Abstract

We compared image restoration methods [Richardson-Lucy (RL), Wiener, and Next-image] with measured “scatter” point-spread-functions, for removing subsurface fluorescence from section-and-image cryo-image volumes. All methods removed haze, delineated single cells from clusters, and improved visualization, but RL best represented structures. Contrast-to-noise and contrast-to-background improvement from RL and Wiener were comparable and 35% better than Next-image. Concerning detection of labeled cells, ROC analyses showed RL ≈Wiener > Next-image >> no processing. Next-image was faster than other methods and less prone to image processing artifacts. RL is recommended for the best restoration of the shape and size of fluorescent structures.

© 2010 OSA

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2010 (2)

D. Roy, M. Gargesha, G. J. Steyer, P. Hakimi, R. W. Hanson, and D. L. Wilson, “Multi-scale Characterization of the PEPCK-Cmus Mouse Through 3D Cryo-Imaging,” Int. J. Biomed. Imaging 2010, 1–12 (2010).
[CrossRef]

P. van Horssen, M. Siebes, I. Hoefer, J. A. Spaan, and J. P. van den Wijngaard, “Improved detection of fluorescently labeled microspheres and vessel architecture with an imaging cryomicrotome,” Med. Biol. Eng. Comput. 48(8), 735–744 (2010).
[CrossRef] [PubMed]

2009 (4)

G. J. Steyer, D. Roy, O. Salvado, M. E. Stone, and D. L. Wilson, “Cryo-Imaging of Fluorescently-Labeled Single Cells in a Mouse,” Proc. Soc. Photo Opt. Instrum. Eng. 7262, 72620W, W8 (2009).
[PubMed]

D. Roy, G. J. Steyer, M. Gargesha, M. E. Stone, and D. L. Wilson, “3D cryo-imaging: a very high-resolution view of the whole mouse,” Anat. Rec. (Hoboken) 292(3), 342–351 (2009).
[CrossRef]

M. Gargesha, M. Qutaish, D. Roy, G. Steyer, H. Bartsch, and D. L. Wilson, “Enhanced Volume Rendering Techniques for High-Resolution Color Cryo-Imaging Data,” Proc. Soc. Photo Opt. Instrum. Eng. 7262, 72655V (2009).
[PubMed]

G. J. Steyer, D. Roy, O. Salvado, M. E. Stone, and D. L. Wilson, “Removal of out-of-plane fluorescence for single cell visualization and quantification in cryo-imaging,” Ann. Biomed. Eng. 37(8), 1613–1628 (2009).
[CrossRef] [PubMed]

2007 (1)

T. Ragan, J. D. Sylvan, K. H. Kim, H. Huang, K. Bahlmann, R. T. Lee, and P. T. So, “High-resolution whole organ imaging using two-photon tissue cytometry,” J. Biomed. Opt. 12(1), 014015 (2007).
[CrossRef] [PubMed]

2006 (1)

P. Sarder and A. Nehorai, “Deconvolution methods for 3-D fluorescence microscopy images,” IEEE Signal Process. Mag. 23(3), 32–45 (2006).
[CrossRef]

2005 (2)

G. D. Li, D. Savvas, E. Arthur, and E. J. Lucy, “A new wide field-of-view confocal imaging system and its applications in drug discovery and pathology,” Proc. Soc. Photo Opt. Instrum. Eng. 6009, 1–16 (2005).

J. A. Spaan, R. ter Wee, J. W. van Teeffelen, G. Streekstra, M. Siebes, C. Kolyva, H. Vink, D. S. Fokkema, and E. VanBavel, “Visualisation of intramural coronary vasculature by an imaging cryomicrotome suggests compartmentalisation of myocardial perfusion areas,” Med. Biol. Eng. Comput. 43(4), 431–435 (2005).
[CrossRef] [PubMed]

2004 (2)

J. C. Szucsik, A. G. Lewis, D. J. Marmer, and J. L. Lessard, “Urogenital tract expression of enhanced green fluorescent protein in transgenic mice driven by a smooth muscle gamma-actin promoter,” J. Urol. 171(2), 944–949 (2004).
[CrossRef] [PubMed]

S. H. Park, J. M. Goo, and C. H. Jo, “Receiver operating characteristic (ROC) curve: practical review for radiologists,” Korean J. Radiol. 5(1), 11–18 (2004).
[CrossRef] [PubMed]

2003 (2)

P. S. Tsai, B. Friedman, A. I. Ifarraguerri, B. D. Thompson, V. Lev-Ram, C. B. Schaffer, Q. Xiong, R. Y. Tsien, J. A. Squier, and D. Kleinfeld, “All-optical histology using ultrashort laser pulses,” Neuron 39(1), 27–41 (2003).
[CrossRef] [PubMed]

J. Mitić, T. Anhut, M. Meier, M. Ducros, A. Serov, and T. Lasser, “Optical sectioning in wide-field microscopy obtained by dynamic structured light illumination and detection based on a smart pixel detector array,” Opt. Lett. 28(9), 698–700 (2003).
[CrossRef] [PubMed]

2001 (1)

W. Wallace, L. H. Schaefer, and J. R. Swedlow, “A workingperson’s guide to deconvolution in light microscopy,” Biotechniques 31(5), 1076–1078, 1080, 1082 passim (2001).
[PubMed]

1997 (1)

1994 (1)

R. L. White, “Image restoration using the damped Richardson-Lucy method,” Proc. Soc. Photo Opt. Instrum. Eng. 2198, 1342–1348 (1994).

