Q. Miao, A. P. Reeves, F. W. Patten, and E. J. Seibel, “Multimodal 3D imaging of cells and tissue: bridging the gap between clinical and research microscopy,” Ann. Biomed. Eng. 40, 263–276 (2012).

[Crossref]

I. R. Çapoglu, C. A. White, J. D. Rogers, H. Subramanian, A. Taflove, and V. Backman, “Numerical simulation of partially coherent broadband optical imaging using the finite-difference time-domain method,” Opt. Lett. 36, 1596–1598 (2011).

[Crossref]

R. L. Coe and E. J. Seibel, “Improved near-field calculations using vectorial diffraction integrals in the finite-difference time-domain method,” J. Opt. Soc. Am. A 28, 1776–1783 (2011).

[Crossref]

N. N. Boustany, S. A. Boppart, and V. Backman, “Microscopic imaging and spectroscopy with scattered light,” Annu. Rev. Biomed. Eng. 12, 285–314 (2010).

[Crossref]

T. Martin, “On the FDTD near-to-far-field transformations for weakly scattering objects,” IEEE Trans. Antennas Propag. 58, 2794–2795 (2010).

[Crossref]

T. H. Chow, W. M. Lee, K. M. Tan, B. K. Ng, and C. J. R. Sheppard, “Resolving interparticle position and optical forces along the axial direction using optical coherence gating,” Appl. Phys. Lett. 97, 231113 (2010).

[Crossref]

J. J. Schwartz, S. Stavrakis, and S. R. Quake, “Colloidal lenses allow high-temperature single-molecule imaging and improve fluorophore photostability,” Nat. Nanotechnol. 5, 127–132 (2009).

[Crossref]

H. Subramanian, H. K. Roy, P. Pradhan, M. J. Goldberg, J. Muldoon, R. E. Brand, C. Sturgis, T. Hensing, D. Ray, A. Bogojevic, J. Mohammed, J. Chang, and V. Backman, “Nanoscale cellular changes in field carcinogenesis detected by partial wave spectroscopy,” Cancer Res. 69, 5357–5363 (2009).

[Crossref]

M. G. Meyer, M. Fauver, J. R. Rahn, T. Neumann, and F. W. Patten, “Automated cell analysis in 2D and 3D: a comparative study,” Pattern Recogn. 42, 141–146 (2009).

[Crossref]

N. Nakajima, “Phase retrieval from a high-numerical-aperture intensity distribution by use of an aperture-array filter,” J. Opt. Soc. Am. A 26, 2172–2180 (2009).

[Crossref]

H. Subramanian, P. Pradhan, Y. Liu, I. R. Capoglu, J. D. Rogers, H. K. Roy, R. E. Brand, and V. Backman, “Partial-wave microscopic spectroscopy detects subwavelength refractive index fluctuations: an application to cancer diagnosis,” Opt. Lett. 34, 518–520 (2009).

[Crossref]

P. Török, P. R. T. Munro, and E. E. Kriezis, “High numerical aperture vectorial imaging in coherent optical microscopes,” Opt. Express 16, 507–523 (2008).

[Crossref]

I. R. Çapoglu, A. Taflove, and V. Backman, “Generation of an incident focused light pulse in FDTD,” Opt. Express 16, 19208–19220 (2008).

[Crossref]

W. Choi, C. Fang-Yen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods 4, 717–719 (2007).

[Crossref]

D. J. Robinson and J. B. Schneider, “On the use of the geometric mean in FDTD near-to-far-field transformations,” IEEE Trans. Antennas Propag. 55, 3204–3211 (2007).

[Crossref]

P. R. T. Munro and P. Török, “Calculation of the image of an arbitrary vectorial electromagnetic field,” Opt. Express 15, 9293–9307 (2007).

[Crossref]

J. B. Schneider and K. Abdijalilov, “Analytic field propagation TFSF boundary for FDTD problems involving planar interfaces: PECs, TE, and TM,” IEEE Trans. Antennas. Propag. 54, 2531–2542 (2006).

