Abstract

Hyperspectral endoscopic imaging has the potential to enhance clinical diagnostics and outcome. Most commercial endoscopes utilize imaging fiber bundles to transmit the collected signal from the patient to the medical operator. These bundles consist of several fiber cores surrounded by a cladding layer creating comb structure-like artifacts, which complicate further analysis, both spatially and spectrally. Here we present an optical fiber pattern removal algorithm which we applied to hyperspectral bronchoscopic images robustly and quantitatively without the need for specific optical or electrical hardware. We validate the performance of the pattern removal by using a novel hyperspectral phasor approach. This algorithm can be generalized to all forms of fiber bundle hyperspectral endoscopy.

© 2018 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

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References

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  1. J. Kaluzny, H. Li, W. Liu, P. Nesper, J. Park, H. F. Zhang, and A. A. Fawzi, “Bayer Filter Snapshot Hyperspectral Fundus Camera for Human Retinal Imaging,” Curr. Eye Res. 42(4), 629–635 (2017).
    [Crossref] [PubMed]
  2. M. Eiter, S. Rupp, and C. Winter, “Physically motivated reconstruction of fiberscopic images,” in Proceedings - International Conference on Pattern Recognition, 2006, vol. 3, pp. 599–602.
  3. B. A. Flusberg, E. D. Cocker, W. Piyawattanametha, J. C. Jung, E. L. M. Cheung, and M. J. Schnitzer, “Fiber-optic fluorescence imaging,” Nat. Methods 2(12), 941–950 (2005).
    [Crossref] [PubMed]
  4. G. J. Tearney, S. A. Boppart, B. E. Bouma, M. E. Brezinski, N. J. Weissman, J. F. Southern, and J. G. Fujimoto, “Scanning single-mode fiber optic catheter-endoscope for optical coherence tomography,” Opt. Lett. 21(7), 543–545 (1996).
    [Crossref] [PubMed]
  5. J. Bec, J. E. Phipps, D. Gorpas, D. Ma, H. Fatakdawala, K. B. Margulies, J. A. Southard, and L. Marcu, “In vivo label-free structural and biochemical imaging of coronary arteries using an integrated ultrasound and multispectral fluorescence lifetime catheter system,” Sci. Rep. 7(1), 8960 (2017).
    [Crossref] [PubMed]
  6. K. Carlson, M. Chidley, K.-B. Sung, M. Descour, A. Gillenwater, M. Follen, and R. Richards-Kortum, “In vivo fiber-optic confocal reflectance microscope with an injection-molded plastic miniature objective lens,” Appl. Opt. 44(10), 1792–1797 (2005).
    [Crossref] [PubMed]
  7. B. E. Sherlock, J. E. Phipps, J. Bec, and L. Marcu, “Simultaneous, label-free, multispectral fluorescence lifetime imaging and optical coherence tomography using a double-clad fiber,” Opt. Lett. 42(19), 3753–3756 (2017).
    [Crossref] [PubMed]
  8. D. L. Dickensheets and G. S. Kino, “Micromachined scanning confocal optical microscope,” Opt. Lett. 21(10), 764–766 (1996).
    [Crossref] [PubMed]
  9. D. Ma, J. Bec, D. Gorpas, D. Yankelevich, and L. Marcu, “Technique for real-time tissue characterization based on scanning multispectral fluorescence lifetime spectroscopy (ms-TRFS),” Biomed. Opt. Express 6(3), 987–1002 (2015).
    [Crossref] [PubMed]
  10. R. T. Kester, N. Bedard, L. Gao, and T. S. Tkaczyk, “Real-time snapshot hyperspectral imaging endoscope,” J. Biomed. Opt. 16(5), 056005 (2011).
    [Crossref] [PubMed]
  11. N. Bedard and T. S. Tkaczyk, “Snapshot spectrally encoded fluorescence imaging through a fiber bundle,” J. Biomed. Opt. 17(8), 080508 (2012).
    [Crossref] [PubMed]
  12. W. G. M. Geraets, A. N. van Daatselaar, and J. G. C. Verheij, “An efficient filling algorithm for counting regions,” Comput. Methods Programs Biomed. 76(1), 1–11 (2004).
    [Crossref] [PubMed]
  13. D. T. Lee and B. J. Schachter, “Two algorithms for constructing a Delaunay triangulation,” Int. J. Comput. Inf. Sci. 9(3), 219–242 (1980).
    [Crossref]
  14. S. Rupp, C. Winter, and M. Elter, “Evaluation of spatial interpolation strategies for the removal of comb-structure in fiber-optic images,” in Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009, 2009, pp. 3677–3680.
    [Crossref]
  15. J. A. Scott, “83.48 Some Examples of the Use of Areal Coordinates in Triangle Geometry,” Math. Gaz. 83(498), 472–477 (1999).
    [Crossref]
  16. F. Cutrale, V. Trivedi, L. A. Trinh, C.-L. Chiu, J. M. Choi, M. S. Artiga, and S. E. Fraser, “Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging,” Nat. Methods 14(2), 149–152 (2017).
    [Crossref] [PubMed]
  17. M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, and H. Burkhardt, “XuvTools: Free, fast and reliable stitching of large 3D datasets,” J. Microsc. 233(1), 42–60 (2009).
    [Crossref] [PubMed]