1982 (1)

L. A. Shepp and Y. Vardi, “Maximum likelihood reconstruction for emission tomography,” IEEE Trans. Med. Imaging 1(2), 113–122 (1982).
[CrossRef] [PubMed]

1974 (1)

L. B. Lucy, “An iterative technique for the rectification of observed distributions,” Astron. J. 79, 745–754 (1974).
[CrossRef]

1972 (1)

Anhut, T.

Arthur, E.

G. D. Li, D. Savvas, E. Arthur, and E. J. Lucy, “A new wide field-of-view confocal imaging system and its applications in drug discovery and pathology,” Proc. Soc. Photo Opt. Instrum. Eng. 6009, 1–16 (2005).

Bahlmann, K.

T. Ragan, J. D. Sylvan, K. H. Kim, H. Huang, K. Bahlmann, R. T. Lee, and P. T. So, “High-resolution whole organ imaging using two-photon tissue cytometry,” J. Biomed. Opt. 12(1), 014015 (2007).
[CrossRef] [PubMed]

Bartsch, H.

M. Gargesha, M. Qutaish, D. Roy, G. Steyer, H. Bartsch, and D. L. Wilson, “Enhanced Volume Rendering Techniques for High-Resolution Color Cryo-Imaging Data,” Proc. Soc. Photo Opt. Instrum. Eng. 7262, 72655V (2009).
[PubMed]

Ducros, M.

Fokkema, D. S.

J. A. Spaan, R. ter Wee, J. W. van Teeffelen, G. Streekstra, M. Siebes, C. Kolyva, H. Vink, D. S. Fokkema, and E. VanBavel, “Visualisation of intramural coronary vasculature by an imaging cryomicrotome suggests compartmentalisation of myocardial perfusion areas,” Med. Biol. Eng. Comput. 43(4), 431–435 (2005).
[CrossRef] [PubMed]

Friedman, B.

P. S. Tsai, B. Friedman, A. I. Ifarraguerri, B. D. Thompson, V. Lev-Ram, C. B. Schaffer, Q. Xiong, R. Y. Tsien, J. A. Squier, and D. Kleinfeld, “All-optical histology using ultrashort laser pulses,” Neuron 39(1), 27–41 (2003).
[CrossRef] [PubMed]

Gargesha, M.

D. Roy, M. Gargesha, G. J. Steyer, P. Hakimi, R. W. Hanson, and D. L. Wilson, “Multi-scale Characterization of the PEPCK-Cmus Mouse Through 3D Cryo-Imaging,” Int. J. Biomed. Imaging 2010, 1–12 (2010).
[CrossRef]

M. Gargesha, M. Qutaish, D. Roy, G. Steyer, H. Bartsch, and D. L. Wilson, “Enhanced Volume Rendering Techniques for High-Resolution Color Cryo-Imaging Data,” Proc. Soc. Photo Opt. Instrum. Eng. 7262, 72655V (2009).
[PubMed]

D. Roy, G. J. Steyer, M. Gargesha, M. E. Stone, and D. L. Wilson, “3D cryo-imaging: a very high-resolution view of the whole mouse,” Anat. Rec. (Hoboken) 292(3), 342–351 (2009).
[CrossRef]

Goo, J. M.

S. H. Park, J. M. Goo, and C. H. Jo, “Receiver operating characteristic (ROC) curve: practical review for radiologists,” Korean J. Radiol. 5(1), 11–18 (2004).
[CrossRef] [PubMed]

Hakimi, P.

D. Roy, M. Gargesha, G. J. Steyer, P. Hakimi, R. W. Hanson, and D. L. Wilson, “Multi-scale Characterization of the PEPCK-Cmus Mouse Through 3D Cryo-Imaging,” Int. J. Biomed. Imaging 2010, 1–12 (2010).
[CrossRef]

Hanson, R. W.

D. Roy, M. Gargesha, G. J. Steyer, P. Hakimi, R. W. Hanson, and D. L. Wilson, “Multi-scale Characterization of the PEPCK-Cmus Mouse Through 3D Cryo-Imaging,” Int. J. Biomed. Imaging 2010, 1–12 (2010).
[CrossRef]

Hoefer, I.

P. van Horssen, M. Siebes, I. Hoefer, J. A. Spaan, and J. P. van den Wijngaard, “Improved detection of fluorescently labeled microspheres and vessel architecture with an imaging cryomicrotome,” Med. Biol. Eng. Comput. 48(8), 735–744 (2010).
[CrossRef] [PubMed]

Huang, H.

T. Ragan, J. D. Sylvan, K. H. Kim, H. Huang, K. Bahlmann, R. T. Lee, and P. T. So, “High-resolution whole organ imaging using two-photon tissue cytometry,” J. Biomed. Opt. 12(1), 014015 (2007).
[CrossRef] [PubMed]

Ifarraguerri, A. I.

P. S. Tsai, B. Friedman, A. I. Ifarraguerri, B. D. Thompson, V. Lev-Ram, C. B. Schaffer, Q. Xiong, R. Y. Tsien, J. A. Squier, and D. Kleinfeld, “All-optical histology using ultrashort laser pulses,” Neuron 39(1), 27–41 (2003).
[CrossRef] [PubMed]

Jo, C. H.

