Abstract

The author proposes a method to identify the three-dimensional positions of fluorescent biomarkers by recording just two images. In the proposed method, the x and y positions of all fluorescent markers are recorded in the first exposure, and the z positions are obtained from a blurred image in the second exposure. The author has verified this method using a specimen with 1μm deep grooves and applied it to measuring chromatic aberration and the separation between two biological probes in fluorescence in situ hybridization cells. The method offers the advantage of greatly reduced data storage requirements.

© 2011 Optical Society of America

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2010 (3)

2009 (2)

T. Dertinger, R. Colyer, G. Lyer, S. Weiss, and J. Enderlein, “Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI),” Proc. Natl. Acad. Sci. 106, 22287–22292(2009).
[CrossRef] [PubMed]

S. R. P. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu, R. J. Twieg, R. Piestun, and W. E. Moerner, “Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function,” Proc. Natl. Acad. Sci. 106, 2995–2999 (2009).
[CrossRef] [PubMed]

2008 (2)

J. Rosen and G. Brooker, “Non-scanning motionless fluorescence three-dimensional holographic microscopy,” Nat. Photonics 2, 190–195 (2008).
[CrossRef]

H. Shroff, C. G. Galbraith, J. A. Galbraith, and E. Betzig, “Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics,” Nat. Methods 5, 417–423 (2008).
[CrossRef] [PubMed]

2007 (2)

L. Holtzer, T. Meckel, and T. Schmidt, “Nanometric three-dimensional tracking of individual quantum dots in cells,” Appl. Phys. Lett. 90, 053902 (2007).
[CrossRef]

A. Veeraraghavan, R. Raskar, A. Agrawal, A. Mohan, and J. Tumblin, “Dappled photography: Mask enhanced cameras for heterodyned light fields and coded aperture refocusing,” ACM Trans. Graphics 26, 69-1–69-12 (2007).
[CrossRef]

2006 (5)

M. Levoy, R. Ng, A. Adams, M. Footer, and M. Horowitz, “Light field microscopy,” ACM Trans. Graphics 25, 924–934(2006).
[CrossRef]

T. Indukuri, P. Koonath, and B. Jalali, “Three-dimensional integration of metal-oxide-semiconductor transistor with subterranean photonics in silicon,” Appl. Phys. Lett. 88, 121108 (2006).
[CrossRef]

K. Kishima, “Analysis of defects in an electric and photonic double-layer substrate made by separation-by-implanted-oxygen three-dimensional sculpting,” Appl. Phys. Lett. 89, 201109 (2006).
[CrossRef]

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313, 1642–1645(2006).
[CrossRef] [PubMed]

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3, 793–796 (2006).
[CrossRef] [PubMed]

2005 (2)

2004 (1)

T. J. Lynch, D. W. Bell, R. Sordella, S. Gurubhagavatula, R. A. Okimoto, B. W. Brannigan, P. L. Harris, S. M. Haserlat, J. G. Supko, F. G. Haluska, D. N. Louis, D. C. Christiani, J. Settleman, and D. A. Haber, “Activating mutations in the epidermal growth factor receptor underlying responsiveness of non–small-cell lung cancer to Gefitinib,” N. Engl. J. Med. 350, 2129–2139(2004).
[CrossRef] [PubMed]

2003 (1)

W. A. Nevin, D. L. Gay, and V. Higgs, “Photoluminescence study of interfacial defects in direct-bonded silicon wafers,” J. Electrochem. Soc. 150, G591–G596 (2003).
[CrossRef]

2002 (1)

1999 (1)

1995 (1)

1994 (1)

1988 (1)

D. Pinkel, J. Landegent, C. Collins, J. Fuscoe, R. Segraves, J. Lucas, and J. Gray, “Fluorescence in situ hybridization with human chromosome-specific libraries: Detection of trisomy 21 translocations of chromosome 4,” Proc. Natl. Acad. Sci. 85, 9138–9142 (1988).
[CrossRef] [PubMed]

1986 (1)

D. Pinkel, T. Straume, and J. W. Gray, “Cytogenetic analysis using quantitative, high-sensitivity, fluorescence hybridization,” Proc. Natl. Acad. Sci. USA 83, 2934–2938 (1986).
[CrossRef] [PubMed]

Adachi, N.

M. Uemura, Y. Niwa, N. Kakazu, N. Adachi, and K. Kinoshita, “Chromosomal manipulation by site-specific recombinases and fluorescent protein-based vectors,” PLoS One 5, e9846(2010).
[CrossRef] [PubMed]

Adams, A.

M. Levoy, R. Ng, A. Adams, M. Footer, and M. Horowitz, “Light field microscopy,” ACM Trans. Graphics 25, 924–934(2006).
[CrossRef]

Agrawal, A.