2017 (4)

J. Kaluzny, H. Li, W. Liu, P. Nesper, J. Park, H. F. Zhang, and A. A. Fawzi, “Bayer Filter Snapshot Hyperspectral Fundus Camera for Human Retinal Imaging,” Curr. Eye Res. 42(4), 629–635 (2017).
[Crossref] [PubMed]

J. Bec, J. E. Phipps, D. Gorpas, D. Ma, H. Fatakdawala, K. B. Margulies, J. A. Southard, and L. Marcu, “In vivo label-free structural and biochemical imaging of coronary arteries using an integrated ultrasound and multispectral fluorescence lifetime catheter system,” Sci. Rep. 7(1), 8960 (2017).
[Crossref] [PubMed]

B. E. Sherlock, J. E. Phipps, J. Bec, and L. Marcu, “Simultaneous, label-free, multispectral fluorescence lifetime imaging and optical coherence tomography using a double-clad fiber,” Opt. Lett. 42(19), 3753–3756 (2017).
[Crossref] [PubMed]

F. Cutrale, V. Trivedi, L. A. Trinh, C.-L. Chiu, J. M. Choi, M. S. Artiga, and S. E. Fraser, “Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging,” Nat. Methods 14(2), 149–152 (2017).
[Crossref] [PubMed]

2015 (1)

2012 (1)

N. Bedard and T. S. Tkaczyk, “Snapshot spectrally encoded fluorescence imaging through a fiber bundle,” J. Biomed. Opt. 17(8), 080508 (2012).
[Crossref] [PubMed]

2011 (1)

R. T. Kester, N. Bedard, L. Gao, and T. S. Tkaczyk, “Real-time snapshot hyperspectral imaging endoscope,” J. Biomed. Opt. 16(5), 056005 (2011).
[Crossref] [PubMed]

2009 (1)

M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, and H. Burkhardt, “XuvTools: Free, fast and reliable stitching of large 3D datasets,” J. Microsc. 233(1), 42–60 (2009).
[Crossref] [PubMed]

2005 (2)

2004 (1)

W. G. M. Geraets, A. N. van Daatselaar, and J. G. C. Verheij, “An efficient filling algorithm for counting regions,” Comput. Methods Programs Biomed. 76(1), 1–11 (2004).
[Crossref] [PubMed]

1999 (1)

J. A. Scott, “83.48 Some Examples of the Use of Areal Coordinates in Triangle Geometry,” Math. Gaz. 83(498), 472–477 (1999).
[Crossref]

1996 (2)

1980 (1)

D. T. Lee and B. J. Schachter, “Two algorithms for constructing a Delaunay triangulation,” Int. J. Comput. Inf. Sci. 9(3), 219–242 (1980).
[Crossref]

Artiga, M. S.

