Abstract

A two stage statistical model based on texture and shape for fully automatic choroidal segmentation of normal and pathologic eyes obtained by a 1060 nm optical coherence tomography (OCT) system is developed. A novel dynamic programming approach is implemented to determine location of the retinal pigment epithelium/ Bruch’s membrane /choriocapillaris (RBC) boundary. The choroid–sclera interface (CSI) is segmented using a statistical model. The algorithm is robust even in presence of speckle noise, low signal (thick choroid), retinal pigment epithelium (RPE) detachments and atrophy, drusen, shadowing and other artifacts. Evaluation against a set of 871 manually segmented cross-sectional scans from 12 eyes achieves an average error rate of 13%, computed per tomogram as a ratio of incorrectly classified pixels and the total layer surface. For the first time a fully automatic choroidal segmentation algorithm is successfully applied to a wide range of clinical volumetric OCT data.

© 2011 OSA

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2011 (4)

M. Esmaeelpour, B. Považay, B. Hermann, B. Hofer, V. Kajic, S. L. Hale, R. V. North, W. Drexler, and N. J. Sheen, “Mapping choroidal and retinal thickness variation in type 2 diabetes using three-dimensional 1060-nm optical coherence tomography,” Invest. Ophthalmol. Vis. Sci.52(8), 5311–5316 (2011).
[CrossRef] [PubMed]

A. K. Mishra, P. W. Fieguth, and D. A. Clausi, “Decoupled active contour (DAC) for boundary detection,” IEEE Trans. Pattern Anal. Mach. Intell.33(2), 310–324 (2011).
[CrossRef] [PubMed]

J. Molnár, D. Chetverikov, D. Cabrera DeBuc, W. Gao, and G. Somfai, “Layer extraction in rodent retinal images acquired by optical coherence tomography,” Mach. Vis. Appl. (2011).
[CrossRef]

K. A. Vermeer, J. van der Schoot, H. G. Lemij, and J. F. de Boer, “Automated segmentation by pixel classification of retinal layers in ophthalmic OCT images,” Biomed. Opt. Express2(6), 1743–1756 (2011).
[CrossRef] [PubMed]

2010 (6)

M. A. Mayer, J. Hornegger, C. Y. Mardin, and R. P. Tornow, “Retinal Nerve Fiber Layer Segmentation on FD-OCT Scans of Normal Subjects and Glaucoma Patients,” Biomed. Opt. Express1(5), 1358–1383 (2010).
[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. Express18(18), 19413–19428 (2010).
[CrossRef] [PubMed]

M. V. Sarunic, A. Yazdanpanah, E. Gibson, J. Xu, Y. Bai, S. Lee, H. U. Saragovi, and M. F. Beg, “Longitudinal study of retinal degeneration in a rat using spectral domain optical coherence tomography,” Opt. Express18(22), 23435–23441 (2010).
[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. Express18(20), 21293–21307 (2010).
[CrossRef] [PubMed]

M. Esmaeelpour, B. Povazay, B. Hermann, B. Hofer, V. Kajic, K. Kapoor, N. J. Sheen, R. V. North, and W. Drexler, “Three-dimensional 1060-nm OCT: choroidal thickness maps in normal subjects and improved posterior segment visualization in cataract patients,” Invest. Ophthalmol. Vis. Sci.51(10), 5260–5266 (2010).
[CrossRef] [PubMed]

V. Kajić, B. Povazay, B. Hermann, B. Hofer, D. Marshall, P. L. Rosin, and W. Drexler, “Robust segmentation of intraretinal layers in the normal human fovea using a novel statistical model based on texture and shape analysis,” Opt. Express18(14), 14730–14744 (2010).
[CrossRef] [PubMed]

2009 (1)

B. Povazay, B. Hermann, B. Hofer, V. Kajić, E. Simpson, T. Bridgford, and W. Drexler, “Wide-field optical coherence tomography of the choroid in vivo,” Invest. Ophthalmol. Vis. Sci.50(4), 1856–1863 (2009).
[CrossRef] [PubMed]

2008 (1)

M. K. Garvin, M. D. Abramoff, 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. Imaging27(10), 1495–1505 (2008).
[CrossRef] [PubMed]

2007 (1)

2005 (4)

2004 (1)

J. Matas, O. Chum, M. Urban, and T. Pajdla, “Robust wide-baseline stereo from maximally stable extremal regions,” Image Vis. Comput.22(10), 761–767 (2004).
[CrossRef]

2001 (2)

T. F. Cootes, G. J. Edwards, and C. J. Taylor, “Active appearance models,” IEEE Trans. Pattern Anal. Mach. Intell.23(6), 681–685 (2001).
[CrossRef]

D. Koozekanani, K. Boyer, and C. Roberts, “Retinal thickness measurements from optical coherence tomography using a Markov boundary model,” IEEE Trans. Med. Imaging20(9), 900–916 (2001).
[CrossRef] [PubMed]

1997 (1)