A. Veeraraghavan, R. Raskar, A. Agrawal, A. Mohan, and J. Tumblin, “Dappled photography: Mask enhanced cameras for heterodyned light fields and coded aperture refocusing,” ACM Trans. Graphics 26, 69-1–69-12 (2007).
[CrossRef]

Bates, M.

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3, 793–796 (2006).
[CrossRef] [PubMed]

Bell, D. W.

T. J. Lynch, D. W. Bell, R. Sordella, S. Gurubhagavatula, R. A. Okimoto, B. W. Brannigan, P. L. Harris, S. M. Haserlat, J. G. Supko, F. G. Haluska, D. N. Louis, D. C. Christiani, J. Settleman, and D. A. Haber, “Activating mutations in the epidermal growth factor receptor underlying responsiveness of non–small-cell lung cancer to Gefitinib,” N. Engl. J. Med. 350, 2129–2139(2004).
[CrossRef] [PubMed]

Bernet, S.

Betzig, E.

H. Shroff, C. G. Galbraith, J. A. Galbraith, and E. Betzig, “Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics,” Nat. Methods 5, 417–423 (2008).
[CrossRef] [PubMed]

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313, 1642–1645(2006).
[CrossRef] [PubMed]

Biteen, J. S.

S. R. P. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu, R. J. Twieg, R. Piestun, and W. E. Moerner, “Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function,” Proc. Natl. Acad. Sci. 106, 2995–2999 (2009).
[CrossRef] [PubMed]

Bonifacino, J. S.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313, 1642–1645(2006).
[CrossRef] [PubMed]

Brannigan, B. W.

T. J. Lynch, D. W. Bell, R. Sordella, S. Gurubhagavatula, R. A. Okimoto, B. W. Brannigan, P. L. Harris, S. M. Haserlat, J. G. Supko, F. G. Haluska, D. N. Louis, D. C. Christiani, J. Settleman, and D. A. Haber, “Activating mutations in the epidermal growth factor receptor underlying responsiveness of non–small-cell lung cancer to Gefitinib,” N. Engl. J. Med. 350, 2129–2139(2004).
[CrossRef] [PubMed]

Brooker, G.

J. Rosen and G. Brooker, “Non-scanning motionless fluorescence three-dimensional holographic microscopy,” Nat. Photonics 2, 190–195 (2008).
[CrossRef]

Cathey, W. T.

Christiani, D. C.

T. J. Lynch, D. W. Bell, R. Sordella, S. Gurubhagavatula, R. A. Okimoto, B. W. Brannigan, P. L. Harris, S. M. Haserlat, J. G. Supko, F. G. Haluska, D. N. Louis, D. C. Christiani, J. Settleman, and D. A. Haber, “Activating mutations in the epidermal growth factor receptor underlying responsiveness of non–small-cell lung cancer to Gefitinib,” N. Engl. J. Med. 350, 2129–2139(2004).
[CrossRef] [PubMed]

Collins, C.

D. Pinkel, J. Landegent, C. Collins, J. Fuscoe, R. Segraves, J. Lucas, and J. Gray, “Fluorescence in situ hybridization with human chromosome-specific libraries: Detection of trisomy 21 translocations of chromosome 4,” Proc. Natl. Acad. Sci. 85, 9138–9142 (1988).
[CrossRef] [PubMed]

Colyer, R.

T. Dertinger, R. Colyer, G. Lyer, S. Weiss, and J. Enderlein, “Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI),” Proc. Natl. Acad. Sci. 106, 22287–22292(2009).
[CrossRef] [PubMed]

Cremer, C.

Dalgarno, H. I. C.

Dalgarno, P. A.

Davidson, M. W.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313, 1642–1645(2006).
[CrossRef] [PubMed]

Dertinger, T.

T. Dertinger, R. Colyer, G. Lyer, S. Weiss, and J. Enderlein, “Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI),” Proc. Natl. Acad. Sci. 106, 22287–22292(2009).
[CrossRef] [PubMed]

Dowski, E. R.

Enderlein, J.

T. Dertinger, R. Colyer, G. Lyer, S. Weiss, and J. Enderlein, “Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI),” Proc. Natl. Acad. Sci. 106, 22287–22292(2009).
[CrossRef] [PubMed]

Fassl, S.

Footer, M.

M. Levoy, R. Ng, A. Adams, M. Footer, and M. Horowitz, “Light field microscopy,” ACM Trans. Graphics 25, 924–934(2006).
[CrossRef]

Franck, T.

Fuscoe, J.

D. Pinkel, J. Landegent, C. Collins, J. Fuscoe, R. Segraves, J. Lucas, and J. Gray, “Fluorescence in situ hybridization with human chromosome-specific libraries: Detection of trisomy 21 translocations of chromosome 4,” Proc. Natl. Acad. Sci. 85, 9138–9142 (1988).
[CrossRef] [PubMed]

Galbraith, C. G.