F. Cutrale, V. Trivedi, L. A. Trinh, C.-L. Chiu, J. M. Choi, M. S. Artiga, and S. E. Fraser, “Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging,” Nat. Methods 14(2), 149–152 (2017).
[Crossref] [PubMed]

Bec, J.

Bedard, N.

N. Bedard and T. S. Tkaczyk, “Snapshot spectrally encoded fluorescence imaging through a fiber bundle,” J. Biomed. Opt. 17(8), 080508 (2012).
[Crossref] [PubMed]

R. T. Kester, N. Bedard, L. Gao, and T. S. Tkaczyk, “Real-time snapshot hyperspectral imaging endoscope,” J. Biomed. Opt. 16(5), 056005 (2011).
[Crossref] [PubMed]

Boppart, S. A.

Bouma, B. E.

Brezinski, M. E.

Burkhardt, H.

M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, and H. Burkhardt, “XuvTools: Free, fast and reliable stitching of large 3D datasets,” J. Microsc. 233(1), 42–60 (2009).
[Crossref] [PubMed]

Carlson, K.

Cheung, E. L. M.

B. A. Flusberg, E. D. Cocker, W. Piyawattanametha, J. C. Jung, E. L. M. Cheung, and M. J. Schnitzer, “Fiber-optic fluorescence imaging,” Nat. Methods 2(12), 941–950 (2005).
[Crossref] [PubMed]

Chidley, M.

Chiu, C.-L.

F. Cutrale, V. Trivedi, L. A. Trinh, C.-L. Chiu, J. M. Choi, M. S. Artiga, and S. E. Fraser, “Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging,” Nat. Methods 14(2), 149–152 (2017).
[Crossref] [PubMed]

Choi, J. M.

F. Cutrale, V. Trivedi, L. A. Trinh, C.-L. Chiu, J. M. Choi, M. S. Artiga, and S. E. Fraser, “Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging,” Nat. Methods 14(2), 149–152 (2017).
[Crossref] [PubMed]

Cocker, E. D.

B. A. Flusberg, E. D. Cocker, W. Piyawattanametha, J. C. Jung, E. L. M. Cheung, and M. J. Schnitzer, “Fiber-optic fluorescence imaging,” Nat. Methods 2(12), 941–950 (2005).
[Crossref] [PubMed]

Cutrale, F.

F. Cutrale, V. Trivedi, L. A. Trinh, C.-L. Chiu, J. M. Choi, M. S. Artiga, and S. E. Fraser, “Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging,” Nat. Methods 14(2), 149–152 (2017).
[Crossref] [PubMed]

Descour, M.

Dickensheets, D. L.

Driever, W.

M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, and H. Burkhardt, “XuvTools: Free, fast and reliable stitching of large 3D datasets,” J. Microsc. 233(1), 42–60 (2009).
[Crossref] [PubMed]

Elter, M.

S. Rupp, C. Winter, and M. Elter, “Evaluation of spatial interpolation strategies for the removal of comb-structure in fiber-optic images,” in Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009, 2009, pp. 3677–3680.
[Crossref]

Emmenlauer, M.

M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, and H. Burkhardt, “XuvTools: Free, fast and reliable stitching of large 3D datasets,” J. Microsc. 233(1), 42–60 (2009).
[Crossref] [PubMed]

Fatakdawala, H.

J. Bec, J. E. Phipps, D. Gorpas, D. Ma, H. Fatakdawala, K. B. Margulies, J. A. Southard, and L. Marcu, “In vivo label-free structural and biochemical imaging of coronary arteries using an integrated ultrasound and multispectral fluorescence lifetime catheter system,” Sci. Rep. 7(1), 8960 (2017).
[Crossref] [PubMed]

Fawzi, A. A.