Z. Q. Yin, T. J. Vaegan, T. J. Millar, P. Beaumont, and S. Sarks, “Widespread choroidal insufficiency in primary open-angle glaucoma,” J. Glaucoma6(1), 23–32 (1997).
[CrossRef] [PubMed]

1994 (1)

D. S. McLeod and G. A. Lutty, “High-resolution histologic analysis of the human choroidal vasculature,” Invest. Ophthalmol. Vis. Sci.35(11), 3799–3811 (1994).
[PubMed]

1977 (1)

W. R. Green and S. N. Key, “Senile macular degeneration: a histopathologic study,” Trans. Am. Ophthalmol. Soc.75, 180–254 (1977).
[PubMed]

1976 (1)

S. H. Sarks, “Ageing and degeneration in the macular region: a clinico-pathological study,” Br. J. Ophthalmol.60(5), 324–341 (1976).
[CrossRef] [PubMed]

Abramoff, M. D.

M. K. Garvin, M. D. Abramoff, 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. Imaging27(10), 1495–1505 (2008).
[CrossRef] [PubMed]

Akkin, T.

Araie, M.

Bai, Y.

Baraniuk, R. G.

I. W. Selesnick, R. G. Baraniuk, and N. G. Kingsbury, “The Dual-Tree Complex Wavelet Transform,” IEEE Signal Process. Mag.22(6), 123–151 (2005).
[CrossRef]

Beaumont, P.

Z. Q. Yin, T. J. Vaegan, T. J. Millar, P. Beaumont, and S. Sarks, “Widespread choroidal insufficiency in primary open-angle glaucoma,” J. Glaucoma6(1), 23–32 (1997).
[CrossRef] [PubMed]

Beg, M. F.

Boyer, K.

D. Koozekanani, K. Boyer, and C. Roberts, “Retinal thickness measurements from optical coherence tomography using a Markov boundary model,” IEEE Trans. Med. Imaging20(9), 900–916 (2001).
[CrossRef] [PubMed]

Bridgford, T.

B. Povazay, B. Hermann, B. Hofer, V. Kajić, E. Simpson, T. Bridgford, and W. Drexler, “Wide-field optical coherence tomography of the choroid in vivo,” Invest. Ophthalmol. Vis. Sci.50(4), 1856–1863 (2009).
[CrossRef] [PubMed]

Cabrera DeBuc, D.

J. Molnár, D. Chetverikov, D. Cabrera DeBuc, W. Gao, and G. Somfai, “Layer extraction in rodent retinal images acquired by optical coherence tomography,” Mach. Vis. Appl. (2011).
[CrossRef]

Cabrera Fernández, D.

Cense, B.

Chan, K.

Chan, R.

Chen, T.

Chetverikov, D.

J. Molnár, D. Chetverikov, D. Cabrera DeBuc, W. Gao, and G. Somfai, “Layer extraction in rodent retinal images acquired by optical coherence tomography,” Mach. Vis. Appl. (2011).
[CrossRef]

Chiu, S. J.

Choi, S. S.

Chum, O.

J. Matas, O. Chum, M. Urban, and T. Pajdla, “Robust wide-baseline stereo from maximally stable extremal regions,” Image Vis. Comput.22(10), 761–767 (2004).
[CrossRef]

Clausi, D. A.

A. K. Mishra, P. W. Fieguth, and D. A. Clausi, “Decoupled active contour (DAC) for boundary detection,” IEEE Trans. Pattern Anal. Mach. Intell.33(2), 310–324 (2011).
[CrossRef] [PubMed]

Cootes, T. F.

T. F. Cootes, G. J. Edwards, and C. J. Taylor, “Active appearance models,” IEEE Trans. Pattern Anal. Mach. Intell.23(6), 681–685 (2001).
[CrossRef]

de Boer, J.

de Boer, J. F.

Drexler, W.

M. Esmaeelpour, B. Považay, B. Hermann, B. Hofer, V. Kajic, S. L. Hale, R. V. North, W. Drexler, and N. J. Sheen, “Mapping choroidal and retinal thickness variation in type 2 diabetes using three-dimensional 1060-nm optical coherence tomography,” Invest. Ophthalmol. Vis. Sci.52(8), 5311–5316 (2011).
[CrossRef] [PubMed]

M. Esmaeelpour, B. Povazay, B. Hermann, B. Hofer, V. Kajic, K. Kapoor, N. J. Sheen, R. V. North, and W. Drexler, “Three-dimensional 1060-nm OCT: choroidal thickness maps in normal subjects and improved posterior segment visualization in cataract patients,” Invest. Ophthalmol. Vis. Sci.51(10), 5260–5266 (2010).
[CrossRef] [PubMed]

V. Kajić, B. Povazay, B. Hermann, B. Hofer, D. Marshall, P. L. Rosin, and W. Drexler, “Robust segmentation of intraretinal layers in the normal human fovea using a novel statistical model based on texture and shape analysis,” Opt. Express18(14), 14730–14744 (2010).
[CrossRef] [PubMed]

B. Povazay, B. Hermann, B. Hofer, V. Kajić, E. Simpson, T. Bridgford, and W. Drexler, “Wide-field optical coherence tomography of the choroid in vivo,” Invest. Ophthalmol. Vis. Sci.50(4), 1856–1863 (2009).
[CrossRef] [PubMed]

Edwards, G. J.