H. Shroff, C. G. Galbraith, J. A. Galbraith, and E. Betzig, “Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics,” Nat. Methods 5, 417–423 (2008).
[CrossRef] [PubMed]

Galbraith, J. A.

H. Shroff, C. G. Galbraith, J. A. Galbraith, and E. Betzig, “Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics,” Nat. Methods 5, 417–423 (2008).
[CrossRef] [PubMed]

Gay, D. L.

W. A. Nevin, D. L. Gay, and V. Higgs, “Photoluminescence study of interfacial defects in direct-bonded silicon wafers,” J. Electrochem. Soc. 150, G591–G596 (2003).
[CrossRef]

Goodman, J. W.

J. W. Goodman, Introduction to Fourier Optics (Roberts, 2004).

Gray, J.

D. Pinkel, J. Landegent, C. Collins, J. Fuscoe, R. Segraves, J. Lucas, and J. Gray, “Fluorescence in situ hybridization with human chromosome-specific libraries: Detection of trisomy 21 translocations of chromosome 4,” Proc. Natl. Acad. Sci. 85, 9138–9142 (1988).
[CrossRef] [PubMed]

Gray, J. W.

D. Pinkel, T. Straume, and J. W. Gray, “Cytogenetic analysis using quantitative, high-sensitivity, fluorescence hybridization,” Proc. Natl. Acad. Sci. USA 83, 2934–2938 (1986).
[CrossRef] [PubMed]

Greenaway, A. H.

Gunn, C.

C. Gunn, “CMOS photonics for high-speed interconnects,” Micro. IEEE 26, 58–66 (2005).
[CrossRef]

Gurubhagavatula, S.

T. J. Lynch, D. W. Bell, R. Sordella, S. Gurubhagavatula, R. A. Okimoto, B. W. Brannigan, P. L. Harris, S. M. Haserlat, J. G. Supko, F. G. Haluska, D. N. Louis, D. C. Christiani, J. Settleman, and D. A. Haber, “Activating mutations in the epidermal growth factor receptor underlying responsiveness of non–small-cell lung cancer to Gefitinib,” N. Engl. J. Med. 350, 2129–2139(2004).
[CrossRef] [PubMed]

Haber, D. A.

T. J. Lynch, D. W. Bell, R. Sordella, S. Gurubhagavatula, R. A. Okimoto, B. W. Brannigan, P. L. Harris, S. M. Haserlat, J. G. Supko, F. G. Haluska, D. N. Louis, D. C. Christiani, J. Settleman, and D. A. Haber, “Activating mutations in the epidermal growth factor receptor underlying responsiveness of non–small-cell lung cancer to Gefitinib,” N. Engl. J. Med. 350, 2129–2139(2004).
[CrossRef] [PubMed]

Haluska, F. G.

T. J. Lynch, D. W. Bell, R. Sordella, S. Gurubhagavatula, R. A. Okimoto, B. W. Brannigan, P. L. Harris, S. M. Haserlat, J. G. Supko, F. G. Haluska, D. N. Louis, D. C. Christiani, J. Settleman, and D. A. Haber, “Activating mutations in the epidermal growth factor receptor underlying responsiveness of non–small-cell lung cancer to Gefitinib,” N. Engl. J. Med. 350, 2129–2139(2004).
[CrossRef] [PubMed]

Harris, P. L.

T. J. Lynch, D. W. Bell, R. Sordella, S. Gurubhagavatula, R. A. Okimoto, B. W. Brannigan, P. L. Harris, S. M. Haserlat, J. G. Supko, F. G. Haluska, D. N. Louis, D. C. Christiani, J. Settleman, and D. A. Haber, “Activating mutations in the epidermal growth factor receptor underlying responsiveness of non–small-cell lung cancer to Gefitinib,” N. Engl. J. Med. 350, 2129–2139(2004).
[CrossRef] [PubMed]

Haserlat, S. M.

T. J. Lynch, D. W. Bell, R. Sordella, S. Gurubhagavatula, R. A. Okimoto, B. W. Brannigan, P. L. Harris, S. M. Haserlat, J. G. Supko, F. G. Haluska, D. N. Louis, D. C. Christiani, J. Settleman, and D. A. Haber, “Activating mutations in the epidermal growth factor receptor underlying responsiveness of non–small-cell lung cancer to Gefitinib,” N. Engl. J. Med. 350, 2129–2139(2004).
[CrossRef] [PubMed]

Heintzmann, R.

Hell, S. W.

Hess, H. F.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313, 1642–1645(2006).
[CrossRef] [PubMed]

Higgs, V.

