An approach to automated retinal layer segmentation in SDOCT images
-
2018-05-03 https://doi.org/10.14419/ijet.v7i2.25.12371 -
Image Analysis, Noise in Imaging Systems, Image Detection Systems, Transforms, Computational Imaging, Optical Coherence Tomography, Ophthalmology. -
Abstract
The optical coherence tomography (OCT) imaging technique is a precise and well-known approach to the diagnosis of retinal layers. The pathological changes in the retina challenge the accuracy of computational segmentation approaches in the evaluation and identification of defects in the boundary layer. The layer segmentations and boundary detections are distorted by noise in the computation. In this work, we propose a fully automated segmentation algorithm using a denoising technique called the Boisterous Obscure Ratio (BOR) for human and mammal retina. First, the BOR is derived using noise detection, i.e., from the Robust Outlyingness Ratio (ROR). It is then applied to edge and layer detection using a gradient-based deformable contour model. Second, the image is vectorised. In this method, a cluster and column intensity grid is applied to identify and determine the unsegmented layers. Using the layer intensity and a region growth seed point algorithm, segmentation of the prominent layers is achieved. The automatic BOR method is an image segmentation process that determines the eight layers in retinal spectral domain optical coherence tomography images. The highlight of the BOR method is that the results produced are accurate, highly substantial, and effective, although time consuming.
Â
-
References
[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, Optical coherence tomography, Science, Vol.254, No.5035, (1991)1178-1181.
[2] J. G. Fujimoto, W. Drexler, J. S. Schuman, and C. K. Hitzenberger, "Optical Coherence Tomography (OCT) in ophthalmology: introduction," Opt. Express, vol.17, No.5, 3978-3979.
[3] Nazli Demirkaya, Hille W. van Dijk, Sanne M. van Schuppen, Michael D. Abr`amoff, Mona K. Garvin, Milan Sonka, Reinier O. Schlingemann, and Frank D. Verbraak, "Effect of Age on Individual Retinal Layer Thickness in Normal Eyes as Measured With Spectral-Domain Optical Coherence Tomography", Invest. Ophthalmol. Vis. Sci., vol. 54, no. 7, pp.4934-4940, 2013.
[4] Delia Cabrera DeBuc, A Review of Algorithms for Segmentation of Retinal Image Data Using Optical Coherence Tomography Computer and Information Science, Artificial Intelligence, "Image Segmentation", book edited by Pei-Gee Ho, 2011. pp. 15-54.
[5] S. Sadigh, A. V. Cideciyan, A. Sumaroka, W. C. Huang, X. Luo, M. Swider, J. D. Steinberg, D. Stambolian, and and Samuel G. Jacobson, "Abnormal Thickening as well as Thinning of the Photoreceptor Layer in Intermediate Age-Related Macular Degeneration," Invest. Ophthalmol. Vis. Sci, vol. 54, pp. 1603-1612, 2013.
[6] T. Loupas and W.N. McDicken and PL Allan, "An adaptive weighted median filter for speckle suppression in medical ultrasonic images," IEEE Trans. Circuits Syst, vol. 36, pp. 129-135, 1989.
[7] Sung-jeo and Yong Hoon Lee, "Center Weighted Median Filters and Their Applications to Image enhancement," IEEE Trans. Circuits Syst, vol. 38, pp. 984-993, 1991.
[8] D. C. Fern?ndez, H. M. Salinas, and C. A. Puliafito, "Automated detection of retinal layer structures on optical coherence tomography images," Opt. express, vol. 13, pp. 10200-10216, 2005.
[9] A. Yazdanpanah, G. Hamarneh, B. R. Smith, and and Marinko V. Sarunic, "Intra-retinal layer segmentation in optical coherence tomography using an active contour approach," Med Image Comput Comput Assist Interv, pp. 649-656, 2009.
[10] Mayer, MA, Tornow, RP, Bock, R, Hornegger, J. a. Kruse, and FE, "Automatic Nerve Fiber Layer Segmentation and Geometry Correction on Spectral Domain OCT Images Using Fuzzy C-Means Clustering," Invest. Ophthalmol. Vis. Sci, vol. 49, 2008.