T. F. Cootes, G. J. Edwards, and C. J. Taylor, “Active appearance models,” IEEE Trans. Pattern Anal. Mach. Intell.23(6), 681–685 (2001).
[CrossRef]

Esmaeelpour, M.

M. Esmaeelpour, B. Považay, B. Hermann, B. Hofer, V. Kajic, S. L. Hale, R. V. North, W. Drexler, and N. J. Sheen, “Mapping choroidal and retinal thickness variation in type 2 diabetes using three-dimensional 1060-nm optical coherence tomography,” Invest. Ophthalmol. Vis. Sci.52(8), 5311–5316 (2011).
[CrossRef] [PubMed]

M. Esmaeelpour, B. Povazay, B. Hermann, B. Hofer, V. Kajic, K. Kapoor, N. J. Sheen, R. V. North, and W. Drexler, “Three-dimensional 1060-nm OCT: choroidal thickness maps in normal subjects and improved posterior segment visualization in cataract patients,” Invest. Ophthalmol. Vis. Sci.51(10), 5260–5266 (2010).
[CrossRef] [PubMed]

Farsiu, S.

Fieguth, P. W.

A. K. Mishra, P. W. Fieguth, and D. A. Clausi, “Decoupled active contour (DAC) for boundary detection,” IEEE Trans. Pattern Anal. Mach. Intell.33(2), 310–324 (2011).
[CrossRef] [PubMed]

Fukuma, Y.

Gao, W.

J. Molnár, D. Chetverikov, D. Cabrera DeBuc, W. Gao, and G. Somfai, “Layer extraction in rodent retinal images acquired by optical coherence tomography,” Mach. Vis. Appl. (2011).
[CrossRef]

Garvin, M. K.

M. K. Garvin, M. D. Abramoff, 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. Imaging27(10), 1495–1505 (2008).
[CrossRef] [PubMed]

Gibson, E.

Green, W. R.

W. R. Green and S. N. Key, “Senile macular degeneration: a histopathologic study,” Trans. Am. Ophthalmol. Soc.75, 180–254 (1977).
[PubMed]

Guy, C. L.

M. Scholz, F. Kaplan, C. L. Guy, J. Kopka, and J. Selbig, “Non-linear PCA: a missing data approach,” Bioinformatics21(20), 3887–3895 (2005).
[CrossRef] [PubMed]

Hale, S. L.

M. Esmaeelpour, B. Považay, B. Hermann, B. Hofer, V. Kajic, S. L. Hale, R. V. North, W. Drexler, and N. J. Sheen, “Mapping choroidal and retinal thickness variation in type 2 diabetes using three-dimensional 1060-nm optical coherence tomography,” Invest. Ophthalmol. Vis. Sci.52(8), 5311–5316 (2011).
[CrossRef] [PubMed]

Hangai, M.

Hermann, B.

M. Esmaeelpour, B. Považay, B. Hermann, B. Hofer, V. Kajic, S. L. Hale, R. V. North, W. Drexler, and N. J. Sheen, “Mapping choroidal and retinal thickness variation in type 2 diabetes using three-dimensional 1060-nm optical coherence tomography,” Invest. Ophthalmol. Vis. Sci.52(8), 5311–5316 (2011).
[CrossRef] [PubMed]

M. Esmaeelpour, B. Povazay, B. Hermann, B. Hofer, V. Kajic, K. Kapoor, N. J. Sheen, R. V. North, and W. Drexler, “Three-dimensional 1060-nm OCT: choroidal thickness maps in normal subjects and improved posterior segment visualization in cataract patients,” Invest. Ophthalmol. Vis. Sci.51(10), 5260–5266 (2010).
[CrossRef] [PubMed]

V. Kajić, B. Povazay, B. Hermann, B. Hofer, D. Marshall, P. L. Rosin, and W. Drexler, “Robust segmentation of intraretinal layers in the normal human fovea using a novel statistical model based on texture and shape analysis,” Opt. Express18(14), 14730–14744 (2010).
[CrossRef] [PubMed]

B. Povazay, B. Hermann, B. Hofer, V. Kajić, E. Simpson, T. Bridgford, and W. Drexler, “Wide-field optical coherence tomography of the choroid in vivo,” Invest. Ophthalmol. Vis. Sci.50(4), 1856–1863 (2009).
[CrossRef] [PubMed]

Hofer, B.

