Physiol. (1)

Z. Liu, Y. Hu, X. Yu, J. Xi, X. Fan, C.-M. Tse, A. C. Myers, P. J. Pasricha, X. Li, and S. Yu, “Allergen challenge sensitizes TRPA1 in vagal sensory neurons and afferent C-fiber subtypes in guinea pig esophagus,” Am. J. Physiol. Gastrointest. Liver Physiol. 308(6), G482–G488 (2015).
[Crossref] [PubMed]

Biomed. Opt. Express (3)

Gastroenterology (1)

Z. Liu, J. Xi, M. Tse, A. C. Myers, X. D. Li, P. J. Pasricha, and S. Yu, “Allergic inflammation-induced structural and functional changes in esophageal epithelium in a guinea pig model of eosinophilic esophagitis,” Gastroenterology 5(5), 92 (2014).
[Crossref]

Gastrointest. Endosc. (2)

H. Yoo, D. Kang, A. J. Katz, G. Y. Lauwers, N. S. Nishioka, Y. Yagi, P. Tanpowpong, J. Namati, B. E. Bouma, and G. J. Tearney, “Reflectance confocal microscopy for the diagnosis of eosinophilic esophagitis: a pilot study conducted on biopsy specimens,” Gastrointest. Endosc. 74(5), 992–1000 (2011).
[Crossref] [PubMed]

P. R. Pfau, M. V. Sivak, A. Chak, M. Kinnard, R. C. Wong, G. A. Isenberg, J. A. Izatt, A. Rollins, and V. Westphal, “Criteria for the diagnosis of dysplasia by endoscopic optical coherence tomography,” Gastrointest. Endosc. 58(2), 196–202 (2003).
[Crossref] [PubMed]

IEEE T. Pattern Anal. (1)

Y. Boykov, O. Veksler, and R. Zabih, “Fast approximate energy minimization via graph cuts,” IEEE T. Pattern Anal. 23(11), 1222–1239 (2001).
[Crossref]

IEEE Trans. Med. Imaging (1)

M. K. Garvin, M. D. Abràmoff, R. Kardon, S. R. Russell, X. Wu, and M. Sonka, “Intraretinal layer segmentation of macular optical coherence tomography images using optimal 3-D graph search,” IEEE Trans. Med. Imaging 27(10), 1495–1505 (2008).
[Crossref] [PubMed]

Invest. Ophthalmol. Vis. Sci. (3)

J. M. Wessel, F. K. Horn, R. P. Tornow, M. Schmid, C. Y. Mardin, F. E. Kruse, A. G. Juenemann, and R. Laemmer, “Longitudinal analysis of progression in glaucoma using spectral-domain optical coherence tomography,” Invest. Ophthalmol. Vis. Sci. 54(5), 3613–3620 (2013).
[Crossref] [PubMed]

Z. M. Dong, G. Wollstein, and J. S. Schuman, “Clinical utility of optical coherence tomography in glaucoma,” Invest. Ophthalmol. Vis. Sci. 57(9), OCT556 (2016).
[Crossref] [PubMed]

S. J. Chiu, J. A. Izatt, R. V. O’Connell, K. P. Winter, C. A. Toth, and S. Farsiu, “Validated automatic segmentation of AMD pathology including drusen and geographic atrophy in SD-OCT images,” Invest. Ophthalmol. Vis. Sci. 53(1), 53–61 (2012).
[Crossref] [PubMed]

J. Biomed. Opt. (5)

Y. Liang, W. Yuan, J. Mavadia-Shukla, and X. Li, “Optical clearing for luminal organ imaging with ultrahigh-resolution optical coherence tomography,” J. Biomed. Opt. 21(8), 081211 (2016).
[Crossref] [PubMed]

M. J. Cobb, Y. Chen, R. A. Underwood, M. L. Usui, J. Olerud, and X. Li, “Noninvasive assessment of cutaneous wound healing using ultrahigh-resolution optical coherence tomography,” J. Biomed. Opt. 11(6), 064002 (2006).
[Crossref] [PubMed]

R. J. Zawadzki, A. R. Fuller, D. F. Wiley, B. Hamann, S. S. Choi, and J. S. Werner, “Adaptation of a support vector machine algorithm for segmentation and visualization of retinal structures in volumetric optical coherence tomography data sets,” J. Biomed. Opt. 12(4), 041206 (2007).
[Crossref] [PubMed]

Y. Gan, D. Tsay, S. B. Amir, C. C. Marboe, and C. P. Hendon, “Automated classification of optical coherence tomography images of human atrial tissue,” J. Biomed. Opt. 21(10), 101407 (2016).
[Crossref] [PubMed]

B. Keller, D. Cunefare, D. S. Grewal, T. H. Mahmoud, J. A. Izatt, and S. Farsiu, “Length-adaptive graph search for automatic segmentation of pathological features in optical coherence tomography images,” J. Biomed. Opt. 21(7), 076015 (2016).
[Crossref] [PubMed]