J. Kaluzny, H. Li, W. Liu, P. Nesper, J. Park, H. F. Zhang, and A. A. Fawzi, “Bayer Filter Snapshot Hyperspectral Fundus Camera for Human Retinal Imaging,” Curr. Eye Res. 42(4), 629–635 (2017).
[Crossref] [PubMed]

Filippi, A.

M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, and H. Burkhardt, “XuvTools: Free, fast and reliable stitching of large 3D datasets,” J. Microsc. 233(1), 42–60 (2009).
[Crossref] [PubMed]

Flusberg, B. A.

B. A. Flusberg, E. D. Cocker, W. Piyawattanametha, J. C. Jung, E. L. M. Cheung, and M. J. Schnitzer, “Fiber-optic fluorescence imaging,” Nat. Methods 2(12), 941–950 (2005).
[Crossref] [PubMed]

Follen, M.

Fraser, S. E.

F. Cutrale, V. Trivedi, L. A. Trinh, C.-L. Chiu, J. M. Choi, M. S. Artiga, and S. E. Fraser, “Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging,” Nat. Methods 14(2), 149–152 (2017).
[Crossref] [PubMed]

Fujimoto, J. G.

Gao, L.

R. T. Kester, N. Bedard, L. Gao, and T. S. Tkaczyk, “Real-time snapshot hyperspectral imaging endoscope,” J. Biomed. Opt. 16(5), 056005 (2011).
[Crossref] [PubMed]

Geraets, W. G. M.

W. G. M. Geraets, A. N. van Daatselaar, and J. G. C. Verheij, “An efficient filling algorithm for counting regions,” Comput. Methods Programs Biomed. 76(1), 1–11 (2004).
[Crossref] [PubMed]

Gillenwater, A.

Gorpas, D.

J. Bec, J. E. Phipps, D. Gorpas, D. Ma, H. Fatakdawala, K. B. Margulies, J. A. Southard, and L. Marcu, “In vivo label-free structural and biochemical imaging of coronary arteries using an integrated ultrasound and multispectral fluorescence lifetime catheter system,” Sci. Rep. 7(1), 8960 (2017).
[Crossref] [PubMed]

D. Ma, J. Bec, D. Gorpas, D. Yankelevich, and L. Marcu, “Technique for real-time tissue characterization based on scanning multispectral fluorescence lifetime spectroscopy (ms-TRFS),” Biomed. Opt. Express 6(3), 987–1002 (2015).
[Crossref] [PubMed]

Griffa, A.

M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, and H. Burkhardt, “XuvTools: Free, fast and reliable stitching of large 3D datasets,” J. Microsc. 233(1), 42–60 (2009).
[Crossref] [PubMed]

Jung, J. C.

B. A. Flusberg, E. D. Cocker, W. Piyawattanametha, J. C. Jung, E. L. M. Cheung, and M. J. Schnitzer, “Fiber-optic fluorescence imaging,” Nat. Methods 2(12), 941–950 (2005).
[Crossref] [PubMed]

Kaluzny, J.

J. Kaluzny, H. Li, W. Liu, P. Nesper, J. Park, H. F. Zhang, and A. A. Fawzi, “Bayer Filter Snapshot Hyperspectral Fundus Camera for Human Retinal Imaging,” Curr. Eye Res. 42(4), 629–635 (2017).
[Crossref] [PubMed]

Kester, R. T.

R. T. Kester, N. Bedard, L. Gao, and T. S. Tkaczyk, “Real-time snapshot hyperspectral imaging endoscope,” J. Biomed. Opt. 16(5), 056005 (2011).
[Crossref] [PubMed]

Kino, G. S.

Lee, D. T.

D. T. Lee and B. J. Schachter, “Two algorithms for constructing a Delaunay triangulation,” Int. J. Comput. Inf. Sci. 9(3), 219–242 (1980).
[Crossref]

Li, H.

J. Kaluzny, H. Li, W. Liu, P. Nesper, J. Park, H. F. Zhang, and A. A. Fawzi, “Bayer Filter Snapshot Hyperspectral Fundus Camera for Human Retinal Imaging,” Curr. Eye Res. 42(4), 629–635 (2017).
[Crossref] [PubMed]

Liu, W.