M. Esmaeelpour, B. Považay, B. Hermann, B. Hofer, V. Kajic, S. L. Hale, R. V. North, W. Drexler, and N. J. Sheen, “Mapping choroidal and retinal thickness variation in type 2 diabetes using three-dimensional 1060-nm optical coherence tomography,” Invest. Ophthalmol. Vis. Sci.52(8), 5311–5316 (2011).
[CrossRef] [PubMed]

M. Esmaeelpour, B. Povazay, B. Hermann, B. Hofer, V. Kajic, K. Kapoor, N. J. Sheen, R. V. North, and W. Drexler, “Three-dimensional 1060-nm OCT: choroidal thickness maps in normal subjects and improved posterior segment visualization in cataract patients,” Invest. Ophthalmol. Vis. Sci.51(10), 5260–5266 (2010).
[CrossRef] [PubMed]

V. Kajić, B. Povazay, B. Hermann, B. Hofer, D. Marshall, P. L. Rosin, and W. Drexler, “Robust segmentation of intraretinal layers in the normal human fovea using a novel statistical model based on texture and shape analysis,” Opt. Express18(14), 14730–14744 (2010).
[CrossRef] [PubMed]

B. Povazay, B. Hermann, B. Hofer, V. Kajić, E. Simpson, T. Bridgford, and W. Drexler, “Wide-field optical coherence tomography of the choroid in vivo,” Invest. Ophthalmol. Vis. Sci.50(4), 1856–1863 (2009).
[CrossRef] [PubMed]

Hood, D. C.

Hornegger, J.

Izatt, J. A.

Jones, S. M.

Joo, C.

Kajic, V.

M. Esmaeelpour, B. Považay, B. Hermann, B. Hofer, V. Kajic, S. L. Hale, R. V. North, W. Drexler, and N. J. Sheen, “Mapping choroidal and retinal thickness variation in type 2 diabetes using three-dimensional 1060-nm optical coherence tomography,” Invest. Ophthalmol. Vis. Sci.52(8), 5311–5316 (2011).
[CrossRef] [PubMed]

M. Esmaeelpour, B. Povazay, B. Hermann, B. Hofer, V. Kajic, K. Kapoor, N. J. Sheen, R. V. North, and W. Drexler, “Three-dimensional 1060-nm OCT: choroidal thickness maps in normal subjects and improved posterior segment visualization in cataract patients,” Invest. Ophthalmol. Vis. Sci.51(10), 5260–5266 (2010).
[CrossRef] [PubMed]

V. Kajić, B. Povazay, B. Hermann, B. Hofer, D. Marshall, P. L. Rosin, and W. Drexler, “Robust segmentation of intraretinal layers in the normal human fovea using a novel statistical model based on texture and shape analysis,” Opt. Express18(14), 14730–14744 (2010).
[CrossRef] [PubMed]

B. Povazay, B. Hermann, B. Hofer, V. Kajić, E. Simpson, T. Bridgford, and W. Drexler, “Wide-field optical coherence tomography of the choroid in vivo,” Invest. Ophthalmol. Vis. Sci.50(4), 1856–1863 (2009).
[CrossRef] [PubMed]

Kaplan, F.

M. Scholz, F. Kaplan, C. L. Guy, J. Kopka, and J. Selbig, “Non-linear PCA: a missing data approach,” Bioinformatics21(20), 3887–3895 (2005).
[CrossRef] [PubMed]

Kapoor, K.

M. Esmaeelpour, B. Povazay, B. Hermann, B. Hofer, V. Kajic, K. Kapoor, N. J. Sheen, R. V. North, and W. Drexler, “Three-dimensional 1060-nm OCT: choroidal thickness maps in normal subjects and improved posterior segment visualization in cataract patients,” Invest. Ophthalmol. Vis. Sci.51(10), 5260–5266 (2010).
[CrossRef] [PubMed]

Kardon, R.

M. K. Garvin, M. D. Abramoff, 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. Imaging27(10), 1495–1505 (2008).
[CrossRef] [PubMed]

Key, S. N.

W. R. Green and S. N. Key, “Senile macular degeneration: a histopathologic study,” Trans. Am. Ophthalmol. Soc.75, 180–254 (1977).
[PubMed]

Kingsbury, N. G.

I. W. Selesnick, R. G. Baraniuk, and N. G. Kingsbury, “The Dual-Tree Complex Wavelet Transform,” IEEE Signal Process. Mag.22(6), 123–151 (2005).
[CrossRef]

Koozekanani, D.

D. Koozekanani, K. Boyer, and C. Roberts, “Retinal thickness measurements from optical coherence tomography using a Markov boundary model,” IEEE Trans. Med. Imaging20(9), 900–916 (2001).
[CrossRef] [PubMed]

Kopka, J.

M. Scholz, F. Kaplan, C. L. Guy, J. Kopka, and J. Selbig, “Non-linear PCA: a missing data approach,” Bioinformatics21(20), 3887–3895 (2005).
[CrossRef] [PubMed]

Lee, S.

Lemij, H. G.

Li, X. T.

Lutty, G. A.

D. S. McLeod and G. A. Lutty, “High-resolution histologic analysis of the human choroidal vasculature,” Invest. Ophthalmol. Vis. Sci.35(11), 3799–3811 (1994).
[PubMed]

Mardin, C. Y.

Marshall, D.

Matas, J.