S. H. Park, J. M. Goo, and C. H. Jo, “Receiver operating characteristic (ROC) curve: practical review for radiologists,” Korean J. Radiol. 5(1), 11–18 (2004).
[CrossRef] [PubMed]

Juskaitis, R.

Kim, K. H.

T. Ragan, J. D. Sylvan, K. H. Kim, H. Huang, K. Bahlmann, R. T. Lee, and P. T. So, “High-resolution whole organ imaging using two-photon tissue cytometry,” J. Biomed. Opt. 12(1), 014015 (2007).
[CrossRef] [PubMed]

Kleinfeld, D.

P. S. Tsai, B. Friedman, A. I. Ifarraguerri, B. D. Thompson, V. Lev-Ram, C. B. Schaffer, Q. Xiong, R. Y. Tsien, J. A. Squier, and D. Kleinfeld, “All-optical histology using ultrashort laser pulses,” Neuron 39(1), 27–41 (2003).
[CrossRef] [PubMed]

Kolyva, C.

J. A. Spaan, R. ter Wee, J. W. van Teeffelen, G. Streekstra, M. Siebes, C. Kolyva, H. Vink, D. S. Fokkema, and E. VanBavel, “Visualisation of intramural coronary vasculature by an imaging cryomicrotome suggests compartmentalisation of myocardial perfusion areas,” Med. Biol. Eng. Comput. 43(4), 431–435 (2005).
[CrossRef] [PubMed]

Lasser, T.

Lee, R. T.

T. Ragan, J. D. Sylvan, K. H. Kim, H. Huang, K. Bahlmann, R. T. Lee, and P. T. So, “High-resolution whole organ imaging using two-photon tissue cytometry,” J. Biomed. Opt. 12(1), 014015 (2007).
[CrossRef] [PubMed]

Lessard, J. L.

J. C. Szucsik, A. G. Lewis, D. J. Marmer, and J. L. Lessard, “Urogenital tract expression of enhanced green fluorescent protein in transgenic mice driven by a smooth muscle gamma-actin promoter,” J. Urol. 171(2), 944–949 (2004).
[CrossRef] [PubMed]

Lev-Ram, V.

P. S. Tsai, B. Friedman, A. I. Ifarraguerri, B. D. Thompson, V. Lev-Ram, C. B. Schaffer, Q. Xiong, R. Y. Tsien, J. A. Squier, and D. Kleinfeld, “All-optical histology using ultrashort laser pulses,” Neuron 39(1), 27–41 (2003).
[CrossRef] [PubMed]

Lewis, A. G.

J. C. Szucsik, A. G. Lewis, D. J. Marmer, and J. L. Lessard, “Urogenital tract expression of enhanced green fluorescent protein in transgenic mice driven by a smooth muscle gamma-actin promoter,” J. Urol. 171(2), 944–949 (2004).
[CrossRef] [PubMed]

Li, G. D.

G. D. Li, D. Savvas, E. Arthur, and E. J. Lucy, “A new wide field-of-view confocal imaging system and its applications in drug discovery and pathology,” Proc. Soc. Photo Opt. Instrum. Eng. 6009, 1–16 (2005).

Lucy, E. J.

G. D. Li, D. Savvas, E. Arthur, and E. J. Lucy, “A new wide field-of-view confocal imaging system and its applications in drug discovery and pathology,” Proc. Soc. Photo Opt. Instrum. Eng. 6009, 1–16 (2005).

Lucy, L. B.

L. B. Lucy, “An iterative technique for the rectification of observed distributions,” Astron. J. 79, 745–754 (1974).
[CrossRef]

Marmer, D. J.

J. C. Szucsik, A. G. Lewis, D. J. Marmer, and J. L. Lessard, “Urogenital tract expression of enhanced green fluorescent protein in transgenic mice driven by a smooth muscle gamma-actin promoter,” J. Urol. 171(2), 944–949 (2004).
[CrossRef] [PubMed]

Meier, M.

Mitic, J.

Nehorai, A.

P. Sarder and A. Nehorai, “Deconvolution methods for 3-D fluorescence microscopy images,” IEEE Signal Process. Mag. 23(3), 32–45 (2006).
[CrossRef]

Neil, M. A.

Park, S. H.

S. H. Park, J. M. Goo, and C. H. Jo, “Receiver operating characteristic (ROC) curve: practical review for radiologists,” Korean J. Radiol. 5(1), 11–18 (2004).
[CrossRef] [PubMed]

Qutaish, M.

M. Gargesha, M. Qutaish, D. Roy, G. Steyer, H. Bartsch, and D. L. Wilson, “Enhanced Volume Rendering Techniques for High-Resolution Color Cryo-Imaging Data,” Proc. Soc. Photo Opt. Instrum. Eng. 7262, 72655V (2009).
[PubMed]

Ragan, T.

T. Ragan, J. D. Sylvan, K. H. Kim, H. Huang, K. Bahlmann, R. T. Lee, and P. T. So, “High-resolution whole organ imaging using two-photon tissue cytometry,” J. Biomed. Opt. 12(1), 014015 (2007).
[CrossRef] [PubMed]

Richardson, W. H.

Roy, D.