[Crossref]

P. Török, P. R. T. Munro, and E. E. Kriezis, “Rigorous near- to far-field transformation for vectorial diffraction calculations and its numerical implementation,” J. Opt. Soc. Am. A 23, 713–722 (2006).

[Crossref]

X. Ma, J. Q. Lu, R. S. Brock, K. M. Jacobs, P. Yang, and X.-H. Hu, “Determination of complex refractive index of polystyrene microspheres from 370 to 1610 nm,” Phys. Med. Biol. 48, 4165–4172 (2003).

[Crossref]

N. Martini, J. Bewersdorf, and S. W. Hell, “A new high-aperture glycerol immersion objective lens and its application to 3D-fluorescence microscopy,” J. Microsc. 206, 146–151 (2002).

[Crossref]

M. Totzeck, “Numerical simulation of high-NA quantitative polarization microscopy and corresponding near-fields,” Optik 112, 399–406 (2001).

[Crossref]

R. Drezek, A. Dunn, and R. Richards-Kortum, “A pulsed finite-difference time-domain (FDTD) method for calculating light scattering from biological cells over broad wavelength ranges,” Opt. Express 6, 147–157 (2000).

[Crossref]

J. A. Roden and S. D. Gedney, “Convolution PML (CPML): an efficient FDTD implementation of the CFS–PML for arbitrary media,” Microw. Opt. Technol. Lett. 27, 334–339 (2000).

[Crossref]

M. G. L. Gustafsson, “Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy,” J. Microsc. 198, 82–87 (2000).

[Crossref]

T. Martin, “An improved near- to far-zone transformation for the finite-difference time-domain method,” IEEE Trans. Antennas Propag. 46, 1263–1271 (1998).

[Crossref]

C. Smithpeter, A. K. Dunn, R. Drezek, T. Collier, and R. Richards-Kortum, “Near real time confocal microscopy of cultured amelanotic cells: sources of signal, contrast agents and limits of contrast,” J. Biomed. Opt. 3, 429–436 (1998).

[Crossref]

I. T. Young, “Quantitative microscopy,” IEEE Eng. Med. Biol. 15, 59–66 (1996).

[Crossref]

G. Gouesbet, “Generalized Lorenz–Mie theory and applications,” Part. Part. Syst. Charact. 11, 22–34 (1994).

[Crossref]

J. P. Berenger, “A perfectly matched layer for the absorption of electromagnetic waves,” J. Comput. Phys. 114, 185–200 (1994).

[Crossref]

D. Merewether, R. Fisher, and F. W. Smith, “On implementing a numeric Huygen’s source scheme in a finite difference program to illuminate scattering bodies,” IEEE Trans. Nucl. Sci. 27, 1829–1833 (1980).

[Crossref]

K. Yee, “Numerical solution of initial boundary value problems involving Maxwell’s equations in isotropic media,” IEEE Trans. Antennas Propag. 14, 302–307 (1966).

[Crossref]

B. Richards and E. Wolf, “Electromagnetic diffraction in optical systems. II. Structure of the image field in an aplanatic system,” Proc. R. Soc. A 253, 358–379 (1959).

[Crossref]

J. B. Schneider and K. Abdijalilov, “Analytic field propagation TFSF boundary for FDTD problems involving planar interfaces: PECs, TE, and TM,” IEEE Trans. Antennas. Propag. 54, 2531–2542 (2006).

[Crossref]

I. R. Çapoglu, C. A. White, J. D. Rogers, H. Subramanian, A. Taflove, and V. Backman, “Numerical simulation of partially coherent broadband optical imaging using the finite-difference time-domain method,” Opt. Lett. 36, 1596–1598 (2011).

[Crossref]

N. N. Boustany, S. A. Boppart, and V. Backman, “Microscopic imaging and spectroscopy with scattered light,” Annu. Rev. Biomed. Eng. 12, 285–314 (2010).

[Crossref]

H. Subramanian, H. K. Roy, P. Pradhan, M. J. Goldberg, J. Muldoon, R. E. Brand, C. Sturgis, T. Hensing, D. Ray, A. Bogojevic, J. Mohammed, J. Chang, and V. Backman, “Nanoscale cellular changes in field carcinogenesis detected by partial wave spectroscopy,” Cancer Res. 69, 5357–5363 (2009).