J. Matas, O. Chum, M. Urban, and T. Pajdla, “Robust wide-baseline stereo from maximally stable extremal regions,” Image Vis. Comput.22(10), 761–767 (2004).
[CrossRef]

Mayer, M. A.

McLeod, D. S.

D. S. McLeod and G. A. Lutty, “High-resolution histologic analysis of the human choroidal vasculature,” Invest. Ophthalmol. Vis. Sci.35(11), 3799–3811 (1994).
[PubMed]

Millar, T. J.

Z. Q. Yin, T. J. Vaegan, T. J. Millar, P. Beaumont, and S. Sarks, “Widespread choroidal insufficiency in primary open-angle glaucoma,” J. Glaucoma6(1), 23–32 (1997).
[CrossRef] [PubMed]

Mishra, A. K.

A. K. Mishra, P. W. Fieguth, and D. A. Clausi, “Decoupled active contour (DAC) for boundary detection,” IEEE Trans. Pattern Anal. Mach. Intell.33(2), 310–324 (2011).
[CrossRef] [PubMed]

Molnár, J.

J. Molnár, D. Chetverikov, D. Cabrera DeBuc, W. Gao, and G. Somfai, “Layer extraction in rodent retinal images acquired by optical coherence tomography,” Mach. Vis. Appl. (2011).
[CrossRef]

Mujat, M.

Nicholas, P.

North, R. V.

M. Esmaeelpour, B. Považay, B. Hermann, B. Hofer, V. Kajic, S. L. Hale, R. V. North, W. Drexler, and N. J. Sheen, “Mapping choroidal and retinal thickness variation in type 2 diabetes using three-dimensional 1060-nm optical coherence tomography,” Invest. Ophthalmol. Vis. Sci.52(8), 5311–5316 (2011).
[CrossRef] [PubMed]

M. Esmaeelpour, B. Povazay, B. Hermann, B. Hofer, V. Kajic, K. Kapoor, N. J. Sheen, R. V. North, and W. Drexler, “Three-dimensional 1060-nm OCT: choroidal thickness maps in normal subjects and improved posterior segment visualization in cataract patients,” Invest. Ophthalmol. Vis. Sci.51(10), 5260–5266 (2010).
[CrossRef] [PubMed]

Oliver, S. S.

Pajdla, T.

J. Matas, O. Chum, M. Urban, and T. Pajdla, “Robust wide-baseline stereo from maximally stable extremal regions,” Image Vis. Comput.22(10), 761–767 (2004).
[CrossRef]

Park, B.

Povazay, B.

M. Esmaeelpour, B. Povazay, B. Hermann, B. Hofer, V. Kajic, K. Kapoor, N. J. Sheen, R. V. North, and W. Drexler, “Three-dimensional 1060-nm OCT: choroidal thickness maps in normal subjects and improved posterior segment visualization in cataract patients,” Invest. Ophthalmol. Vis. Sci.51(10), 5260–5266 (2010).
[CrossRef] [PubMed]

V. Kajić, B. Povazay, B. Hermann, B. Hofer, D. Marshall, P. L. Rosin, and W. Drexler, “Robust segmentation of intraretinal layers in the normal human fovea using a novel statistical model based on texture and shape analysis,” Opt. Express18(14), 14730–14744 (2010).
[CrossRef] [PubMed]

B. Povazay, B. Hermann, B. Hofer, V. Kajić, E. Simpson, T. Bridgford, and W. Drexler, “Wide-field optical coherence tomography of the choroid in vivo,” Invest. Ophthalmol. Vis. Sci.50(4), 1856–1863 (2009).
[CrossRef] [PubMed]

Považay, B.

M. Esmaeelpour, B. Považay, B. Hermann, B. Hofer, V. Kajic, S. L. Hale, R. V. North, W. Drexler, and N. J. Sheen, “Mapping choroidal and retinal thickness variation in type 2 diabetes using three-dimensional 1060-nm optical coherence tomography,” Invest. Ophthalmol. Vis. Sci.52(8), 5311–5316 (2011).
[CrossRef] [PubMed]

Puliafito, C. A.

Raza, A. S.

Reisman, C. A.

Roberts, C.

D. Koozekanani, K. Boyer, and C. Roberts, “Retinal thickness measurements from optical coherence tomography using a Markov boundary model,” IEEE Trans. Med. Imaging20(9), 900–916 (2001).
[CrossRef] [PubMed]

Rosin, P. L.

Russell, S. R.

M. K. Garvin, M. D. Abramoff, 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. Imaging27(10), 1495–1505 (2008).
[CrossRef] [PubMed]

Salinas, H. M.

Saragovi, H. U.

Sarks, S.

Z. Q. Yin, T. J. Vaegan, T. J. Millar, P. Beaumont, and S. Sarks, “Widespread choroidal insufficiency in primary open-angle glaucoma,” J. Glaucoma6(1), 23–32 (1997).
[CrossRef] [PubMed]

Sarks, S. H.

S. H. Sarks, “Ageing and degeneration in the macular region: a clinico-pathological study,” Br. J. Ophthalmol.60(5), 324–341 (1976).
[CrossRef] [PubMed]

Sarunic, M. V.