W. A. Nevin, D. L. Gay, and V. Higgs, “Photoluminescence study of interfacial defects in direct-bonded silicon wafers,” J. Electrochem. Soc. 150, G591–G596 (2003).
[CrossRef]

Hodge, D.

Holtzer, L.

L. Holtzer, T. Meckel, and T. Schmidt, “Nanometric three-dimensional tracking of individual quantum dots in cells,” Appl. Phys. Lett. 90, 053902 (2007).
[CrossRef]

Horowitz, M.

M. Levoy, R. Ng, A. Adams, M. Footer, and M. Horowitz, “Light field microscopy,” ACM Trans. Graphics 25, 924–934(2006).
[CrossRef]

Indukuri, T.

T. Indukuri, P. Koonath, and B. Jalali, “Three-dimensional integration of metal-oxide-semiconductor transistor with subterranean photonics in silicon,” Appl. Phys. Lett. 88, 121108 (2006).
[CrossRef]

Jalali, B.

T. Indukuri, P. Koonath, and B. Jalali, “Three-dimensional integration of metal-oxide-semiconductor transistor with subterranean photonics in silicon,” Appl. Phys. Lett. 88, 121108 (2006).
[CrossRef]

Jovin, T. M.

Kakazu, N.

M. Uemura, Y. Niwa, N. Kakazu, N. Adachi, and K. Kinoshita, “Chromosomal manipulation by site-specific recombinases and fluorescent protein-based vectors,” PLoS One 5, e9846(2010).
[CrossRef] [PubMed]

Keil, U.

Khan, S.

Kinoshita, K.

M. Uemura, Y. Niwa, N. Kakazu, N. Adachi, and K. Kinoshita, “Chromosomal manipulation by site-specific recombinases and fluorescent protein-based vectors,” PLoS One 5, e9846(2010).
[CrossRef] [PubMed]

Kishima, K.

K. Kishima, “Analysis of defects in an electric and photonic double-layer substrate made by separation-by-implanted-oxygen three-dimensional sculpting,” Appl. Phys. Lett. 89, 201109 (2006).
[CrossRef]

Klar, T. A.

Koonath, P.

T. Indukuri, P. Koonath, and B. Jalali, “Three-dimensional integration of metal-oxide-semiconductor transistor with subterranean photonics in silicon,” Appl. Phys. Lett. 88, 121108 (2006).
[CrossRef]

Kuthirummal, S.

H. Nagahara, S. Kuthirummal, C. Zhou, and S. K. Nayar, “Flexible depth of field photography,” in Proceedings of European Conference on Computer Vision (ECCV) (Springer-Verlag, 2008), pp. 60–73.

Lambert, R.

Landegent, J.

D. Pinkel, J. Landegent, C. Collins, J. Fuscoe, R. Segraves, J. Lucas, and J. Gray, “Fluorescence in situ hybridization with human chromosome-specific libraries: Detection of trisomy 21 translocations of chromosome 4,” Proc. Natl. Acad. Sci. 85, 9138–9142 (1988).
[CrossRef] [PubMed]

Levoy, M.

M. Levoy, R. Ng, A. Adams, M. Footer, and M. Horowitz, “Light field microscopy,” ACM Trans. Graphics 25, 924–934(2006).
[CrossRef]

Liao, L.

Lindwasser, O. W.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313, 1642–1645(2006).
[CrossRef] [PubMed]

Lippincott, J.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313, 1642–1645(2006).
[CrossRef] [PubMed]

Liu, A.

Liu, N.

S. R. P. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu, R. J. Twieg, R. Piestun, and W. E. Moerner, “Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function,” Proc. Natl. Acad. Sci. 106, 2995–2999 (2009).
[CrossRef] [PubMed]

Logan, D. C.

Lord, S. J.

S. R. P. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu, R. J. Twieg, R. Piestun, and W. E. Moerner, “Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function,” Proc. Natl. Acad. Sci. 106, 2995–2999 (2009).
[CrossRef] [PubMed]

Louis, D. N.

T. J. Lynch, D. W. Bell, R. Sordella, S. Gurubhagavatula, R. A. Okimoto, B. W. Brannigan, P. L. Harris, S. M. Haserlat, J. G. Supko, F. G. Haluska, D. N. Louis, D. C. Christiani, J. Settleman, and D. A. Haber, “Activating mutations in the epidermal growth factor receptor underlying responsiveness of non–small-cell lung cancer to Gefitinib,” N. Engl. J. Med. 350, 2129–2139(2004).
[CrossRef] [PubMed]

Lucas, J.

D. Pinkel, J. Landegent, C. Collins, J. Fuscoe, R. Segraves, J. Lucas, and J. Gray, “Fluorescence in situ hybridization with human chromosome-specific libraries: Detection of trisomy 21 translocations of chromosome 4,” Proc. Natl. Acad. Sci. 85, 9138–9142 (1988).
[CrossRef] [PubMed]

Lyer, G.