[11] M. A. Mayer, J. Hornegger, C. Y. Mardin, and and Ralf P. Tornow, "Retinal nerve fiber layer segmentation on FD-OCT scans of normal subjects and glaucoma patients," Biomed Opt Express, vol. 1, pp. 1358-1383, 2010.
[12] I. Ghorbel, F. Rossant, I. Bloch, S. Tick, and M. Paques, "Automated segmentation of macular layers in OCT images and quantitative evaluation of performances," Pattern Recogn, vol. 44, pp. 81590-81603, 2011.
[13] K. A. Vermeer, J. van der Schoot, H. G. Lemij, and and J. F. de Boer, "Automated segmentation by pixel classification of retinal layers in ophthalmic OCT images," Biomed. Opt. Express, vol. 2, no. 6, pp. 1743-1756, 2011.
[14] Q. Yang, C. A. Reisman, Z. Wang, Y. Fukuma, M. Hangai, N. Yoshimura, A. Tomidokoro, M. Araie, A. S. Raza, D. C. Hood, and a. K. Chan, "Automated layer segmentation of macular OCT images using dual-scale gradient information," Opt. express, vol. 18, no. 20, pp. 21293-21307, 2010.
[15] M. D. Abramoff, K. Lee, M. Niemeijer, Wallace L. M. Alward, E. C. Greenlee, M. K. Garvin, M. Sonka, and and Young H. Kwon, "Automated Segmentation of the Cup and Rim from Spectral Domain OCT of the Optic Nerve Head," Invest. Ophthalmol. Vis. Sci, vol. 50, no. 12, pp. 5778-5784, 2009.
[16] K. Lee, M. Niemeijer, M. K. Garvin, Y. H. Kwon, M. Sonka, and and Michael D. Abramoff, "Segmentation of the Optic Disc in 3D-OCT Scans of the Optic Nerve Head," IEEE Trans. Med. Imag, vol. 29, no. 1, pp. 159-168, 2010.
[17] Q. G, L. K, D. M, G. MK, A. MD, and S. M, "Three-dimensional analysis of retinal layer texture: Identification of fluid-filled regions in SD-OCT of the macula," IEEE Trans. Med. Imag, vol. 29, no. 6, pp. 1321-1330, 2010.
[18] S. J. Chiu, X. T. Li, P. Nicholas, C. A. Toth, J. A. Izatt, and a. S. Farsiu, "Automatic segmentation of seven retinal layers in SDOCT images congruent with expert manual segmentation," Opt express, vol. 18, no. 18, pp. 19413-19428, 2010.
[19] R. Kafieh, H. Rabbani, M. D. Abramoff, and a. M. Sonka, "Intra-retinal layer segmentation of 3D optical coherence tomography using coarse grained diffusion map," Med. Image Anal, vol. 17, no. 8, pp. 907-928, 2012.
[20] Kafieh R, Rabbani H, Kermani S, "A review of algorithms for segmentation of optical coherence tomography from retina", J Med Sign Sens., Vol.3, No.1, pp.45-60, 2012.
[21] Nakano N, Hangai M, Nakanishi H, Mori S, Nukada M, Kotera Y, Ikeda HO, Nakamura H, Nonaka A, Yoshimura N., "Macular Ganglion Cell Layer Imaging in Preperimetric Glaucoma with Speckle Noise-Reduced Spectral Domain Optical Coherence Tomography", Ophthalmology, Vol. 118, No.12, pp.2414-2426, 2011.
[22] Kim M, Lee SJ, Han J, Yu SY, Kwak HW., "Segmentation error and macular thickness measurements obtained with spectral-domain optical coherence tomography devices in neovascular age-related macular degeneration", Ind J Ophthalmol., Vol.61, No.5, pp.213-217, 2013.
[23] Priyam Chatterjee and Peyman Milanfar, "Patch-Based Near-Optimal Image Denoising," IEEE Trans Med Imaging. Vol.21, No.4, pp1635-1649, 2012.
[24] Jianbing Xu, Haiyan Ou, Cuiru Sun, Po Ching Chui, Victor X. D. Yang, Edmund Y. Lam, and Kenneth K. Y. Wonga, "Wavelet domain compounding for speckle reduction in optical coherence tomography," J. Biomed. Opt., Vol.18, No.9, 096002, 2013.
