Performance evaluation of automated segmentation software on optical coherence tomography volume data

Journal of Biophotonics

Volumn 9, Issue 5, 2016, Pages 478-489

  Tian, Jing ^a   Varga, Boglarka ^b   Tatrai, Erika ^b   Fanni, Palya ^b   Somfai, Gabor Mark ^b   Smiddy, William E ^a   Debuc, Delia Cabrera ^a  

^a UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

^b SEMMELWEIS UNIVERSITY   (Hungary)

Author keywords

Automated segmentation software; Ground truth; Optical coherence tomography; Performance evaluation; Spectralis SD OCT

Indexed keywords

AUTOMATION; OPHTHALMOLOGY; TOMOGRAPHY;

AUTOMATED SEGMENTATION; CLINICAL SETTINGS; COMMON GROUND; GROUND TRUTH; PERFORMANCE EVALUATION; SEGMENTATION ALGORITHMS; SPECTRALIS SD-OCT; VALIDATION PROCESS;

OPTICAL TOMOGRAPHY;

ALGORITHM; DIAGNOSTIC IMAGING; HUMAN; OPTICAL COHERENCE TOMOGRAPHY; REPRODUCIBILITY; RETINA; SOFTWARE;

ALGORITHMS; HUMANS; REPRODUCIBILITY OF RESULTS; RETINA; SOFTWARE; TOMOGRAPHY, OPTICAL COHERENCE;

EID: 84960434380     PISSN: 1864063X     EISSN: 18640648     Source Type: Journal    
DOI: 10.1002/jbio.201500239     Document Type: Review

References (43)