T. Dertinger, R. Colyer, G. Lyer, S. Weiss, and J. Enderlein, “Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI),” Proc. Natl. Acad. Sci. 106, 22287–22292(2009).
[CrossRef] [PubMed]

Lynch, T. J.

T. J. Lynch, D. W. Bell, R. Sordella, S. Gurubhagavatula, R. A. Okimoto, B. W. Brannigan, P. L. Harris, S. M. Haserlat, J. G. Supko, F. G. Haluska, D. N. Louis, D. C. Christiani, J. Settleman, and D. A. Haber, “Activating mutations in the epidermal growth factor receptor underlying responsiveness of non–small-cell lung cancer to Gefitinib,” N. Engl. J. Med. 350, 2129–2139(2004).
[CrossRef] [PubMed]

Maurer, C.

Meckel, T.

L. Holtzer, T. Meckel, and T. Schmidt, “Nanometric three-dimensional tracking of individual quantum dots in cells,” Appl. Phys. Lett. 90, 053902 (2007).
[CrossRef]

Moerner, W. E.

S. R. P. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu, R. J. Twieg, R. Piestun, and W. E. Moerner, “Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function,” Proc. Natl. Acad. Sci. 106, 2995–2999 (2009).
[CrossRef] [PubMed]

Mohan, A.

A. Veeraraghavan, R. Raskar, A. Agrawal, A. Mohan, and J. Tumblin, “Dappled photography: Mask enhanced cameras for heterodyned light fields and coded aperture refocusing,” ACM Trans. Graphics 26, 69-1–69-12 (2007).
[CrossRef]

Morse, M.

Nagahara, H.

H. Nagahara, S. Kuthirummal, C. Zhou, and S. K. Nayar, “Flexible depth of field photography,” in Proceedings of European Conference on Computer Vision (ECCV) (Springer-Verlag, 2008), pp. 60–73.

Nayar, S. K.

H. Nagahara, S. Kuthirummal, C. Zhou, and S. K. Nayar, “Flexible depth of field photography,” in Proceedings of European Conference on Computer Vision (ECCV) (Springer-Verlag, 2008), pp. 60–73.

Nevin, W. A.

W. A. Nevin, D. L. Gay, and V. Higgs, “Photoluminescence study of interfacial defects in direct-bonded silicon wafers,” J. Electrochem. Soc. 150, G591–G596 (2003).
[CrossRef]

Ng, R.

M. Levoy, R. Ng, A. Adams, M. Footer, and M. Horowitz, “Light field microscopy,” ACM Trans. Graphics 25, 924–934(2006).
[CrossRef]

Niwa, Y.

M. Uemura, Y. Niwa, N. Kakazu, N. Adachi, and K. Kinoshita, “Chromosomal manipulation by site-specific recombinases and fluorescent protein-based vectors,” PLoS One 5, e9846(2010).
[CrossRef] [PubMed]

Okimoto, R. A.

T. J. Lynch, D. W. Bell, R. Sordella, S. Gurubhagavatula, R. A. Okimoto, B. W. Brannigan, P. L. Harris, S. M. Haserlat, J. G. Supko, F. G. Haluska, D. N. Louis, D. C. Christiani, J. Settleman, and D. A. Haber, “Activating mutations in the epidermal growth factor receptor underlying responsiveness of non–small-cell lung cancer to Gefitinib,” N. Engl. J. Med. 350, 2129–2139(2004).
[CrossRef] [PubMed]

Olenych, S.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313, 1642–1645(2006).
[CrossRef] [PubMed]

Paterson, L.

Patterson, G. H.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313, 1642–1645(2006).
[CrossRef] [PubMed]

Pavani, S. R. P.

S. R. P. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu, R. J. Twieg, R. Piestun, and W. E. Moerner, “Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function,” Proc. Natl. Acad. Sci. 106, 2995–2999 (2009).
[CrossRef] [PubMed]

Piestun, R.

S. R. P. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu, R. J. Twieg, R. Piestun, and W. E. Moerner, “Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function,” Proc. Natl. Acad. Sci. 106, 2995–2999 (2009).
[CrossRef] [PubMed]

Pinkel, D.

D. Pinkel, J. Landegent, C. Collins, J. Fuscoe, R. Segraves, J. Lucas, and J. Gray, “Fluorescence in situ hybridization with human chromosome-specific libraries: Detection of trisomy 21 translocations of chromosome 4,” Proc. Natl. Acad. Sci. 85, 9138–9142 (1988).
[CrossRef] [PubMed]

D. Pinkel, T. Straume, and J. W. Gray, “Cytogenetic analysis using quantitative, high-sensitivity, fluorescence hybridization,” Proc. Natl. Acad. Sci. USA 83, 2934–2938 (1986).
[CrossRef] [PubMed]

Putoud, A.