J. Sci. Comput. (1)

L. A. Vese and S. J. Osher, “Modeling textures with total variation minimization and oscillating patterns in image processing,” J. Sci. Comput. 19(1/3), 553–572 (2003).
[Crossref]

Med. Eng. Phys. (1)

M. Baroni, P. Fortunato, and A. La Torre, “Towards quantitative analysis of retinal features in optical coherence tomography,” Med. Eng. Phys. 29(4), 432–441 (2007).
[Crossref] [PubMed]

Nat. Med. (1)

M. J. Gora, J. S. Sauk, R. W. Carruth, K. A. Gallagher, M. J. Suter, N. S. Nishioka, L. E. Kava, M. Rosenberg, B. E. Bouma, and G. J. Tearney, “Tethered capsule endomicroscopy enables less invasive imaging of gastrointestinal tract microstructure,” Nat. Med. 19(2), 238–240 (2013).
[Crossref] [PubMed]

Numer. Math. (1)

E. W. Dijkstra, “A note on two problems in connexion with graphs,” Numer. Math. 1(1), 269–271 (1959).
[Crossref]

Opt. Express (7)

S. J. Chiu, X. T. Li, P. Nicholas, C. A. Toth, J. A. Izatt, and S. Farsiu, “Automatic segmentation of seven retinal layers in SDOCT images congruent with expert manual segmentation,” Opt. Express 18(18), 19413–19428 (2010).
[Crossref] [PubMed]

M. Mujat, R. Chan, B. Cense, B. Park, C. Joo, T. Akkin, T. Chen, and J. de Boer, “Retinal nerve fiber layer thickness map determined from optical coherence tomography images,” Opt. Express 13(23), 9480–9491 (2005).
[Crossref] [PubMed]

A. Mishra, A. Wong, K. Bizheva, and D. A. Clausi, “Intra-retinal layer segmentation in optical coherence tomography images,” Opt. Express 17(26), 23719–23728 (2009).
[Crossref] [PubMed]

T. Fabritius, S. Makita, M. Miura, R. Myllylä, and Y. Yasuno, “Automated segmentation of the macula by optical coherence tomography,” Opt. Express 17(18), 15659–15669 (2009).
[Crossref] [PubMed]

D. C. Adler, C. Zhou, T.-H. Tsai, J. Schmitt, Q. Huang, H. Mashimo, and J. G. Fujimoto, “Three-dimensional endomicroscopy of the human colon using optical coherence tomography,” Opt. Express 17(2), 784–796 (2009).
[Crossref] [PubMed]

D. Cabrera Fernández, H. M. Salinas, and C. A. Puliafito, “Automated detection of retinal layer structures on optical coherence tomography images,” Opt. Express 13(25), 10200–10216 (2005).
[Crossref] [PubMed]

Q. Yang, C. A. Reisman, Z. Wang, Y. Fukuma, M. Hangai, N. Yoshimura, A. Tomidokoro, M. Araie, A. S. Raza, D. C. Hood, and K. Chan, “Automated layer segmentation of macular OCT images using dual-scale gradient information,” Opt. Express 18(20), 21293–21307 (2010).
[Crossref] [PubMed]

Opt. Lett. (4)

Physica D (1)

L. I. Rudin, S. Osher, and E. Fatemi, “Nonlinear total variation based noise removal algorithms,” Physica D 60(1-4), 259–268 (1992).
[Crossref]

Q. Appl. Math. (1)

R. Bellman, “On a routing problem,” Q. Appl. Math. 16(1), 87–90 (1958).
[Crossref]

Science (2)

D. Huang, E. A. Swanson, C. P. Lin, J. S. Schuman, W. G. Stinson, W. Chang, M. R. Hee, T. Flotte, K. Gregory, C. A. Puliafito, and et, “Optical coherence tomography,” Science 254(5035), 1178–1181 (1991).
[Crossref] [PubMed]

G. J. Tearney, M. E. Brezinski, B. E. Bouma, S. A. Boppart, C. Pitris, J. F. Southern, and J. G. Fujimoto, “In vivo endoscopic optical biopsy with optical coherence tomography,” Science 276(5321), 2037–2039 (1997).
[Crossref] [PubMed]

SIAM J. Imaging Sci. (1)

A. Beck and M. Teboulle, “A fast iterative shrinkage-thresholding algorithm for linear inverse problems,” SIAM J. Imaging Sci. 2(1), 183–202 (2009).
[Crossref]

Other (7)

M. Sonka, V. Hlavac, and R. Boyle, Image Processing, Analysis, and Machine Vision (Cengage Learning, 2014).

L. R. Ford, Jr. and D. R. Fulkerson, Flows in Networks (Princeton University Press, 2015).

E. DiBenedetto, Real Analysis (Springer Science & Business Media, 2012).

S. Boyd and L. Vandenberghe, Convex Optimization (Cambridge University Press, 2004).

L. Xu, C. Lu, Y. Xu, and J. Jia, “Image smoothing via L0 gradient minimization,” in ACM Transactions on Graphics (TOG), (ACM, 2011), 174.