Scholz, M.

M. Scholz, F. Kaplan, C. L. Guy, J. Kopka, and J. Selbig, “Non-linear PCA: a missing data approach,” Bioinformatics21(20), 3887–3895 (2005).
[CrossRef] [PubMed]

Selbig, J.

M. Scholz, F. Kaplan, C. L. Guy, J. Kopka, and J. Selbig, “Non-linear PCA: a missing data approach,” Bioinformatics21(20), 3887–3895 (2005).
[CrossRef] [PubMed]

Selesnick, I. W.

I. W. Selesnick, R. G. Baraniuk, and N. G. Kingsbury, “The Dual-Tree Complex Wavelet Transform,” IEEE Signal Process. Mag.22(6), 123–151 (2005).
[CrossRef]

Sheen, N. J.

M. Esmaeelpour, B. Považay, B. Hermann, B. Hofer, V. Kajic, S. L. Hale, R. V. North, W. Drexler, and N. J. Sheen, “Mapping choroidal and retinal thickness variation in type 2 diabetes using three-dimensional 1060-nm optical coherence tomography,” Invest. Ophthalmol. Vis. Sci.52(8), 5311–5316 (2011).
[CrossRef] [PubMed]

M. Esmaeelpour, B. Povazay, B. Hermann, B. Hofer, V. Kajic, K. Kapoor, N. J. Sheen, R. V. North, and W. Drexler, “Three-dimensional 1060-nm OCT: choroidal thickness maps in normal subjects and improved posterior segment visualization in cataract patients,” Invest. Ophthalmol. Vis. Sci.51(10), 5260–5266 (2010).
[CrossRef] [PubMed]

Simpson, E.

B. Povazay, B. Hermann, B. Hofer, V. Kajić, E. Simpson, T. Bridgford, and W. Drexler, “Wide-field optical coherence tomography of the choroid in vivo,” Invest. Ophthalmol. Vis. Sci.50(4), 1856–1863 (2009).
[CrossRef] [PubMed]

Somfai, G.

J. Molnár, D. Chetverikov, D. Cabrera DeBuc, W. Gao, and G. Somfai, “Layer extraction in rodent retinal images acquired by optical coherence tomography,” Mach. Vis. Appl. (2011).
[CrossRef]

Sonka, M.

M. K. Garvin, M. D. Abramoff, 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. Imaging27(10), 1495–1505 (2008).
[CrossRef] [PubMed]

Taylor, C. J.

T. F. Cootes, G. J. Edwards, and C. J. Taylor, “Active appearance models,” IEEE Trans. Pattern Anal. Mach. Intell.23(6), 681–685 (2001).
[CrossRef]

Tomidokoro, A.

Tornow, R. P.

Toth, C. A.

Urban, M.

J. Matas, O. Chum, M. Urban, and T. Pajdla, “Robust wide-baseline stereo from maximally stable extremal regions,” Image Vis. Comput.22(10), 761–767 (2004).
[CrossRef]

Vaegan, T. J.

Z. Q. Yin, T. J. Vaegan, T. J. Millar, P. Beaumont, and S. Sarks, “Widespread choroidal insufficiency in primary open-angle glaucoma,” J. Glaucoma6(1), 23–32 (1997).
[CrossRef] [PubMed]

van der Schoot, J.

Vermeer, K. A.

Wang, Z.

Werner, J. S.

Wu, X.

M. K. Garvin, M. D. Abramoff, 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. Imaging27(10), 1495–1505 (2008).
[CrossRef] [PubMed]

Xu, J.

Yang, Q.

Yazdanpanah, A.

Yin, Z. Q.

Z. Q. Yin, T. J. Vaegan, T. J. Millar, P. Beaumont, and S. Sarks, “Widespread choroidal insufficiency in primary open-angle glaucoma,” J. Glaucoma6(1), 23–32 (1997).
[CrossRef] [PubMed]

Yoshimura, N.

Zawadzki, R. J.

Bioinformatics (1)

M. Scholz, F. Kaplan, C. L. Guy, J. Kopka, and J. Selbig, “Non-linear PCA: a missing data approach,” Bioinformatics21(20), 3887–3895 (2005).
[CrossRef] [PubMed]

Biomed. Opt. Express (2)

Br. J. Ophthalmol. (1)

S. H. Sarks, “Ageing and degeneration in the macular region: a clinico-pathological study,” Br. J. Ophthalmol.60(5), 324–341 (1976).
[CrossRef] [PubMed]

IEEE Signal Process. Mag. (1)

I. W. Selesnick, R. G. Baraniuk, and N. G. Kingsbury, “The Dual-Tree Complex Wavelet Transform,” IEEE Signal Process. Mag.22(6), 123–151 (2005).
[CrossRef]

IEEE Trans. Med. Imaging (2)

M. K. Garvin, M. D. Abramoff, 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. Imaging27(10), 1495–1505 (2008).
[CrossRef] [PubMed]