Raskar, R.

A. Veeraraghavan, R. Raskar, A. Agrawal, A. Mohan, and J. Tumblin, “Dappled photography: Mask enhanced cameras for heterodyned light fields and coded aperture refocusing,” ACM Trans. Graphics 26, 69-1–69-12 (2007).
[CrossRef]

Ritsch-Marte, M.

Rosen, J.

J. Rosen and G. Brooker, “Non-scanning motionless fluorescence three-dimensional holographic microscopy,” Nat. Photonics 2, 190–195 (2008).
[CrossRef]

Rubin, D.

Rust, M. J.

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3, 793–796 (2006).
[CrossRef] [PubMed]

Samara-Rubio, D.

Schmidt, T.

L. Holtzer, T. Meckel, and T. Schmidt, “Nanometric three-dimensional tracking of individual quantum dots in cells,” Appl. Phys. Lett. 90, 053902 (2007).
[CrossRef]

Segraves, R.

D. Pinkel, J. Landegent, C. Collins, J. Fuscoe, R. Segraves, J. Lucas, and J. Gray, “Fluorescence in situ hybridization with human chromosome-specific libraries: Detection of trisomy 21 translocations of chromosome 4,” Proc. Natl. Acad. Sci. 85, 9138–9142 (1988).
[CrossRef] [PubMed]

Settleman, J.

T. J. Lynch, D. W. Bell, R. Sordella, S. Gurubhagavatula, R. A. Okimoto, B. W. Brannigan, P. L. Harris, S. M. Haserlat, J. G. Supko, F. G. Haluska, D. N. Louis, D. C. Christiani, J. Settleman, and D. A. Haber, “Activating mutations in the epidermal growth factor receptor underlying responsiveness of non–small-cell lung cancer to Gefitinib,” N. Engl. J. Med. 350, 2129–2139(2004).
[CrossRef] [PubMed]

Shroff, H.

H. Shroff, C. G. Galbraith, J. A. Galbraith, and E. Betzig, “Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics,” Nat. Methods 5, 417–423 (2008).
[CrossRef] [PubMed]

Sordella, R.

T. J. Lynch, D. W. Bell, R. Sordella, S. Gurubhagavatula, R. A. Okimoto, B. W. Brannigan, P. L. Harris, S. M. Haserlat, J. G. Supko, F. G. Haluska, D. N. Louis, D. C. Christiani, J. Settleman, and D. A. Haber, “Activating mutations in the epidermal growth factor receptor underlying responsiveness of non–small-cell lung cancer to Gefitinib,” N. Engl. J. Med. 350, 2129–2139(2004).
[CrossRef] [PubMed]

Sougrat, R.

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313, 1642–1645(2006).
[CrossRef] [PubMed]

Straume, T.

D. Pinkel, T. Straume, and J. W. Gray, “Cytogenetic analysis using quantitative, high-sensitivity, fluorescence hybridization,” Proc. Natl. Acad. Sci. USA 83, 2934–2938 (1986).
[CrossRef] [PubMed]

Supko, J. G.

T. J. Lynch, D. W. Bell, R. Sordella, S. Gurubhagavatula, R. A. Okimoto, B. W. Brannigan, P. L. Harris, S. M. Haserlat, J. G. Supko, F. G. Haluska, D. N. Louis, D. C. Christiani, J. Settleman, and D. A. Haber, “Activating mutations in the epidermal growth factor receptor underlying responsiveness of non–small-cell lung cancer to Gefitinib,” N. Engl. J. Med. 350, 2129–2139(2004).
[CrossRef] [PubMed]

Thompson, M. A.

S. R. P. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu, R. J. Twieg, R. Piestun, and W. E. Moerner, “Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function,” Proc. Natl. Acad. Sci. 106, 2995–2999 (2009).
[CrossRef] [PubMed]

Towers, D. P.

Tumblin, J.

A. Veeraraghavan, R. Raskar, A. Agrawal, A. Mohan, and J. Tumblin, “Dappled photography: Mask enhanced cameras for heterodyned light fields and coded aperture refocusing,” ACM Trans. Graphics 26, 69-1–69-12 (2007).
[CrossRef]

Twieg, R. J.

S. R. P. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu, R. J. Twieg, R. Piestun, and W. E. Moerner, “Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function,” Proc. Natl. Acad. Sci. 106, 2995–2999 (2009).
[CrossRef] [PubMed]

Uemura, M.

M. Uemura, Y. Niwa, N. Kakazu, N. Adachi, and K. Kinoshita, “Chromosomal manipulation by site-specific recombinases and fluorescent protein-based vectors,” PLoS One 5, e9846(2010).
[CrossRef] [PubMed]

Veeraraghavan, A.