[Crossref]

H. Subramanian, P. Pradhan, Y. Liu, I. R. Capoglu, J. D. Rogers, H. K. Roy, R. E. Brand, and V. Backman, “Partial-wave microscopic spectroscopy detects subwavelength refractive index fluctuations: an application to cancer diagnosis,” Opt. Lett. 34, 518–520 (2009).

[Crossref]

I. R. Çapoglu, A. Taflove, and V. Backman, “Generation of an incident focused light pulse in FDTD,” Opt. Express 16, 19208–19220 (2008).

[Crossref]

I. R. Capoglu, J. D. Rogers, A. Taflove, and V. Backman, “The microscope in a computer: Image synthesis from three-dimensional full-vector solutions of Maxwell’s equations at the nanometer scale,” Prog. Opt.57, 1–91 (2012).

[Crossref]

W. Choi, C. Fang-Yen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods 4, 717–719 (2007).

[Crossref]

J. P. Berenger, “A perfectly matched layer for the absorption of electromagnetic waves,” J. Comput. Phys. 114, 185–200 (1994).

[Crossref]

N. Martini, J. Bewersdorf, and S. W. Hell, “A new high-aperture glycerol immersion objective lens and its application to 3D-fluorescence microscopy,” J. Microsc. 206, 146–151 (2002).

[Crossref]

H. Subramanian, H. K. Roy, P. Pradhan, M. J. Goldberg, J. Muldoon, R. E. Brand, C. Sturgis, T. Hensing, D. Ray, A. Bogojevic, J. Mohammed, J. Chang, and V. Backman, “Nanoscale cellular changes in field carcinogenesis detected by partial wave spectroscopy,” Cancer Res. 69, 5357–5363 (2009).

[Crossref]

N. N. Boustany, S. A. Boppart, and V. Backman, “Microscopic imaging and spectroscopy with scattered light,” Annu. Rev. Biomed. Eng. 12, 285–314 (2010).

[Crossref]

M. Born and E. Wolf, Principles of Optics: Electromagnetic Theory of Propagation, Interference and Diffraction of Light (Pergamon, 1980).

N. N. Boustany, S. A. Boppart, and V. Backman, “Microscopic imaging and spectroscopy with scattered light,” Annu. Rev. Biomed. Eng. 12, 285–314 (2010).

[Crossref]

H. Subramanian, H. K. Roy, P. Pradhan, M. J. Goldberg, J. Muldoon, R. E. Brand, C. Sturgis, T. Hensing, D. Ray, A. Bogojevic, J. Mohammed, J. Chang, and V. Backman, “Nanoscale cellular changes in field carcinogenesis detected by partial wave spectroscopy,” Cancer Res. 69, 5357–5363 (2009).

[Crossref]

H. Subramanian, P. Pradhan, Y. Liu, I. R. Capoglu, J. D. Rogers, H. K. Roy, R. E. Brand, and V. Backman, “Partial-wave microscopic spectroscopy detects subwavelength refractive index fluctuations: an application to cancer diagnosis,” Opt. Lett. 34, 518–520 (2009).

[Crossref]

X. Ma, J. Q. Lu, R. S. Brock, K. M. Jacobs, P. Yang, and X.-H. Hu, “Determination of complex refractive index of polystyrene microspheres from 370 to 1610 nm,” Phys. Med. Biol. 48, 4165–4172 (2003).

[Crossref]

J. P. Brody and S. R. Quake, “A self-assembled microlensing rotational probe,” Appl. Phys. Lett. 74, 144–146 (1999).

[Crossref]

H. Subramanian, P. Pradhan, Y. Liu, I. R. Capoglu, J. D. Rogers, H. K. Roy, R. E. Brand, and V. Backman, “Partial-wave microscopic spectroscopy detects subwavelength refractive index fluctuations: an application to cancer diagnosis,” Opt. Lett. 34, 518–520 (2009).