[25] Markus A. Mayer, Anja Borsdorf, Martin Wagner, Joachim Hornegger, Christian Y. Mardin, and Ralf P. Tornow, "Wavelet denoising of multiframe optical coherence tomography data," Biomed. Opt. Express. 3(3), 572-589 (2012).
[26] Maciej Szkulmowski, Iwona Gorczynska, Daniel Szlag, Marcin Sylwestrzak, Andrzej Kowalczyk, and Maciej Wojtkowski, "Efficient reduction of speckle noise in Optical Coherence Tomography", Optics Express, Vol. 20, No. 2, pp.1337-1359, 2012.
[27] Bo Xiong and Zhouping Yin, "A Universal Denoising Framework with a New Impulse Detector and Nonlocal Means", IEEE Trans Biomed Eng, Vol. 21, No. 4, pp. 1663-1675, 2012.
[28] R. Maronna, R. Martin, and V. Yohar, "Robust Statistics: Theory and Methods." Chichester, U.K.: Wiley, 2006.
[29] Yazdanpanah, G. Hamarneh, B. R. Smith, and M. V. Sarunic, "Segmentation of intra-retinal layers from optical coherence tomography images using an active contour approach," IEEE Trans Med Imaging , Vol. 30, No. 2, pp. 484-496, 2011.
[30] Kalpana Saini, M. L. Dewal, and Manojkumar Rohit, "A Fast Region-Based Active Contour Model for Boundary Detection of Echocardiographic Images", J Digit Imaging. Vol. 25, No.2, pp.271-278, 2012.
[31] Mishra A. K., Fieguth P. W., and Clausi D. A., "Decoupled active contour (DAC) for boundary detection," IEEE Trans. Pattern Anal. Mach. Intell., Vol. 33, No. 2, pp.310-324, 2011.
[32] Giuseppe Papari, Nicolai Petkov, "Edge and line oriented contour detection: State of the art", Image and Vision Computing, Vol. 29, No. 2-3, pp. 79-103, 2011.
[33] Sylvain Paris, Samuel W. Hasinoff, Jan Kautz, "Local Laplacian filters: edge-aware image processing with a Laplacian pyramid." ACM Transactions on Graphics, Vol.30, No. 4, Article No. 68, 2011.
[34] Y. Y. Liu, M. Chen, H. Ishikawa, G. Wollstein, J. S. Schuman, and J. M. Rehg, "Automated macular pathology diagnosis in retinal OCT images using multi-scale spatial pyramid and local binary patterns in texture and shape encoding," Med. Image Anal., Vol. 15, No. 5, pp. 748-759, 2011.
[35] P. J. Burt and E. H. Adelson, "The Laplacian pyramid as a compact image code," IEEE Trans. Commun., Vol. 31, No. 4, pp. 532- 540, 1983.
[36] William McIlhagga, "The Canny Edge Detector Revisited", International Journal of Computer Vision, Vol. 91, No. 3, pp 251-261, 2011.
[37] Nadia Payet, Sinisa Todorovic, "SLEDGE: Sequential Labeling of Image Edges for Boundary Detection", Vol.104, No. 1, pp.15-37, 2013.
[38] Sahirzeeshan Ali, Anant Madabhushi, "An Integrated Region-, Boundary-, Shape-Based Active Contour for Multiple Object Overlap Resolution in Histological Imagery", IEEE Transactions on Medical Imaging, Vol. 31, No. 7, pp.1448-1460, 2012.
[39] Kenya Kusunose, Tomoaki Chono, Tomotsugu Tabata, Hirotsugu Yamada, Masataka Sata, "Echocardiographic image tracker with a speckle adaptive noise reduction filter for the automatic measurement of the left atrial volume curve", Eur heart j. cardiovasc. Imaging, Vol. 15, No. 5, pp. 509, 2014.
[40] W. Jeffrey Elias, Zhong A. Zheng, Paul Domer, Mark Quigg, Nader Pouratian , "Validation of connectivity-based thalamic segmentation with direct electrophysiologic recordings from human sensory thalamus", NeuroImage, Vol. 59, No. 3, pp.2025-2034, 2012.
[41] C.W. Chen, J. Luo, K.J. Parker, Image segmentation via adaptive k-mean clustering and knowledge based morphological operations with biomedical applications", IEEE Transactions on Image Processing, Vol. 7, No. 12, pp. 1673-1683, 1998.