D. Roy, M. Gargesha, G. J. Steyer, P. Hakimi, R. W. Hanson, and D. L. Wilson, “Multi-scale Characterization of the PEPCK-Cmus Mouse Through 3D Cryo-Imaging,” Int. J. Biomed. Imaging 2010, 1–12 (2010).
[CrossRef]

G. J. Steyer, D. Roy, O. Salvado, M. E. Stone, and D. L. Wilson, “Removal of out-of-plane fluorescence for single cell visualization and quantification in cryo-imaging,” Ann. Biomed. Eng. 37(8), 1613–1628 (2009).
[CrossRef] [PubMed]

M. Gargesha, M. Qutaish, D. Roy, G. Steyer, H. Bartsch, and D. L. Wilson, “Enhanced Volume Rendering Techniques for High-Resolution Color Cryo-Imaging Data,” Proc. Soc. Photo Opt. Instrum. Eng. 7262, 72655V (2009).
[PubMed]

D. Roy, G. J. Steyer, M. Gargesha, M. E. Stone, and D. L. Wilson, “3D cryo-imaging: a very high-resolution view of the whole mouse,” Anat. Rec. (Hoboken) 292(3), 342–351 (2009).
[CrossRef]

G. J. Steyer, D. Roy, O. Salvado, M. E. Stone, and D. L. Wilson, “Cryo-Imaging of Fluorescently-Labeled Single Cells in a Mouse,” Proc. Soc. Photo Opt. Instrum. Eng. 7262, 72620W, W8 (2009).
[PubMed]

Salvado, O.

G. J. Steyer, D. Roy, O. Salvado, M. E. Stone, and D. L. Wilson, “Cryo-Imaging of Fluorescently-Labeled Single Cells in a Mouse,” Proc. Soc. Photo Opt. Instrum. Eng. 7262, 72620W, W8 (2009).
[PubMed]

G. J. Steyer, D. Roy, O. Salvado, M. E. Stone, and D. L. Wilson, “Removal of out-of-plane fluorescence for single cell visualization and quantification in cryo-imaging,” Ann. Biomed. Eng. 37(8), 1613–1628 (2009).
[CrossRef] [PubMed]

Sarder, P.

P. Sarder and A. Nehorai, “Deconvolution methods for 3-D fluorescence microscopy images,” IEEE Signal Process. Mag. 23(3), 32–45 (2006).
[CrossRef]

Savvas, D.

G. D. Li, D. Savvas, E. Arthur, and E. J. Lucy, “A new wide field-of-view confocal imaging system and its applications in drug discovery and pathology,” Proc. Soc. Photo Opt. Instrum. Eng. 6009, 1–16 (2005).

Schaefer, L. H.

W. Wallace, L. H. Schaefer, and J. R. Swedlow, “A workingperson’s guide to deconvolution in light microscopy,” Biotechniques 31(5), 1076–1078, 1080, 1082 passim (2001).
[PubMed]

Schaffer, C. B.

P. S. Tsai, B. Friedman, A. I. Ifarraguerri, B. D. Thompson, V. Lev-Ram, C. B. Schaffer, Q. Xiong, R. Y. Tsien, J. A. Squier, and D. Kleinfeld, “All-optical histology using ultrashort laser pulses,” Neuron 39(1), 27–41 (2003).
[CrossRef] [PubMed]

Serov, A.

Shepp, L. A.

L. A. Shepp and Y. Vardi, “Maximum likelihood reconstruction for emission tomography,” IEEE Trans. Med. Imaging 1(2), 113–122 (1982).
[CrossRef] [PubMed]

Siebes, M.

P. van Horssen, M. Siebes, I. Hoefer, J. A. Spaan, and J. P. van den Wijngaard, “Improved detection of fluorescently labeled microspheres and vessel architecture with an imaging cryomicrotome,” Med. Biol. Eng. Comput. 48(8), 735–744 (2010).
[CrossRef] [PubMed]

J. A. Spaan, R. ter Wee, J. W. van Teeffelen, G. Streekstra, M. Siebes, C. Kolyva, H. Vink, D. S. Fokkema, and E. VanBavel, “Visualisation of intramural coronary vasculature by an imaging cryomicrotome suggests compartmentalisation of myocardial perfusion areas,” Med. Biol. Eng. Comput. 43(4), 431–435 (2005).
[CrossRef] [PubMed]

So, P. T.

T. Ragan, J. D. Sylvan, K. H. Kim, H. Huang, K. Bahlmann, R. T. Lee, and P. T. So, “High-resolution whole organ imaging using two-photon tissue cytometry,” J. Biomed. Opt. 12(1), 014015 (2007).
[CrossRef] [PubMed]

Spaan, J. A.

P. van Horssen, M. Siebes, I. Hoefer, J. A. Spaan, and J. P. van den Wijngaard, “Improved detection of fluorescently labeled microspheres and vessel architecture with an imaging cryomicrotome,” Med. Biol. Eng. Comput. 48(8), 735–744 (2010).
[CrossRef] [PubMed]

J. A. Spaan, R. ter Wee, J. W. van Teeffelen, G. Streekstra, M. Siebes, C. Kolyva, H. Vink, D. S. Fokkema, and E. VanBavel, “Visualisation of intramural coronary vasculature by an imaging cryomicrotome suggests compartmentalisation of myocardial perfusion areas,” Med. Biol. Eng. Comput. 43(4), 431–435 (2005).
[CrossRef] [PubMed]

Squier, J. A.