[Crossref]

I. R. Capoglu, J. D. Rogers, A. Taflove, and V. Backman, “The microscope in a computer: Image synthesis from three-dimensional full-vector solutions of Maxwell’s equations at the nanometer scale,” Prog. Opt.57, 1–91 (2012).

[Crossref]

I. R. Çapoglu, C. A. White, J. D. Rogers, H. Subramanian, A. Taflove, and V. Backman, “Numerical simulation of partially coherent broadband optical imaging using the finite-difference time-domain method,” Opt. Lett. 36, 1596–1598 (2011).

[Crossref]

I. R. Çapoglu, A. Taflove, and V. Backman, “Generation of an incident focused light pulse in FDTD,” Opt. Express 16, 19208–19220 (2008).

[Crossref]

H. Subramanian, H. K. Roy, P. Pradhan, M. J. Goldberg, J. Muldoon, R. E. Brand, C. Sturgis, T. Hensing, D. Ray, A. Bogojevic, J. Mohammed, J. Chang, and V. Backman, “Nanoscale cellular changes in field carcinogenesis detected by partial wave spectroscopy,” Cancer Res. 69, 5357–5363 (2009).

[Crossref]

W. Choi, C. Fang-Yen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods 4, 717–719 (2007).

[Crossref]

T. H. Chow, W. M. Lee, K. M. Tan, B. K. Ng, and C. J. R. Sheppard, “Resolving interparticle position and optical forces along the axial direction using optical coherence gating,” Appl. Phys. Lett. 97, 231113 (2010).

[Crossref]

C. Smithpeter, A. K. Dunn, R. Drezek, T. Collier, and R. Richards-Kortum, “Near real time confocal microscopy of cultured amelanotic cells: sources of signal, contrast agents and limits of contrast,” J. Biomed. Opt. 3, 429–436 (1998).

[Crossref]

W. Choi, C. Fang-Yen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods 4, 717–719 (2007).

[Crossref]

R. Drezek, A. Dunn, and R. Richards-Kortum, “A pulsed finite-difference time-domain (FDTD) method for calculating light scattering from biological cells over broad wavelength ranges,” Opt. Express 6, 147–157 (2000).

[Crossref]

R. Drezek, A. Dunn, and R. Richards-Kortum, “Light scattering from cells: finite-difference time-domain simulations and goniometric measurements,” Appl. Opt. 38, 3651–3661 (1999).

[Crossref]

C. Smithpeter, A. K. Dunn, R. Drezek, T. Collier, and R. Richards-Kortum, “Near real time confocal microscopy of cultured amelanotic cells: sources of signal, contrast agents and limits of contrast,” J. Biomed. Opt. 3, 429–436 (1998).

[Crossref]

R. Drezek, A. Dunn, and R. Richards-Kortum, “A pulsed finite-difference time-domain (FDTD) method for calculating light scattering from biological cells over broad wavelength ranges,” Opt. Express 6, 147–157 (2000).

[Crossref]

R. Drezek, A. Dunn, and R. Richards-Kortum, “Light scattering from cells: finite-difference time-domain simulations and goniometric measurements,” Appl. Opt. 38, 3651–3661 (1999).

[Crossref]

C. Smithpeter, A. K. Dunn, R. Drezek, T. Collier, and R. Richards-Kortum, “Near real time confocal microscopy of cultured amelanotic cells: sources of signal, contrast agents and limits of contrast,” J. Biomed. Opt. 3, 429–436 (1998).

[Crossref]

W. Choi, C. Fang-Yen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods 4, 717–719 (2007).

[Crossref]

M. G. Meyer, M. Fauver, J. R. Rahn, T. Neumann, and F. W. Patten, “Automated cell analysis in 2D and 3D: a comparative study,” Pattern Recogn. 42, 141–146 (2009).

[Crossref]

M. Fauver, E. J. Seibel, J. R. Rahn, M. G. Meyer, F. W. Patten, T. Neumann, and A. C. Nelson, “Three-dimensional imaging of single isolated cell nuclei using optical projection tomography,” Opt. Express 13, 4210–4223 (2005).