J. Kaluzny, H. Li, W. Liu, P. Nesper, J. Park, H. F. Zhang, and A. A. Fawzi, “Bayer Filter Snapshot Hyperspectral Fundus Camera for Human Retinal Imaging,” Curr. Eye Res. 42(4), 629–635 (2017).
[Crossref] [PubMed]

Ma, D.

J. Bec, J. E. Phipps, D. Gorpas, D. Ma, H. Fatakdawala, K. B. Margulies, J. A. Southard, and L. Marcu, “In vivo label-free structural and biochemical imaging of coronary arteries using an integrated ultrasound and multispectral fluorescence lifetime catheter system,” Sci. Rep. 7(1), 8960 (2017).
[Crossref] [PubMed]

D. Ma, J. Bec, D. Gorpas, D. Yankelevich, and L. Marcu, “Technique for real-time tissue characterization based on scanning multispectral fluorescence lifetime spectroscopy (ms-TRFS),” Biomed. Opt. Express 6(3), 987–1002 (2015).
[Crossref] [PubMed]

Marcu, L.

Margulies, K. B.

J. Bec, J. E. Phipps, D. Gorpas, D. Ma, H. Fatakdawala, K. B. Margulies, J. A. Southard, and L. Marcu, “In vivo label-free structural and biochemical imaging of coronary arteries using an integrated ultrasound and multispectral fluorescence lifetime catheter system,” Sci. Rep. 7(1), 8960 (2017).
[Crossref] [PubMed]

Nesper, P.

J. Kaluzny, H. Li, W. Liu, P. Nesper, J. Park, H. F. Zhang, and A. A. Fawzi, “Bayer Filter Snapshot Hyperspectral Fundus Camera for Human Retinal Imaging,” Curr. Eye Res. 42(4), 629–635 (2017).
[Crossref] [PubMed]

Nitschke, R.

M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, and H. Burkhardt, “XuvTools: Free, fast and reliable stitching of large 3D datasets,” J. Microsc. 233(1), 42–60 (2009).
[Crossref] [PubMed]

Park, J.

J. Kaluzny, H. Li, W. Liu, P. Nesper, J. Park, H. F. Zhang, and A. A. Fawzi, “Bayer Filter Snapshot Hyperspectral Fundus Camera for Human Retinal Imaging,” Curr. Eye Res. 42(4), 629–635 (2017).
[Crossref] [PubMed]

Phipps, J. E.

J. Bec, J. E. Phipps, D. Gorpas, D. Ma, H. Fatakdawala, K. B. Margulies, J. A. Southard, and L. Marcu, “In vivo label-free structural and biochemical imaging of coronary arteries using an integrated ultrasound and multispectral fluorescence lifetime catheter system,” Sci. Rep. 7(1), 8960 (2017).
[Crossref] [PubMed]

B. E. Sherlock, J. E. Phipps, J. Bec, and L. Marcu, “Simultaneous, label-free, multispectral fluorescence lifetime imaging and optical coherence tomography using a double-clad fiber,” Opt. Lett. 42(19), 3753–3756 (2017).
[Crossref] [PubMed]

Piyawattanametha, W.

B. A. Flusberg, E. D. Cocker, W. Piyawattanametha, J. C. Jung, E. L. M. Cheung, and M. J. Schnitzer, “Fiber-optic fluorescence imaging,” Nat. Methods 2(12), 941–950 (2005).
[Crossref] [PubMed]

Ponti, A.

M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, and H. Burkhardt, “XuvTools: Free, fast and reliable stitching of large 3D datasets,” J. Microsc. 233(1), 42–60 (2009).
[Crossref] [PubMed]

Richards-Kortum, R.

Ronneberger, O.

M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, and H. Burkhardt, “XuvTools: Free, fast and reliable stitching of large 3D datasets,” J. Microsc. 233(1), 42–60 (2009).
[Crossref] [PubMed]

Rupp, S.