P. S. Tsai, B. Friedman, A. I. Ifarraguerri, B. D. Thompson, V. Lev-Ram, C. B. Schaffer, Q. Xiong, R. Y. Tsien, J. A. Squier, and D. Kleinfeld, “All-optical histology using ultrashort laser pulses,” Neuron 39(1), 27–41 (2003).
[CrossRef] [PubMed]

Steyer, G.

M. Gargesha, M. Qutaish, D. Roy, G. Steyer, H. Bartsch, and D. L. Wilson, “Enhanced Volume Rendering Techniques for High-Resolution Color Cryo-Imaging Data,” Proc. Soc. Photo Opt. Instrum. Eng. 7262, 72655V (2009).
[PubMed]

Steyer, G. J.

D. Roy, M. Gargesha, G. J. Steyer, P. Hakimi, R. W. Hanson, and D. L. Wilson, “Multi-scale Characterization of the PEPCK-Cmus Mouse Through 3D Cryo-Imaging,” Int. J. Biomed. Imaging 2010, 1–12 (2010).
[CrossRef]

G. J. Steyer, D. Roy, O. Salvado, M. E. Stone, and D. L. Wilson, “Cryo-Imaging of Fluorescently-Labeled Single Cells in a Mouse,” Proc. Soc. Photo Opt. Instrum. Eng. 7262, 72620W, W8 (2009).
[PubMed]

G. J. Steyer, D. Roy, O. Salvado, M. E. Stone, and D. L. Wilson, “Removal of out-of-plane fluorescence for single cell visualization and quantification in cryo-imaging,” Ann. Biomed. Eng. 37(8), 1613–1628 (2009).
[CrossRef] [PubMed]

D. Roy, G. J. Steyer, M. Gargesha, M. E. Stone, and D. L. Wilson, “3D cryo-imaging: a very high-resolution view of the whole mouse,” Anat. Rec. (Hoboken) 292(3), 342–351 (2009).
[CrossRef]

Stone, M. E.

D. Roy, G. J. Steyer, M. Gargesha, M. E. Stone, and D. L. Wilson, “3D cryo-imaging: a very high-resolution view of the whole mouse,” Anat. Rec. (Hoboken) 292(3), 342–351 (2009).
[CrossRef]

G. J. Steyer, D. Roy, O. Salvado, M. E. Stone, and D. L. Wilson, “Cryo-Imaging of Fluorescently-Labeled Single Cells in a Mouse,” Proc. Soc. Photo Opt. Instrum. Eng. 7262, 72620W, W8 (2009).
[PubMed]

G. J. Steyer, D. Roy, O. Salvado, M. E. Stone, and D. L. Wilson, “Removal of out-of-plane fluorescence for single cell visualization and quantification in cryo-imaging,” Ann. Biomed. Eng. 37(8), 1613–1628 (2009).
[CrossRef] [PubMed]

Streekstra, G.

J. A. Spaan, R. ter Wee, J. W. van Teeffelen, G. Streekstra, M. Siebes, C. Kolyva, H. Vink, D. S. Fokkema, and E. VanBavel, “Visualisation of intramural coronary vasculature by an imaging cryomicrotome suggests compartmentalisation of myocardial perfusion areas,” Med. Biol. Eng. Comput. 43(4), 431–435 (2005).
[CrossRef] [PubMed]

Swedlow, J. R.

W. Wallace, L. H. Schaefer, and J. R. Swedlow, “A workingperson’s guide to deconvolution in light microscopy,” Biotechniques 31(5), 1076–1078, 1080, 1082 passim (2001).
[PubMed]

Sylvan, J. D.

T. Ragan, J. D. Sylvan, K. H. Kim, H. Huang, K. Bahlmann, R. T. Lee, and P. T. So, “High-resolution whole organ imaging using two-photon tissue cytometry,” J. Biomed. Opt. 12(1), 014015 (2007).
[CrossRef] [PubMed]

Szucsik, J. C.

J. C. Szucsik, A. G. Lewis, D. J. Marmer, and J. L. Lessard, “Urogenital tract expression of enhanced green fluorescent protein in transgenic mice driven by a smooth muscle gamma-actin promoter,” J. Urol. 171(2), 944–949 (2004).
[CrossRef] [PubMed]

ter Wee, R.

J. A. Spaan, R. ter Wee, J. W. van Teeffelen, G. Streekstra, M. Siebes, C. Kolyva, H. Vink, D. S. Fokkema, and E. VanBavel, “Visualisation of intramural coronary vasculature by an imaging cryomicrotome suggests compartmentalisation of myocardial perfusion areas,” Med. Biol. Eng. Comput. 43(4), 431–435 (2005).
[CrossRef] [PubMed]

Thompson, B. D.

P. S. Tsai, B. Friedman, A. I. Ifarraguerri, B. D. Thompson, V. Lev-Ram, C. B. Schaffer, Q. Xiong, R. Y. Tsien, J. A. Squier, and D. Kleinfeld, “All-optical histology using ultrashort laser pulses,” Neuron 39(1), 27–41 (2003).
[CrossRef] [PubMed]

Tsai, P. S.