R. C. Gonzalez and R. E. Woods, “Digital Image Processing,” (Prentice Hall, 2002).

M. Haeker, M. Sonka, R. Kardon, V. A. Shah, X. Wu, and M. D. Abràmoff, “Automated segmentation of intraretinal layers from macular optical coherence tomography images,” in Medical Imaging, (International Society for Optics and Photonics, 2007), 651214.

Supplementary Material (1)

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» Visualization 1: MPG (3044 KB)      Movie 1

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Figures (6)

Fig. 1
Fig. 1

Histology of guinea pig esophagus. SC: stratum corneum; EP: epithelium; LP: lamina propria; MM: muscularis mucosae; SM: submucosa; MP: muscularis propria.

Fig. 2
Fig. 2

Representative endoscopic OCT images of guinea pig esophagus before and after L1-L0 norm minimization based de-noising and smoothing procedures. (a)-(c) are the original OCT image, image after the de-noising procedure, and image after the de-noising and smoothing procedures, respectively; (d)-(f) are the representative intensity profiles along imaging depth (in the units of pixel) corresponding to the A-scan labeled with red dashed vertical lines in (a)-(c).

Fig. 3
Fig. 3

Segmentation of a representative endoscopic OCT image. (a) Representative cross-section in vivo OCT image of guinea pig esophagus. (b) Segmentation result of (a), with lines of different colors indicating the layer boundaries. Red circles indicate areas of dramatic kinks of tissues layers. Deep red: boundary 1, SC surface; red: boundary 2, SC/EP interface; orange: boundary 3, EP/LP interface; yellow: boundary 4, LP/MM interface; green: boundary 5, MM/SM interface; cyan: boundary 6, SM/MP interface.

Fig. 4
Fig. 4

Segmentation of the representative ill-posed endoscopic OCT images with different challenges. OCT images of a guinea pig esophagus with steep slopes in layer boundaries, partially blocked view, and local distortions, are shown in (a), (c), and (e), respectively. Areas boxed with red solid lines in (a), (c), and (e) indicate the challenging areas of each image. (b), (d), and (f) show the corresponding segmentation results of (a), (c) and (e), respectively.

Fig. 5
Fig. 5

Optical staining of representative endoscopic OCT images. (a-b): OCT image of guinea pig esophagus and its optical staining version in Cartesian coordinates. (c-d): OCT image of guinea pig esophagus and its optical staining version in polar coordination. Red box in (a) contains a residual portion of the plastic sheath was exclude from optical staining.

Fig. 6
Fig. 6

Two representative OCT images of guinea pig esophagus segmented with our method for a control (a) and an EoE model (b). (c) Comparison of the esophageal layer thickness for a guinea pig EoE model and control. SC: stratum corneum; EP: epithelium; LP: lamina propria; MM: muscularis mucosae; SM: submucosa. “*” indicates the thickness difference between the EoE model and control is statistically significant with a P-value less than 1 × 10−7 for all five layers (based on two-tailed Welch’s t-test, n = 20).

Tables (1)

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Table 1 Automatic versus manual segmentation of layer thickness for guinea pig esophagus

Equations (14)

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J ε ( u ) = λ Ω | g u | 2 d x d y + Ω ε 2 + | u | 2 d x d y ,
{ u = g + 1 2 λ ( u ε 2 + | u | 2 ) in Ω , and u n = 0 on Ω , ,
J s ( I s ) = λ s Ω | u I s | 2 d x d y + I s 0 ,
J s ( I s , D ) = λ s Ω | u I s | 2 d x d y + λ d Ω ( | D h x I s | 2 + | D v y I s | 2 ) d x d y + D 0 ,
J s ( I s ) = λ s Ω | u I s | 2 d x d y + λ d Ω ( | D h x I s | 2 + | D v y I s | 2 ) d x d y ,
J s ( D ) = λ d Ω ( | D h x I s | 2 + | D v y I s | 2 ) d x d y + D 0 .
k = 1 13 [ 0 1 2 1 0 1 2 3 2 1 0 0 0 0 0 -1 -2 -3 -2 -1 0 -1 -2 -1 0 ] ,
g r a d = k I s .
g r a d N m = g r a d min ( g r a d ) max ( g r a d ) min ( g r a d ) ,
C ( i , j ) = 1 g r a d N m ( i , j ) .
W ( i , j ) ( m , n ) = { , i f ( m , n ) N e i g h b o r ( i , j ) C ( i , j ) + C ( m , n ) , i f ( m , n ) N e i g h b o r ( i , j ) ,
N e i g h b o r ( i , j ) = { ( k , l ) | k [ i 1 , i + 1 ] , l [ j 1 , j + 1 ] , | k i | + | l j | 0 }
φ ( y ) = a y n ,
I ( x , y ) = I s ( x , y ) / φ ( y ) .