S. Rupp, C. Winter, and M. Elter, “Evaluation of spatial interpolation strategies for the removal of comb-structure in fiber-optic images,” in Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009, 2009, pp. 3677–3680.
[Crossref]

Schachter, B. J.

D. T. Lee and B. J. Schachter, “Two algorithms for constructing a Delaunay triangulation,” Int. J. Comput. Inf. Sci. 9(3), 219–242 (1980).
[Crossref]

Schnitzer, M. J.

B. A. Flusberg, E. D. Cocker, W. Piyawattanametha, J. C. Jung, E. L. M. Cheung, and M. J. Schnitzer, “Fiber-optic fluorescence imaging,” Nat. Methods 2(12), 941–950 (2005).
[Crossref] [PubMed]

Schwarb, P.

M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, and H. Burkhardt, “XuvTools: Free, fast and reliable stitching of large 3D datasets,” J. Microsc. 233(1), 42–60 (2009).
[Crossref] [PubMed]

Scott, J. A.

J. A. Scott, “83.48 Some Examples of the Use of Areal Coordinates in Triangle Geometry,” Math. Gaz. 83(498), 472–477 (1999).
[Crossref]

Sherlock, B. E.

Southard, J. A.

J. Bec, J. E. Phipps, D. Gorpas, D. Ma, H. Fatakdawala, K. B. Margulies, J. A. Southard, and L. Marcu, “In vivo label-free structural and biochemical imaging of coronary arteries using an integrated ultrasound and multispectral fluorescence lifetime catheter system,” Sci. Rep. 7(1), 8960 (2017).
[Crossref] [PubMed]

Southern, J. F.

Sung, K.-B.

Tearney, G. J.

Tkaczyk, T. S.

N. Bedard and T. S. Tkaczyk, “Snapshot spectrally encoded fluorescence imaging through a fiber bundle,” J. Biomed. Opt. 17(8), 080508 (2012).
[Crossref] [PubMed]

R. T. Kester, N. Bedard, L. Gao, and T. S. Tkaczyk, “Real-time snapshot hyperspectral imaging endoscope,” J. Biomed. Opt. 16(5), 056005 (2011).
[Crossref] [PubMed]

Trinh, L. A.

F. Cutrale, V. Trivedi, L. A. Trinh, C.-L. Chiu, J. M. Choi, M. S. Artiga, and S. E. Fraser, “Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging,” Nat. Methods 14(2), 149–152 (2017).
[Crossref] [PubMed]

Trivedi, V.

F. Cutrale, V. Trivedi, L. A. Trinh, C.-L. Chiu, J. M. Choi, M. S. Artiga, and S. E. Fraser, “Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging,” Nat. Methods 14(2), 149–152 (2017).
[Crossref] [PubMed]

van Daatselaar, A. N.

W. G. M. Geraets, A. N. van Daatselaar, and J. G. C. Verheij, “An efficient filling algorithm for counting regions,” Comput. Methods Programs Biomed. 76(1), 1–11 (2004).
[Crossref] [PubMed]

Verheij, J. G. C.

W. G. M. Geraets, A. N. van Daatselaar, and J. G. C. Verheij, “An efficient filling algorithm for counting regions,” Comput. Methods Programs Biomed. 76(1), 1–11 (2004).
[Crossref] [PubMed]

Weissman, N. J.

Winter, C.

S. Rupp, C. Winter, and M. Elter, “Evaluation of spatial interpolation strategies for the removal of comb-structure in fiber-optic images,” in Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009, 2009, pp. 3677–3680.
[Crossref]

Yankelevich, D.

Zhang, H. F.