[42] Mohandass G, Ananda Natarajan R, "layer segmentation and detection of GA and Drusen from SD-OCT images", J. theor. Appl. inf. tech., Vol. 60, No.1, pp.9-20, 2014.
[43] Mohandass G, Ananda Natarajan R & Hari Krishnan G, "Comparative analysis of optical coherence tomography retinal images using multidimensional and cluster methods.", Biomed Res- India, Vol.26 No. 2, 2015.
[44] Graham Auger, Stephen Winder, "Spectral Domain OCT: An Aid to Diagnosis and Surgical Planning of Retinal Detachments," J. of Ophthalmology, Vol. 2011. Article ID 725362, 2011.
[45] P. Jindahra, T. R. Hedges, C. E. Mendoza-Santiesteban, G. T. Plant, "Optical coherence tomography of the retina: applications in neurology," Curr. Opin. Neurol., Vol. 23, No. 1, pp. 16-23, 2010.
[46] S. Saidha, S. B. Syc, M. A. Ibrahim, C. Eckstein, C. V. Warner, S. K. Farrell, J. D. Oakley, M. K. Durbin, S. A. Meyer, L. J. Balcer, E. M. Frohman, J. M. Rosenzweig, S. D. Newsome, J. N. Ratchford, Q. D. Nguyen, and P. A. Calabresi, "Primary retinal pathology in multiple sclerosis as detected by optical coherence tomography," Brain, Vol. 134, No. 11, pp. 518-533, 2011.
[47] Kijas JW, Cideciyan AV, Aleman TS, Pianta MJ, Pearce-Kelling SE, Miller BJ, Jacobson SG, Aguirre GD, Acland GM, "Naturally occurring rhodopsin mutation in the dog causes retinal dysfunction and degeneration mimicking human dominant retinitis pigmentosa", Proc. Natl. Acad. Sci. U S A., Vol. 99, No. 9, pp.6328-6333, 2002.
[48] G. Huber, S. C. Beck, C. Grimm, A. Sahaboglu-Tekgoz, F. Paquet-Durand, A. Wenzel, P. Humphries, T. M. Redmond, M. W. Seeliger, and M. D. Fischer, "Spectral domain optical coherence tomography in mouse models of retinal degeneration," Invest. Ophthalmol. Vis. Sci., Vol.50, No. 12, pp.5888-5895, 2009.
[49] Y. Muraoka, H. O. Ikeda, N. Nakano, M. Hangai, Y. Toda, K. Okamoto-Furuta, H. Kohda, M. Kondo, H. Terasaki, A. Kakizuka, and N. Yoshimura, "Real-time imaging of rabbit retina with retinal degeneration by using spectral-domain optical coherence tomography", PloS One, 2012.
[50] Randa S. Eshaqa, William S. Wrightb, Norman R. Harrisa,"Oxygen delivery, consumption, and conversion to reactive oxygen species in experimental models of diabetic retinopathy", Redox biology, vol.2, pp. 661-666, 2014.
[51] Olena Puzyeyeva, Wai Ching Lam, John G. Flanagan, Michael H. Brent, Robert G. Devenyi, Mark S. Mandelcorn, Tien Wong, and Christopher Hudson, "High-Resolution Optical Coherence Tomography Retinal Imaging: A Case Series Illustrating Potential and Limitations", Journal of Ophthalmology, Vol. 2011, Article ID 764183, 2011.
[52] Tae Joong Eom, Yeh-Chan Ahn, Chang-Seok Kim, and Zhongping Chen, "Calibration and characterization protocol for spectral-domain optical coherence tomography using fiber Bragg gratings," J. Biomed. Opt., Vol. 16, No.3, 030501-3, 2011.
[53] C. Sull, L. N. Vuong, and L. L. Price, "Comparison of spectral/Fourier domain optical coherence tomography instruments for assessment of normal macular thickness," Retina, Vol. 30, No. 2, pp. 235-245, 2010.
-
Downloads
-
How to Cite
G, M., Krishnan G, H., & R J, H. (2018). An approach to automated retinal layer segmentation in SDOCT images. International Journal of Engineering & Technology, 7(2.25), 56-63. https://doi.org/10.14419/ijet.v7i2.25.12371Received date: 2018-05-03
Accepted date: 2018-05-03
Published date: 2018-05-03