D. Koozekanani, K. Boyer, and C. Roberts, “Retinal thickness measurements from optical coherence tomography using a Markov boundary model,” IEEE Trans. Med. Imaging20(9), 900–916 (2001).
[CrossRef] [PubMed]

IEEE Trans. Pattern Anal. Mach. Intell. (2)

A. K. Mishra, P. W. Fieguth, and D. A. Clausi, “Decoupled active contour (DAC) for boundary detection,” IEEE Trans. Pattern Anal. Mach. Intell.33(2), 310–324 (2011).
[CrossRef] [PubMed]

T. F. Cootes, G. J. Edwards, and C. J. Taylor, “Active appearance models,” IEEE Trans. Pattern Anal. Mach. Intell.23(6), 681–685 (2001).
[CrossRef]

Image Vis. Comput. (1)

J. Matas, O. Chum, M. Urban, and T. Pajdla, “Robust wide-baseline stereo from maximally stable extremal regions,” Image Vis. Comput.22(10), 761–767 (2004).
[CrossRef]

Invest. Ophthalmol. Vis. Sci. (4)

B. Povazay, B. Hermann, B. Hofer, V. Kajić, E. Simpson, T. Bridgford, and W. Drexler, “Wide-field optical coherence tomography of the choroid in vivo,” Invest. Ophthalmol. Vis. Sci.50(4), 1856–1863 (2009).
[CrossRef] [PubMed]

M. Esmaeelpour, B. Považay, B. Hermann, B. Hofer, V. Kajic, S. L. Hale, R. V. North, W. Drexler, and N. J. Sheen, “Mapping choroidal and retinal thickness variation in type 2 diabetes using three-dimensional 1060-nm optical coherence tomography,” Invest. Ophthalmol. Vis. Sci.52(8), 5311–5316 (2011).
[CrossRef] [PubMed]

M. Esmaeelpour, B. Povazay, B. Hermann, B. Hofer, V. Kajic, K. Kapoor, N. J. Sheen, R. V. North, and W. Drexler, “Three-dimensional 1060-nm OCT: choroidal thickness maps in normal subjects and improved posterior segment visualization in cataract patients,” Invest. Ophthalmol. Vis. Sci.51(10), 5260–5266 (2010).
[CrossRef] [PubMed]

D. S. McLeod and G. A. Lutty, “High-resolution histologic analysis of the human choroidal vasculature,” Invest. Ophthalmol. Vis. Sci.35(11), 3799–3811 (1994).
[PubMed]

J. Glaucoma (1)

Z. Q. Yin, T. J. Vaegan, T. J. Millar, P. Beaumont, and S. Sarks, “Widespread choroidal insufficiency in primary open-angle glaucoma,” J. Glaucoma6(1), 23–32 (1997).
[CrossRef] [PubMed]

J. Opt. Soc. Am. A (1)

Mach. Vis. Appl. (1)

J. Molnár, D. Chetverikov, D. Cabrera DeBuc, W. Gao, and G. Somfai, “Layer extraction in rodent retinal images acquired by optical coherence tomography,” Mach. Vis. Appl. (2011).
[CrossRef]

Opt. Express (6)

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. Express13(23), 9480–9491 (2005).
[CrossRef] [PubMed]

M. V. Sarunic, A. Yazdanpanah, E. Gibson, J. Xu, Y. Bai, S. Lee, H. U. Saragovi, and M. F. Beg, “Longitudinal study of retinal degeneration in a rat using spectral domain optical coherence tomography,” Opt. Express18(22), 23435–23441 (2010).
[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. Express18(20), 21293–21307 (2010).
[CrossRef] [PubMed]

D. Cabrera Fernández, H. M. Salinas, and C. A. Puliafito, “Automated detection of retinal layer structures on optical coherence tomography images,” Opt. Express13(25), 10200–10216 (2005).
[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. Express18(18), 19413–19428 (2010).
[CrossRef] [PubMed]

V. Kajić, B. Povazay, B. Hermann, B. Hofer, D. Marshall, P. L. Rosin, and W. Drexler, “Robust segmentation of intraretinal layers in the normal human fovea using a novel statistical model based on texture and shape analysis,” Opt. Express18(14), 14730–14744 (2010).
[CrossRef] [PubMed]

Trans. Am. Ophthalmol. Soc. (1)

W. R. Green and S. N. Key, “Senile macular degeneration: a histopathologic study,” Trans. Am. Ophthalmol. Soc.75, 180–254 (1977).
[PubMed]

Other (8)

W. Drexler and J. G. Fujimoto, Optical Coherence Tomography: Technology and Applications (Springer, 2008), Vol. 1.

A. Yazdanpanah, G. Hamarneh, B. Smith, and M. Sarunic, “Intra-retinal layer segmentation in optical coherence tomography using an active contour approach,” in Medical Image Computing and Computer-Assisted Intervention—MICCAI 2009 (Springer-Verlag, London, UK, 2009), pp. 649–656.