J. Kaluzny, H. Li, W. Liu, P. Nesper, J. Park, H. F. Zhang, and A. A. Fawzi, “Bayer Filter Snapshot Hyperspectral Fundus Camera for Human Retinal Imaging,” Curr. Eye Res. 42(4), 629–635 (2017).
[Crossref] [PubMed]

Appl. Opt. (1)

Biomed. Opt. Express (1)

Comput. Methods Programs Biomed. (1)

W. G. M. Geraets, A. N. van Daatselaar, and J. G. C. Verheij, “An efficient filling algorithm for counting regions,” Comput. Methods Programs Biomed. 76(1), 1–11 (2004).
[Crossref] [PubMed]

Curr. Eye Res. (1)

J. Kaluzny, H. Li, W. Liu, P. Nesper, J. Park, H. F. Zhang, and A. A. Fawzi, “Bayer Filter Snapshot Hyperspectral Fundus Camera for Human Retinal Imaging,” Curr. Eye Res. 42(4), 629–635 (2017).
[Crossref] [PubMed]

Int. J. Comput. Inf. Sci. (1)

D. T. Lee and B. J. Schachter, “Two algorithms for constructing a Delaunay triangulation,” Int. J. Comput. Inf. Sci. 9(3), 219–242 (1980).
[Crossref]

J. Biomed. Opt. (2)

R. T. Kester, N. Bedard, L. Gao, and T. S. Tkaczyk, “Real-time snapshot hyperspectral imaging endoscope,” J. Biomed. Opt. 16(5), 056005 (2011).
[Crossref] [PubMed]

N. Bedard and T. S. Tkaczyk, “Snapshot spectrally encoded fluorescence imaging through a fiber bundle,” J. Biomed. Opt. 17(8), 080508 (2012).
[Crossref] [PubMed]

J. Microsc. (1)

M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, and H. Burkhardt, “XuvTools: Free, fast and reliable stitching of large 3D datasets,” J. Microsc. 233(1), 42–60 (2009).
[Crossref] [PubMed]

Math. Gaz. (1)

J. A. Scott, “83.48 Some Examples of the Use of Areal Coordinates in Triangle Geometry,” Math. Gaz. 83(498), 472–477 (1999).
[Crossref]

Nat. Methods (2)

F. Cutrale, V. Trivedi, L. A. Trinh, C.-L. Chiu, J. M. Choi, M. S. Artiga, and S. E. Fraser, “Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging,” Nat. Methods 14(2), 149–152 (2017).
[Crossref] [PubMed]

B. A. Flusberg, E. D. Cocker, W. Piyawattanametha, J. C. Jung, E. L. M. Cheung, and M. J. Schnitzer, “Fiber-optic fluorescence imaging,” Nat. Methods 2(12), 941–950 (2005).
[Crossref] [PubMed]

Opt. Lett. (3)

Sci. Rep. (1)

J. Bec, J. E. Phipps, D. Gorpas, D. Ma, H. Fatakdawala, K. B. Margulies, J. A. Southard, and L. Marcu, “In vivo label-free structural and biochemical imaging of coronary arteries using an integrated ultrasound and multispectral fluorescence lifetime catheter system,” Sci. Rep. 7(1), 8960 (2017).
[Crossref] [PubMed]

Other (2)

M. Eiter, S. Rupp, and C. Winter, “Physically motivated reconstruction of fiberscopic images,” in Proceedings - International Conference on Pattern Recognition, 2006, vol. 3, pp. 599–602.

S. Rupp, C. Winter, and M. Elter, “Evaluation of spatial interpolation strategies for the removal of comb-structure in fiber-optic images,” in Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009, 2009, pp. 3677–3680.
[Crossref]

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Figures (7)