A. Veeraraghavan, R. Raskar, A. Agrawal, A. Mohan, and J. Tumblin, “Dappled photography: Mask enhanced cameras for heterodyned light fields and coded aperture refocusing,” ACM Trans. Graphics 26, 69-1–69-12 (2007).
[CrossRef]

Warburton, R. J.

Weiss, S.

T. Dertinger, R. Colyer, G. Lyer, S. Weiss, and J. Enderlein, “Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI),” Proc. Natl. Acad. Sci. 106, 22287–22292(2009).
[CrossRef] [PubMed]

Wichmann, J.

Zhou, C.

H. Nagahara, S. Kuthirummal, C. Zhou, and S. K. Nayar, “Flexible depth of field photography,” in Proceedings of European Conference on Computer Vision (ECCV) (Springer-Verlag, 2008), pp. 60–73.

Zhuang, X.

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3, 793–796 (2006).
[CrossRef] [PubMed]

ACM Trans. Graphics (2)

A. Veeraraghavan, R. Raskar, A. Agrawal, A. Mohan, and J. Tumblin, “Dappled photography: Mask enhanced cameras for heterodyned light fields and coded aperture refocusing,” ACM Trans. Graphics 26, 69-1–69-12 (2007).
[CrossRef]

M. Levoy, R. Ng, A. Adams, M. Footer, and M. Horowitz, “Light field microscopy,” ACM Trans. Graphics 25, 924–934(2006).
[CrossRef]

Appl. Opt. (1)

Appl. Phys. Lett. (3)

T. Indukuri, P. Koonath, and B. Jalali, “Three-dimensional integration of metal-oxide-semiconductor transistor with subterranean photonics in silicon,” Appl. Phys. Lett. 88, 121108 (2006).
[CrossRef]

K. Kishima, “Analysis of defects in an electric and photonic double-layer substrate made by separation-by-implanted-oxygen three-dimensional sculpting,” Appl. Phys. Lett. 89, 201109 (2006).
[CrossRef]

L. Holtzer, T. Meckel, and T. Schmidt, “Nanometric three-dimensional tracking of individual quantum dots in cells,” Appl. Phys. Lett. 90, 053902 (2007).
[CrossRef]

J. Electrochem. Soc. (1)

W. A. Nevin, D. L. Gay, and V. Higgs, “Photoluminescence study of interfacial defects in direct-bonded silicon wafers,” J. Electrochem. Soc. 150, G591–G596 (2003).
[CrossRef]

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

Micro. IEEE (1)

C. Gunn, “CMOS photonics for high-speed interconnects,” Micro. IEEE 26, 58–66 (2005).
[CrossRef]

N. Engl. J. Med. (1)

T. J. Lynch, D. W. Bell, R. Sordella, S. Gurubhagavatula, R. A. Okimoto, B. W. Brannigan, P. L. Harris, S. M. Haserlat, J. G. Supko, F. G. Haluska, D. N. Louis, D. C. Christiani, J. Settleman, and D. A. Haber, “Activating mutations in the epidermal growth factor receptor underlying responsiveness of non–small-cell lung cancer to Gefitinib,” N. Engl. J. Med. 350, 2129–2139(2004).
[CrossRef] [PubMed]

Nat. Methods (2)

M. J. Rust, M. Bates, and X. Zhuang, “Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM),” Nat. Methods 3, 793–796 (2006).
[CrossRef] [PubMed]

H. Shroff, C. G. Galbraith, J. A. Galbraith, and E. Betzig, “Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics,” Nat. Methods 5, 417–423 (2008).
[CrossRef] [PubMed]

Nat. Photonics (1)

J. Rosen and G. Brooker, “Non-scanning motionless fluorescence three-dimensional holographic microscopy,” Nat. Photonics 2, 190–195 (2008).
[CrossRef]

Opt. Express (3)

Opt. Lett. (2)

PLoS One (1)

M. Uemura, Y. Niwa, N. Kakazu, N. Adachi, and K. Kinoshita, “Chromosomal manipulation by site-specific recombinases and fluorescent protein-based vectors,” PLoS One 5, e9846(2010).
[CrossRef] [PubMed]

Proc. Natl. Acad. Sci. (3)

D. Pinkel, J. Landegent, C. Collins, J. Fuscoe, R. Segraves, J. Lucas, and J. Gray, “Fluorescence in situ hybridization with human chromosome-specific libraries: Detection of trisomy 21 translocations of chromosome 4,” Proc. Natl. Acad. Sci. 85, 9138–9142 (1988).
[CrossRef] [PubMed]

T. Dertinger, R. Colyer, G. Lyer, S. Weiss, and J. Enderlein, “Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI),” Proc. Natl. Acad. Sci. 106, 22287–22292(2009).
[CrossRef] [PubMed]