[Crossref]

W. Choi, C. Fang-Yen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods 4, 717–719 (2007).

[Crossref]

D. Merewether, R. Fisher, and F. W. Smith, “On implementing a numeric Huygen’s source scheme in a finite difference program to illuminate scattering bodies,” IEEE Trans. Nucl. Sci. 27, 1829–1833 (1980).

[Crossref]

J. A. Roden and S. D. Gedney, “Convolution PML (CPML): an efficient FDTD implementation of the CFS–PML for arbitrary media,” Microw. Opt. Technol. Lett. 27, 334–339 (2000).

[Crossref]

H. Subramanian, H. K. Roy, P. Pradhan, M. J. Goldberg, J. Muldoon, R. E. Brand, C. Sturgis, T. Hensing, D. Ray, A. Bogojevic, J. Mohammed, J. Chang, and V. Backman, “Nanoscale cellular changes in field carcinogenesis detected by partial wave spectroscopy,” Cancer Res. 69, 5357–5363 (2009).

[Crossref]

C. Guiffaut and K. Mahdjoubi, “Perfect wideband plane wave injector for FDTD method,” in Proceedings of IEEE Antennas Propagation Society International Symposium (IEEE, 2000), pp. 236–239.

M. G. L. Gustafsson, “Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy,” J. Microsc. 198, 82–87 (2000).

[Crossref]

A. Taflove and S. C. Hagness,Computational Electrodynamics: The Finite-Difference Time-Domain Method (Artech House, 2005).

N. Martini, J. Bewersdorf, and S. W. Hell, “A new high-aperture glycerol immersion objective lens and its application to 3D-fluorescence microscopy,” J. Microsc. 206, 146–151 (2002).

[Crossref]

H. Subramanian, H. K. Roy, P. Pradhan, M. J. Goldberg, J. Muldoon, R. E. Brand, C. Sturgis, T. Hensing, D. Ray, A. Bogojevic, J. Mohammed, J. Chang, and V. Backman, “Nanoscale cellular changes in field carcinogenesis detected by partial wave spectroscopy,” Cancer Res. 69, 5357–5363 (2009).

[Crossref]

X. Ma, J. Q. Lu, R. S. Brock, K. M. Jacobs, P. Yang, and X.-H. Hu, “Determination of complex refractive index of polystyrene microspheres from 370 to 1610 nm,” Phys. Med. Biol. 48, 4165–4172 (2003).

[Crossref]

X. Ma, J. Q. Lu, R. S. Brock, K. M. Jacobs, P. Yang, and X.-H. Hu, “Determination of complex refractive index of polystyrene microspheres from 370 to 1610 nm,” Phys. Med. Biol. 48, 4165–4172 (2003).

[Crossref]

A. C. Kak and M. Slaney, Principles of Computerized Tomographic Imaging (IEEE, 1988).

P. Török, P. R. T. Munro, and E. E. Kriezis, “High numerical aperture vectorial imaging in coherent optical microscopes,” Opt. Express 16, 507–523 (2008).

[Crossref]

P. Török, P. R. T. Munro, and E. E. Kriezis, “Rigorous near- to far-field transformation for vectorial diffraction calculations and its numerical implementation,” J. Opt. Soc. Am. A 23, 713–722 (2006).

[Crossref]

T. H. Chow, W. M. Lee, K. M. Tan, B. K. Ng, and C. J. R. Sheppard, “Resolving interparticle position and optical forces along the axial direction using optical coherence gating,” Appl. Phys. Lett. 97, 231113 (2010).

[Crossref]

H. Subramanian, P. Pradhan, Y. Liu, I. R. Capoglu, J. D. Rogers, H. K. Roy, R. E. Brand, and V. Backman, “Partial-wave microscopic spectroscopy detects subwavelength refractive index fluctuations: an application to cancer diagnosis,” Opt. Lett. 34, 518–520 (2009).

[Crossref]

X. Ma, J. Q. Lu, R. S. Brock, K. M. Jacobs, P. Yang, and X.-H. Hu, “Determination of complex refractive index of polystyrene microspheres from 370 to 1610 nm,” Phys. Med. Biol. 48, 4165–4172 (2003).