P. S. Tsai, B. Friedman, A. I. Ifarraguerri, B. D. Thompson, V. Lev-Ram, C. B. Schaffer, Q. Xiong, R. Y. Tsien, J. A. Squier, and D. Kleinfeld, “All-optical histology using ultrashort laser pulses,” Neuron 39(1), 27–41 (2003).
[CrossRef] [PubMed]

Tsien, R. Y.

P. S. Tsai, B. Friedman, A. I. Ifarraguerri, B. D. Thompson, V. Lev-Ram, C. B. Schaffer, Q. Xiong, R. Y. Tsien, J. A. Squier, and D. Kleinfeld, “All-optical histology using ultrashort laser pulses,” Neuron 39(1), 27–41 (2003).
[CrossRef] [PubMed]

van den Wijngaard, J. P.

P. van Horssen, M. Siebes, I. Hoefer, J. A. Spaan, and J. P. van den Wijngaard, “Improved detection of fluorescently labeled microspheres and vessel architecture with an imaging cryomicrotome,” Med. Biol. Eng. Comput. 48(8), 735–744 (2010).
[CrossRef] [PubMed]

van Horssen, P.

P. van Horssen, M. Siebes, I. Hoefer, J. A. Spaan, and J. P. van den Wijngaard, “Improved detection of fluorescently labeled microspheres and vessel architecture with an imaging cryomicrotome,” Med. Biol. Eng. Comput. 48(8), 735–744 (2010).
[CrossRef] [PubMed]

van Teeffelen, J. W.

J. A. Spaan, R. ter Wee, J. W. van Teeffelen, G. Streekstra, M. Siebes, C. Kolyva, H. Vink, D. S. Fokkema, and E. VanBavel, “Visualisation of intramural coronary vasculature by an imaging cryomicrotome suggests compartmentalisation of myocardial perfusion areas,” Med. Biol. Eng. Comput. 43(4), 431–435 (2005).
[CrossRef] [PubMed]

VanBavel, E.

J. A. Spaan, R. ter Wee, J. W. van Teeffelen, G. Streekstra, M. Siebes, C. Kolyva, H. Vink, D. S. Fokkema, and E. VanBavel, “Visualisation of intramural coronary vasculature by an imaging cryomicrotome suggests compartmentalisation of myocardial perfusion areas,” Med. Biol. Eng. Comput. 43(4), 431–435 (2005).
[CrossRef] [PubMed]

Vardi, Y.

L. A. Shepp and Y. Vardi, “Maximum likelihood reconstruction for emission tomography,” IEEE Trans. Med. Imaging 1(2), 113–122 (1982).
[CrossRef] [PubMed]

Vink, H.

J. A. Spaan, R. ter Wee, J. W. van Teeffelen, G. Streekstra, M. Siebes, C. Kolyva, H. Vink, D. S. Fokkema, and E. VanBavel, “Visualisation of intramural coronary vasculature by an imaging cryomicrotome suggests compartmentalisation of myocardial perfusion areas,” Med. Biol. Eng. Comput. 43(4), 431–435 (2005).
[CrossRef] [PubMed]

Wallace, W.

W. Wallace, L. H. Schaefer, and J. R. Swedlow, “A workingperson’s guide to deconvolution in light microscopy,” Biotechniques 31(5), 1076–1078, 1080, 1082 passim (2001).
[PubMed]

White, R. L.

R. L. White, “Image restoration using the damped Richardson-Lucy method,” Proc. Soc. Photo Opt. Instrum. Eng. 2198, 1342–1348 (1994).

Wilson, D. L.

D. Roy, M. Gargesha, G. J. Steyer, P. Hakimi, R. W. Hanson, and D. L. Wilson, “Multi-scale Characterization of the PEPCK-Cmus Mouse Through 3D Cryo-Imaging,” Int. J. Biomed. Imaging 2010, 1–12 (2010).
[CrossRef]

G. J. Steyer, D. Roy, O. Salvado, M. E. Stone, and D. L. Wilson, “Removal of out-of-plane fluorescence for single cell visualization and quantification in cryo-imaging,” Ann. Biomed. Eng. 37(8), 1613–1628 (2009).
[CrossRef] [PubMed]

G. J. Steyer, D. Roy, O. Salvado, M. E. Stone, and D. L. Wilson, “Cryo-Imaging of Fluorescently-Labeled Single Cells in a Mouse,” Proc. Soc. Photo Opt. Instrum. Eng. 7262, 72620W, W8 (2009).
[PubMed]

D. Roy, G. J. Steyer, M. Gargesha, M. E. Stone, and D. L. Wilson, “3D cryo-imaging: a very high-resolution view of the whole mouse,” Anat. Rec. (Hoboken) 292(3), 342–351 (2009).
[CrossRef]

M. Gargesha, M. Qutaish, D. Roy, G. Steyer, H. Bartsch, and D. L. Wilson, “Enhanced Volume Rendering Techniques for High-Resolution Color Cryo-Imaging Data,” Proc. Soc. Photo Opt. Instrum. Eng. 7262, 72655V (2009).
[PubMed]

Wilson, T.

Xiong, Q.