S. R. P. Pavani, M. A. Thompson, J. S. Biteen, S. J. Lord, N. Liu, R. J. Twieg, R. Piestun, and W. E. Moerner, “Three-dimensional, single-molecule fluorescence imaging beyond the diffraction limit by using a double-helix point spread function,” Proc. Natl. Acad. Sci. 106, 2995–2999 (2009).
[CrossRef] [PubMed]

Proc. Natl. Acad. Sci. USA (1)

D. Pinkel, T. Straume, and J. W. Gray, “Cytogenetic analysis using quantitative, high-sensitivity, fluorescence hybridization,” Proc. Natl. Acad. Sci. USA 83, 2934–2938 (1986).
[CrossRef] [PubMed]

Science (1)

E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott, and H. F. Hess, “Imaging intracellular fluorescent proteins at nanometer resolution,” Science 313, 1642–1645(2006).
[CrossRef] [PubMed]

Other (4)

H. Nagahara, S. Kuthirummal, C. Zhou, and S. K. Nayar, “Flexible depth of field photography,” in Proceedings of European Conference on Computer Vision (ECCV) (Springer-Verlag, 2008), pp. 60–73.

J. W. Goodman, Introduction to Fourier Optics (Roberts, 2004).

http://www.abbottmolecular.com/UroVysion_5181.aspx.

http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=CCL-171&Template=cellBiology.

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Figures (15)

Fig. 1
Fig. 1

Procedure for finding the z positions of the fluorescent markers in the traditional method. (a) First step: capturing multiple images with fine intervals in the z direction. A red and a green fluorescent marker are seen in the right and left portion of the image, respectively. They have different focus positions. (b) Second step: plotting the peak brightness data for each fluorescence marker, determining the focal depth, identifying the position of the markers.

Fig. 2
Fig. 2

3D structure to explain the proposed method. Marker A is on the z A plane and marker B is on the z B plane.

Fig. 3
Fig. 3

First step: identifying the x y position of markers using through-focus exposure. (a) Image of fluorescent marker A on imaging device as a function of time t during exposure. (b) Image of markers A and B recorded by through-focus exposure. x y positions of marker A and B are identified as ( X A , Y A ) and ( X B , Y B ) , respectively.

Fig. 4
Fig. 4

Second step: identifying the z position of markers from blurred image. (a) Image of fluorescent marker A on imaging device as a function of time t during exposure. (b) Final blurred images of markers A and B.

Fig. 5
Fig. 5

Experimental setup. Piezo-type stages x y and z stages are placed on the stage of FOV-type fluorescent microscope; Axio Imager Z1 (Carl Ziess). Color digital SLR camera is used.

Fig. 6
Fig. 6

Specimen for verification of the proposed method.

Fig. 7
Fig. 7

Images of fluorescent beads on specimen. (a) Image the first step exposure. The z stage was moved during exposure. (b) Image by the second step exposure. The x y stage and z stage were synchronously moved.

Fig. 8
Fig. 8

Localization process of fluorescent marker in z direction.

Fig. 9
Fig. 9

Results of localization of bead A and B in test specimen.

Fig. 10
Fig. 10

Specimen for measuring chromatic aberration.

Fig. 11
Fig. 11

Images of fluorescent beads of different colors on flat substrate by the second step exposure. The x y stage and z stage were synchronously moved.

Fig. 12
Fig. 12

Results for chromatic aberration measurements. Results of localization of red and green beads on flat substrate.

Fig. 13
Fig. 13

Images of FISH cells of UroVysion Bladder Cancer Kit. Red color fluorescent probe hybridizes to the centromere regions of chromosomes 3 and green probe hybridizes to the centromere regions of chromosomes 7. (a) Image by the first step exposure. The z stage was moved during exposure. (b) Image by the second step exposure. The x y stage and z stage were synchronously moved. (c) Reference image captured with x y and z stages fixed.

Fig. 14
Fig. 14

Cropped blurred images of FISH cells for localization of probe position. (a) Original color (3 color component image) of cropped blurred image (b) Red component of cropped image for localization of probe hybridized to chromosome 3. (c) Green component of cropped image for localization of probe hybridized to chromosome 7.

Fig. 15
Fig. 15

Results for localization of probes of chromosomes 3 and 7. There is a 14 degree difference between chromosome 3 and 7 before correction for the chromatic aberration shown in Fig. 12.

Equations (6)

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

z ( t ) = z start + ( z end z start ) t t ex
x = x 0
y = y 0 .
z ( t ) = z start + ( z end z start ) t t ex
x ( t ) = x 0 + L × cos ( π t t ex )
y ( t ) = y 0 + L × sin ( π t t ex ) .

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