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 J. G. Fujimoto, Science 80, 1178-1181 (1991).
2. A. M. Zysk, F. T. Nguyen, A. L. Oldenburg, D. L. Marks, and S. A. Boppart, J. Biomed. Opt. 12, 051403 (2007).
3. R. Hamdan, R. G. Gonzalez, S. Ghostine, and C. Caussin, Archives of Cardiovascular Diseases 105, 529-534 (2012).
4. C. A. Puliafito, Ophthalmic Surg. Lasers Imaging 41, S5 (2010).
5. J. S. Schuman, C. A. Puliafito, J. G. Fujimoto, and S. D. Jay, Optical Coherence Tomography of Ocular Diseases, 3rd ed. Thorofare: Slack, Inc, 2004.
6. W. Drexler, Journal of Biomedical Optics 9, 47 (2004).
7. A. F. Fercher, Z. Med. Phys. 20, 251-76 (2010).
8. Biopigen Inc, Envisu C-Class SDOCT System | Bioptigen, Inc. [Online]. Available: http://www.bioptigen.com/products/c-class/ [Accessed: 06-Sep-2015].
9. Canon, Canon OCT-HS100 - Eye Care - Canon Europe, 02-Jan-2012. [Online]. Available: http://www.canon-europe.com/medical/eye_care/oct-hs100/ [Accessed: 06-Sep-2015].
10. Optovue Inc, iVUE SD-OCT. [Online]. Available: http://optovue.com/wp-content/uploads/2013/08/iVue-Brochure.pdf [Accessed: 06-Sep-2015].
11. Heidelberg Engineering GmbH, Spectralis HRA+OCT User Manual Software Version 6.0, 2014.
12. D. Koozekanani, K. Boyer, and C. Roberts, IEEE Trans. Med. Imaging 20, 900-916 (2001).
13. D. Cabrera Fernández, H. M. Salinas, and C. A. Puliafito, Opt. Express 13, 10200-10216 (2005).
14. T. Fabritius, S. Makita, M. Miura, R. Myllylä, and Y. Yasuno, Opt. Express 17, 15659-15669 (2009).
15. M. Shahidi, Z. Wang, and R. Zelkha, Am. J. Ophthalmol. 139, 1056-61 (2005).
16. H. Ishikawa, D. M. Stein, G. Wollstein, S. Beaton, J. G. Fujimoto, and J. S. Schuman, Invest. Ophthalmol. Vis. Sci. 46, 2012-7 (2005).
17. G. Gregori and R. W. Knighton, Invest. Ophthalmol. Vis. Sci. 45, 3007 (2004).
18. M. D. Abràmoff, M. K. Garvin, and M. Sonka, IEEE Rev. Biomed. Eng. 3, 169-208 (2010).
19. S. J. Chiu, X. T. Li, P. Nicholas, C. A. Toth, J. A. Izatt, and S. Farsiu, Opt. Express 18, 19413-19428 (2010).
20. M. K. Garvin, M. D. Abràmoff, X. Wu, S. R. Russell, T. L. Burns, and M. Sonka, IEEE Trans. Med. Imaging 28, 1436-144 (2009).
21. A. Lang, A. Carass, M. Hauser, E. S. Sotirchos, P. A. Calabresi, H. S. Ying, and J. L. Prince, Biomed. Opt. Express 4, 1133-52 (2013).
22. P. A. Dufour, L. Ceklic, H. Abdillahi, S. Schroder, S. De Dzanet, U. Wolf-Schnurrbusch, and J. Kowal, IEEE Trans. Med. Imaging 32, 531-543 (2013).
23. A. Yazdanpanah, G. Hamarneh, B. R. Smith, and M. V. Sarunic, IEEE Trans. Med. Imaging 30, 484-96 (2011).
24. V. Kajić, B. Povazay, B. Hermann, B. Hofer, D. Marshall, P. L. Rosin, and W. Drexler, Opt. Express 18, 14730-44 (2010).
25. Q. Chen, T. Leng, L. Zheng, L. Kutzscher, J. Ma, L. de Sisternes, and D. L. Rubin, Med. Image Anal. 17, 1058-72 (2013).
26. M. A. Mayer, J. Hornegger, C. Y. Mardin, and R. P. Tornow, Biomed. Opt. Express 1, 1358-1383 (2010).
27. D. C. DeBuc, A review of algorithms for segmentation of retinal image data using optical coherence tomography (2011).
28. J. D. Oakley, I. Gabilondo, C. Songster, D. Russakoff, A. Green, and P. Villoslada, Invest. Ophthalmol. Vis. Sci. 55, 4790 (2014).
29. J. Tian, B. Varga, G. M. Somfai, W.-H. Lee, W. E. Smiddy, and Delia Cabrera DeBuc, PlosOne 8, 0133908 (2015).
30. K. Lee, M. D. Abramoff, M. Garvin, and M. Sonka, The Iowa Reference Algorithms (Retinal Image Analysis Lab, Iowa Institute for Biomedical Imaging, Iowa City, IA). [Online]. Available: https://www.iibi.uiowa.edu/content/iowa-reference-algorithms-human-and-murine-oct-retinal-layer-analysis-and-display.
31. A. Lang, NITRC: AURA tools : AUtomated Retinal Analysis tools: Tool/Resource Info, 2015. [Online]. Available: http://www.nitrc.org/projects/aura_tools/ [Accessed: 22-Jun-2015].
32. P. A. Dufour, OCT Segmentation Application. [Online]. Available: http://pascaldufour.net/Research/software_data.html [Accessed: 22-Jun-2015].
33. G. Staurenghi, S. Sadda, U. Chakravarthy, and R. F. Spaide, Ophthalmology 121, 1572-1578 (2014).
34. E. W. Dijkstra, Numer. Math. 1, 269-271 (1959).
35. K. Li, X. Wu, D. Z. Chen, and M. Sonka, IEEE Trans. Pattern Anal. Mach. Intell. 28, 119-134 (2006).
36. M. Mayer, Read heidelberg engineering (he) oct raw files., 2011. [Online]. Available: http://www5.informatik.unierlangen.de/fileadmin/Persons/MayerMarkus/openVol.m URL.
37. MathWorks, MATLAB Runtime - MATLAB Compiler. [Online]. Available: http://www.mathworks.com/products/compiler/mcr/?refresh=true [Accessed: 22-Jun-2015].
38. D. DeBuc, E. Tatrai, L. Laurik, B. E. Varga, V. Olvedy, A. Somogyi, W. E. Smiddy, and G. M. Somfai, J. Clin. Exp. Ophthalmol. 04, no. 04, (2013).
39. Z. Hu, M. Nittala, and S. Sadda, Invest. Ophthalmol. Vis. Sci. 54, 5492 (2013).
40. H. Chen, X. Chen, Z. Qiu, D. Xiang, W. Chen, F. Shi, J. Zheng, W. Zhu, and M. Sonka, Sci. Rep. 5, 9269 (2015).
41. K. A. Vermeer, J. van der Schoot, H. G. Lemij, and J. F. de Boer, Invest. Ophthalmol. Vis. Sci. 53, 6102-6108 (2012).
42. T. E. de Carlo, A. Romano, N. K. Waheed, and J. S. Duker, Int. J. Retin. Vitr. 1, 5 (2015).
43. M. Tiemann, History of the OSI | Open Source Initiative, Sciencecommons.org., 2010. [Online]. Available: http://opensource.org/history [Accessed: 07-Sep-2015].