[Crossref]

W. Choi, C. Fang-Yen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods 4, 717–719 (2007).

[Crossref]

X. Ma, J. Q. Lu, R. S. Brock, K. M. Jacobs, P. Yang, and X.-H. Hu, “Determination of complex refractive index of polystyrene microspheres from 370 to 1610 nm,” Phys. Med. Biol. 48, 4165–4172 (2003).

[Crossref]

C. Guiffaut and K. Mahdjoubi, “Perfect wideband plane wave injector for FDTD method,” in Proceedings of IEEE Antennas Propagation Society International Symposium (IEEE, 2000), pp. 236–239.

T. Martin, “On the FDTD near-to-far-field transformations for weakly scattering objects,” IEEE Trans. Antennas Propag. 58, 2794–2795 (2010).

[Crossref]

T. Martin, “An improved near- to far-zone transformation for the finite-difference time-domain method,” IEEE Trans. Antennas Propag. 46, 1263–1271 (1998).

[Crossref]

N. Martini, J. Bewersdorf, and S. W. Hell, “A new high-aperture glycerol immersion objective lens and its application to 3D-fluorescence microscopy,” J. Microsc. 206, 146–151 (2002).

[Crossref]

D. Merewether, R. Fisher, and F. W. Smith, “On implementing a numeric Huygen’s source scheme in a finite difference program to illuminate scattering bodies,” IEEE Trans. Nucl. Sci. 27, 1829–1833 (1980).

[Crossref]

M. G. Meyer, M. Fauver, J. R. Rahn, T. Neumann, and F. W. Patten, “Automated cell analysis in 2D and 3D: a comparative study,” Pattern Recogn. 42, 141–146 (2009).

[Crossref]

M. Fauver, E. J. Seibel, J. R. Rahn, M. G. Meyer, F. W. Patten, T. Neumann, and A. C. Nelson, “Three-dimensional imaging of single isolated cell nuclei using optical projection tomography,” Opt. Express 13, 4210–4223 (2005).

[Crossref]

Q. Miao, A. P. Reeves, F. W. Patten, and E. J. Seibel, “Multimodal 3D imaging of cells and tissue: bridging the gap between clinical and research microscopy,” Ann. Biomed. Eng. 40, 263–276 (2012).

[Crossref]

H. Subramanian, H. K. Roy, P. Pradhan, M. J. Goldberg, J. Muldoon, R. E. Brand, C. Sturgis, T. Hensing, D. Ray, A. Bogojevic, J. Mohammed, J. Chang, and V. Backman, “Nanoscale cellular changes in field carcinogenesis detected by partial wave spectroscopy,” Cancer Res. 69, 5357–5363 (2009).

[Crossref]

H. Subramanian, H. K. Roy, P. Pradhan, M. J. Goldberg, J. Muldoon, R. E. Brand, C. Sturgis, T. Hensing, D. Ray, A. Bogojevic, J. Mohammed, J. Chang, and V. Backman, “Nanoscale cellular changes in field carcinogenesis detected by partial wave spectroscopy,” Cancer Res. 69, 5357–5363 (2009).

[Crossref]

P. Török, P. R. T. Munro, and E. E. Kriezis, “High numerical aperture vectorial imaging in coherent optical microscopes,” Opt. Express 16, 507–523 (2008).

[Crossref]

P. R. T. Munro and P. Török, “Calculation of the image of an arbitrary vectorial electromagnetic field,” Opt. Express 15, 9293–9307 (2007).

[Crossref]

P. Török, P. R. T. Munro, and E. E. Kriezis, “Rigorous near- to far-field transformation for vectorial diffraction calculations and its numerical implementation,” J. Opt. Soc. Am. A 23, 713–722 (2006).

[Crossref]

M. G. Meyer, M. Fauver, J. R. Rahn, T. Neumann, and F. W. Patten, “Automated cell analysis in 2D and 3D: a comparative study,” Pattern Recogn. 42, 141–146 (2009).

[Crossref]

M. Fauver, E. J. Seibel, J. R. Rahn, M. G. Meyer, F. W. Patten, T. Neumann, and A. C. Nelson, “Three-dimensional imaging of single isolated cell nuclei using optical projection tomography,” Opt. Express 13, 4210–4223 (2005).