F. Rossant, I. Ghorbel, I. Bloch, M. Paques, and S. Tick, “Automated segmentation of retinal layers in OCT imaging and derived ophthalmic measures,” in IEEE International Symposium on Biomedical Imaging: from Nano to Macro, 2009. ISBI '09 (IEEE, 2009), pp. 1370–1373.

M. Scholz, M. Fraunholz, and J. Selbig, “Nonlinear principal component analysis: neural network models and applications,” in Principal Manifolds for Data Visualization and Dimension Reduction (Springer, 2007), pp. 44–67.

A. Vedaldi and B. Fulkerson, “VLFeat: an open and portable library of computer vision algorithms” (2008), http://www.vlfeat.org/ .

D. Tolliver, Y. Koutis, H. Ishikawa, J. S. Schuman, and G. L. Miller, “Unassisted segmentation of multiple retinal layers via spectral rounding,” in ARVO 2008 Annual Meeting (Association for Research in Vision and Ophthalmology, 2008), poster.

P. Thevenaz and M. Unser, “A pyramid approach to sub-pixel image fusion based on mutual information,” in International Conference on Image Processing, 1996. Proceedings (1996), vol. 1, pp. 265–268.

I. Perkon, A. Košir, J. Tasič, and M. Diamond, “Whisker detection as a shortest path problem,” presented at Visual Observation and Analysis of Animal and Insect Behavior, Istanbul, Aug. 22, 2010.

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Figures (11)

Fig. 1
Fig. 1

Algorithm overview: both the training and unseen data pass through the pre-processing block. The registration is used only for averaging in z-direction as a despeckling procedure, while the segmentation is independent for each B-scan. A statistical model is subsequently constructed that captures the variance in the training data, which can be then used (dotted line) to segment unseen data.

Fig. 2
Fig. 2

Pre-processing steps for finding ILM and RBC: a is the original image; b is obtained after Canny edge filtering; c shows color coded dominant wavelet domain orientations (from dark red “descending” (−90 deg) angle, to dark blue “ascending” (90 deg).

Fig. 3
Fig. 3

RPE estimate (green line and blue dots) and convex hull (red line).

Fig. 4
Fig. 4

The final result: ILM (red) and RBC (green).

Fig. 5
Fig. 5

A slice from a typical diabetes type 1 eye (patient D), before (a) and after (b) the A-scan optimization. ILM (red), RBC (green), CSI (purple).

Fig. 6
Fig. 6

The algorithm performs well despite the thinning of the RPE in the middle and deep, low signal choroid.

Fig. 7
Fig. 7

The choroid is very thin and has a strong variation in contrast.

Fig. 8
Fig. 8

RPE/RBC and CSI are found despite the extremely thin choroid with a strong signal in the middle as a result of the RPE atrophy.

Fig. 9
Fig. 9

RPE and RBC have an uncommon “inverted” shape.

Fig. 10
Fig. 10

The algorithm correctly interpolated over the drusen, finding a close approximation of the RBC.

Fig. 11
Fig. 11

Choroidal Thickness maps of a diabetes type 1 patient (D, subfigure a) and 5 pathologies (H-L, subfigures b to f).

Tables (2)

Tables Icon

Table 1 Error values on seven eyes with diabetes type 1, expressed as percentage of misclassified pixel relative to the layer area. The total average value is computed as an average of all the patient error values, and is independent of the number of B-scans per stack.

Tables Icon

Table 2 Error values on 5 eyes with various pathologies, about 20 slices manually segmented per stack, expressed as percentage of misclassified pixel relative to the layer area. The total average value is computed as an average of all the patient error values, and is independent of the number of B-scans per stack.

Equations (13)

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

A=( c 11 0 0 c 1m 0 0 c n1 0 0 c nm ), c ij =1I(x,j+1),max(0,ijmp)<x<min(n,i+jmp).
d(sc)= w 1 A(sc,y)+ w 2 | y'' |+ w 3 (1 e w 1 IW(yc,xc, j 1 ) n +e w 2 IW(yc,xc, j 2 ) n IW(yc,xc, ϕ i ) n ) xc= sc1 M yc  sc-1   (mod M) y=A(sc,i)>0 y''=(yyc(ycyp))=(y2*yc+yp) y' ¯ = yyc+(ycyp) 2 = yyp 2 e w 1 = j 2 -j j 2 - j 1 e w 2 =1-e w 1
X=( x 1 x m )=( v 11 v 1n v m1 v mn ), v ij =[of f 1 of f W ].
X=WΣ V T Y= W L T X
Φ gen :z> X ^ Φ extr :X>z
x(xμ(x))/σ(x)
g=G(x,I)
x=S(s)= x ¯ + Q s s g=T(t)= g ¯ + Q g t
A=( aOf f 11 aOf f 1n aOf f u1 aOf f un )
f(s)= G CH (S(s), F MSER (I)) A CH + A PCH
f A ( s A )= G DW (S( s A ),I) G AW (S( s A ),I)
E i B = j=1 j=w | yAu t ij yRe f ij |
E= i=k i=k+1 E i A A + A R ,0<k<b

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