Fig. 1
Fig. 1 System setup. (a) Imaging system configuration. (1) Snapshot CMOS mosaic hyperspectral camera. (2) 1:2.5 matched pair BBAR 400-700nm, 35mm bronchoscope adapter (Thorlabs, Newton, NJ, USA), longpass filter (OD4 – 475nm/25mm, Edmund, Barrington, NJ, USA) and shortpass filter (OD4 – 650nm/25mm, Edmund, Barrington, NJ, USA). (3)(4) Bronchoscope and fiber bundle. (5) Halogen light source (Olympus CLK-4). (6) Light-guide cable (4.25mm, 3m, CF type, Olympus, Tokyo, Japan). (7) Sample. (8) Work station (PC). (9) Ethernet cable. (b) Snapshot mosaic hyperspectral CMOS sensor Bayer filter layout and peak wavelengths of each channel (SM4x4-460-630, IMEC, Leuven, Belgium). (c) Quantum Efficiency (QE) of 16 physical channels.
Fig. 2
Fig. 2 Fiber pattern removal algorithm diagram. (a) Pattern masked white reference image and (f) target image. (b)(g). Localization of fiber cores based on white reference image, same locations applied to target image. (c)(h). Application of Delaunay triangulation to generate Vonoroi diagrams. (d)(i). Apply barycentric interpolation to reconstruct pattern removed image. (e)(j). Resulting Pattern removed image (Channel 6 of 13 shown).
Fig. 3
Fig. 3 Fiber core pixels screening process. (a) Fiber core pixel candidates (magenta circles) after first round of screening. Notice the presence of false positive locations due to the presence of local maxima (b) Second screening identifies false positive coordinates (cyan circles) using relative distance analysis. (c) Fiber core pixels after two rounds of screenings, after removal of incorrect fiber core locations.
Fig. 4
Fig. 4 Barycentric coordinates and interpolation diagram. The vertices   v i ,       i = 1 , 2 , 3     represent fiber cores. Each pixel within the triangle is defined as p. The resulting areas for each pixel p and points v i are defined as A i .
Fig. 5
Fig. 5 Reflectance spectra of six standard color targets at 13 peak wavelengths. Average spectra calculated on calibrated color targets. (Blue crosses) Standard reflectance spectra from manufacturer. (Cyan circles) Recovered reflectance without fiber spectrum calibration. (Magenta crosses) Recovered reflectance with fiber spectrum calibration applied.
Fig. 6
Fig. 6 Hyperspectral Phasor analysis on color targets and color checkers. (column 1) Phasor plots of reference images(35mm lens). (column 2) Phasor plots of fiber pattern masked images. (column 3) Phasor plots of fiber pattern removed images. (column 4) Color targets and color checkers. (row a) Blue color target, SCS-BL-010, Labsphere. (row b) Green color target, SCS-GN-010, Labsphere. (row c) Red color target, SCS-RD-010, Labsphere. (row d) Brown color checker, ColorChecker Classic Card, X-Rite. (row e) Yellow color checker, ColorChecker Classic Card, X-Rite. (row f) Neutral 3.5(grey) color checker, ColorChecker Classic Card, X-Rite.
Fig. 7
Fig. 7 Application example of fiber pattern removal algorithm on exposed mouse trachea. Images were acquired as a “fly-over” with our hyperspectral bronchoscope setup and stitched. Images represent a true-color visualization of the hyperspectral data sets for comparison purpose (a) Pattern masked stitched mouse trachea image. Visible honeycomb pattern affects the quality of the image (b) Pattern removed image. The hyperspectral pattern removing algorithm improves the visualization of the image. Color tones are unchanged, suggesting a reduced presence of spectral artifacts.

Tables (1)

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Table 1 Scatter error and shifted mean error

Equations (6)

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I ( p ) =     A 1 A 1 + A 2 + A 3 I ( v 1 ) + A 2 A 1 + A 2 + A 3 I ( v 2 ) + A 3 A 1 + A 2 + A 3 I ( v 3 )
R o r i g i n a l = E w h i t e r e f E s a m p l e I s a m p l e I d a r k r e f s a m p l e I w h i t e r e f I d a r k r e f w h i t e r e f
R c o r r e c t e d = R o r i g i n a l × T
M S E i   =   ( s i _ w i r i _ ) T ( s i _ w i r i _ ) ,   i = 1 , 2 13
w i = s i _ T r i _ r i _ T r i _ , i = 1 , 2...13
R f i n a l , i =   w i R c o r r e c t , i

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