P. S. Tsai, B. Friedman, A. I. Ifarraguerri, B. D. Thompson, V. Lev-Ram, C. B. Schaffer, Q. Xiong, R. Y. Tsien, J. A. Squier, and D. Kleinfeld, “All-optical histology using ultrashort laser pulses,” Neuron 39(1), 27–41 (2003).
[CrossRef] [PubMed]

Anat. Rec. (Hoboken) (1)

D. Roy, G. J. Steyer, M. Gargesha, M. E. Stone, and D. L. Wilson, “3D cryo-imaging: a very high-resolution view of the whole mouse,” Anat. Rec. (Hoboken) 292(3), 342–351 (2009).
[CrossRef]

Ann. Biomed. Eng. (1)

G. J. Steyer, D. Roy, O. Salvado, M. E. Stone, and D. L. Wilson, “Removal of out-of-plane fluorescence for single cell visualization and quantification in cryo-imaging,” Ann. Biomed. Eng. 37(8), 1613–1628 (2009).
[CrossRef] [PubMed]

Astron. J. (1)

L. B. Lucy, “An iterative technique for the rectification of observed distributions,” Astron. J. 79, 745–754 (1974).
[CrossRef]

Biotechniques (1)

W. Wallace, L. H. Schaefer, and J. R. Swedlow, “A workingperson’s guide to deconvolution in light microscopy,” Biotechniques 31(5), 1076–1078, 1080, 1082 passim (2001).
[PubMed]

IEEE Signal Process. Mag. (1)

P. Sarder and A. Nehorai, “Deconvolution methods for 3-D fluorescence microscopy images,” IEEE Signal Process. Mag. 23(3), 32–45 (2006).
[CrossRef]

IEEE Trans. Med. Imaging (1)

L. A. Shepp and Y. Vardi, “Maximum likelihood reconstruction for emission tomography,” IEEE Trans. Med. Imaging 1(2), 113–122 (1982).
[CrossRef] [PubMed]

Int. J. Biomed. Imaging (1)

D. Roy, M. Gargesha, G. J. Steyer, P. Hakimi, R. W. Hanson, and D. L. Wilson, “Multi-scale Characterization of the PEPCK-Cmus Mouse Through 3D Cryo-Imaging,” Int. J. Biomed. Imaging 2010, 1–12 (2010).
[CrossRef]

J. Biomed. Opt. (1)

T. Ragan, J. D. Sylvan, K. H. Kim, H. Huang, K. Bahlmann, R. T. Lee, and P. T. So, “High-resolution whole organ imaging using two-photon tissue cytometry,” J. Biomed. Opt. 12(1), 014015 (2007).
[CrossRef] [PubMed]

J. Opt. Soc. Am. (1)

J. Urol. (1)

J. C. Szucsik, A. G. Lewis, D. J. Marmer, and J. L. Lessard, “Urogenital tract expression of enhanced green fluorescent protein in transgenic mice driven by a smooth muscle gamma-actin promoter,” J. Urol. 171(2), 944–949 (2004).
[CrossRef] [PubMed]

Korean J. Radiol. (1)

S. H. Park, J. M. Goo, and C. H. Jo, “Receiver operating characteristic (ROC) curve: practical review for radiologists,” Korean J. Radiol. 5(1), 11–18 (2004).
[CrossRef] [PubMed]

Med. Biol. Eng. Comput. (2)

P. van Horssen, M. Siebes, I. Hoefer, J. A. Spaan, and J. P. van den Wijngaard, “Improved detection of fluorescently labeled microspheres and vessel architecture with an imaging cryomicrotome,” Med. Biol. Eng. Comput. 48(8), 735–744 (2010).
[CrossRef] [PubMed]

J. A. Spaan, R. ter Wee, J. W. van Teeffelen, G. Streekstra, M. Siebes, C. Kolyva, H. Vink, D. S. Fokkema, and E. VanBavel, “Visualisation of intramural coronary vasculature by an imaging cryomicrotome suggests compartmentalisation of myocardial perfusion areas,” Med. Biol. Eng. Comput. 43(4), 431–435 (2005).
[CrossRef] [PubMed]

Neuron (1)

P. S. Tsai, B. Friedman, A. I. Ifarraguerri, B. D. Thompson, V. Lev-Ram, C. B. Schaffer, Q. Xiong, R. Y. Tsien, J. A. Squier, and D. Kleinfeld, “All-optical histology using ultrashort laser pulses,” Neuron 39(1), 27–41 (2003).
[CrossRef] [PubMed]

Opt. Lett. (2)

Proc. Soc. Photo Opt. Instrum. Eng. (4)

G. D. Li, D. Savvas, E. Arthur, and E. J. Lucy, “A new wide field-of-view confocal imaging system and its applications in drug discovery and pathology,” Proc. Soc. Photo Opt. Instrum. Eng. 6009, 1–16 (2005).

G. J. Steyer, D. Roy, O. Salvado, M. E. Stone, and D. L. Wilson, “Cryo-Imaging of Fluorescently-Labeled Single Cells in a Mouse,” Proc. Soc. Photo Opt. Instrum. Eng. 7262, 72620W, W8 (2009).
[PubMed]

M. Gargesha, M. Qutaish, D. Roy, G. Steyer, H. Bartsch, and D. L. Wilson, “Enhanced Volume Rendering Techniques for High-Resolution Color Cryo-Imaging Data,” Proc. Soc. Photo Opt. Instrum. Eng. 7262, 72655V (2009).
[PubMed]

R. L. White, “Image restoration using the damped Richardson-Lucy method,” Proc. Soc. Photo Opt. Instrum. Eng. 2198, 1342–1348 (1994).

Other (1)

N. Wiener, ed., Extrapolation, Interpolation, and Smoothing of Stationary Time Series (Wiley, New York, 1949).

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Figures (7)

Fig. 1
Fig. 1

Measured scatter PSF of the cryo-imaging system. Twenty measured PSFs were aligned and averaged. A background value was subtracted. Maximum intensity projections in the YZ (a) and XY (b) planes are shown. The comet tail extends approximately 100 µm and the maximal in-plane spread is 15 µm. The PSF was acquired at a resolution of 5.4x5.4x10 µm using microspheres 0.2 μm diameter

Fig. 2
Fig. 2

Reduction of comet tail artifacts using image restoration algorithms. Microspheres (15.4 μm diameter) were embedded in O.C.T phantom, imaged, and processed. MIPS of a sub volume are shown. The unprocessed image (a) shows the comet tail artifact extending to a depth of ≈100 μm. RL processing (b) removes comet tail artifacts and restores the shape of the bead both in-plane and along Z. Next-image processing (c) reduces the comet tail artifacts but in-plane spread persists. Wiener deconvolution (d) removes comet tail artifacts but the resultant image suffers from high frequency noise and in-plane restoration is not as effective as in RL. Parameters were: voxel size 4x4x5µm3, (RL, 20 iterations, damping factor of 3), and Wiener, NSR = 10−4. Scale bar corresponds to 50 µm

Fig. 3
Fig. 3

Restoration of a single, representative microsphere from the same volume in Fig. 2. Unprocessed image (a) contains significant subsurface fluorescence artifacts and in-plane spread. RL (b), Wiener (c) and Next-image (d) effectively remove subsurface fluorescence. RL gives a truer spatial representation of the microsphere.

Fig. 4
Fig. 4

Reduction of subsurface fluorescence in the various tissue types. Subsurface fluorescence is seen in both the axial (a) and (c) side view. The PSF measured in OCT was subsampled to restore the images. The restored images show reduced subsurface fluorescence in the axial view (b) and the comet tail reduction in the side view (d). RL image restoration parameters, N = 20 iterations and a damping factor of 1. The original image size was 1036x1360x20 with pixel size of 15.6x15.6x40 µm.

Fig. 5
Fig. 5

Isosurface rendering of string of microspheres in the mouse brain trapped in the vasculature. The cluster is oriented along the z-axis of the volume. Two different views of the unprocessed volumes are shown in (a) & (c) and the RL deconvolved volumes are rendered in (b) & (d). Following deconvolution there is better separation between the microspheres along the z-axis. The images were generated from microspheres in the mouse brain. The images were acquired at 15.6x15.6x40 microns. The RL parameters were 20 iterations and a damping factor of 3. The scale bar corresponds to 50 µm.

Fig. 6
Fig. 6

Image restorations by elimination of subsurface fluorescence from fluorescent structures. XY cross sections were obtained from the esophagus of a mouse (a). Unprocessed image shows significance subsurface fluorescence in the lumen of the esophagus. RL image restoration (b) removes the subsurface fluorescence and clearly delineates the esophagus. The brightfield section with the corresponding RL processed fluorescence image is shown in (c) and the region in the box is zoomed in and shown in (d). The images were acquired at a resolution of 15.6x15.6x20 µm. A sub volume of size 337x195x44 containing the esophagus was processed. RL parameters, 20 iterations and 0.3 damping parameter.

Fig. 7
Fig. 7

ROC curves for detection of microspheres in tissue. Following restoration, detection was done using a simple thresholding technique. Areas under the curves (Az) were 0.9977, 0.9985, 0.99894, and 0.99892, for unprocessed, Next-image, RL, and Wiener respectively. The inset shows the curve after zooming in on the x-axis between 0 and 0.01 where there are slight but visually perceptible differences between the curves. The image thresholds for two of the data points are marked as T = 0, T = 1 and T = 3(inset).

Tables (1)

Tables Icon

Table 1 CNRs and CBRs for restored and unprocessed images. The average values were obtained over 200 microspheres in the brain after detection and manual verification

Equations (15)

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

o ( X ) = h ( X X ' ) i ( X ' ) d X '
o ^ = h ^ i ^ + n
I ( ω ) = [ H ( ω ) * O ( ω ) | H ( ω ) | 2 + | N ( ω ) | 2 | I ( ω ) | 2 ]
L ( X ) = exp ( o ( X ) ) ( i ( X ) h ( X ) ) o ( X ) o ( X ) !
ln ( L ) = ( o ln ( i h ) i h ln [ o ! ] ) d X
i ln L i = 0 ;
ln L i = h * o h i 1
i k + 1 = i k . [ h ( X ) o ( X ) h ( X ) i k ]
ln L = f ( g ( X ) ) d X
g = 2 T [ o ln [ i h o ] i h + o ]
f ( y ) = N 1 N + 1 ( 1 y N + 1 ) + y N , y < 1          =  y                                  , y 1
i k + 1 = i k . { [ 1 + g ^ N 1 [ N ( N 1 ) g ^ ] o ( i k h ) i k h } . h d X
i k exp ( μ t s ) ( i k + 1 h ( x , y ) ) = i k 0 t a t f i t t a
i k 0 t a t f i t t a = i k k . ( i k + 1 h ( x , y ) )
F o b j = | R s ( i , k ) μ R s |

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