[Crossref]

T. H. Chow, W. M. Lee, K. M. Tan, B. K. Ng, and C. J. R. Sheppard, “Resolving interparticle position and optical forces along the axial direction using optical coherence gating,” Appl. Phys. Lett. 97, 231113 (2010).

[Crossref]

W. Choi, C. Fang-Yen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods 4, 717–719 (2007).

[Crossref]

Q. Miao, A. P. Reeves, F. W. Patten, and E. J. Seibel, “Multimodal 3D imaging of cells and tissue: bridging the gap between clinical and research microscopy,” Ann. Biomed. Eng. 40, 263–276 (2012).

[Crossref]

M. G. Meyer, M. Fauver, J. R. Rahn, T. Neumann, and F. W. Patten, “Automated cell analysis in 2D and 3D: a comparative study,” Pattern Recogn. 42, 141–146 (2009).

[Crossref]

M. Fauver, E. J. Seibel, J. R. Rahn, M. G. Meyer, F. W. Patten, T. Neumann, and A. C. Nelson, “Three-dimensional imaging of single isolated cell nuclei using optical projection tomography,” Opt. Express 13, 4210–4223 (2005).

[Crossref]

H. Subramanian, P. Pradhan, Y. Liu, I. R. Capoglu, J. D. Rogers, H. K. Roy, R. E. Brand, and V. Backman, “Partial-wave microscopic spectroscopy detects subwavelength refractive index fluctuations: an application to cancer diagnosis,” Opt. Lett. 34, 518–520 (2009).

[Crossref]

H. Subramanian, H. K. Roy, P. Pradhan, M. J. Goldberg, J. Muldoon, R. E. Brand, C. Sturgis, T. Hensing, D. Ray, A. Bogojevic, J. Mohammed, J. Chang, and V. Backman, “Nanoscale cellular changes in field carcinogenesis detected by partial wave spectroscopy,” Cancer Res. 69, 5357–5363 (2009).

[Crossref]

J. J. Schwartz, S. Stavrakis, and S. R. Quake, “Colloidal lenses allow high-temperature single-molecule imaging and improve fluorophore photostability,” Nat. Nanotechnol. 5, 127–132 (2009).

[Crossref]

J. P. Brody and S. R. Quake, “A self-assembled microlensing rotational probe,” Appl. Phys. Lett. 74, 144–146 (1999).

[Crossref]

M. G. Meyer, M. Fauver, J. R. Rahn, T. Neumann, and F. W. Patten, “Automated cell analysis in 2D and 3D: a comparative study,” Pattern Recogn. 42, 141–146 (2009).

[Crossref]

M. Fauver, E. J. Seibel, J. R. Rahn, M. G. Meyer, F. W. Patten, T. Neumann, and A. C. Nelson, “Three-dimensional imaging of single isolated cell nuclei using optical projection tomography,” Opt. Express 13, 4210–4223 (2005).

[Crossref]

H. Subramanian, H. K. Roy, P. Pradhan, M. J. Goldberg, J. Muldoon, R. E. Brand, C. Sturgis, T. Hensing, D. Ray, A. Bogojevic, J. Mohammed, J. Chang, and V. Backman, “Nanoscale cellular changes in field carcinogenesis detected by partial wave spectroscopy,” Cancer Res. 69, 5357–5363 (2009).

[Crossref]

Q. Miao, A. P. Reeves, F. W. Patten, and E. J. Seibel, “Multimodal 3D imaging of cells and tissue: bridging the gap between clinical and research microscopy,” Ann. Biomed. Eng. 40, 263–276 (2012).

[Crossref]

B. Richards and E. Wolf, “Electromagnetic diffraction in optical systems. II. Structure of the image field in an aplanatic system,” Proc. R. Soc. A 253, 358–379 (1959).

[Crossref]

R. Drezek, A. Dunn, and R. Richards-Kortum, “A pulsed finite-difference time-domain (FDTD) method for calculating light scattering from biological cells over broad wavelength ranges,” Opt. Express 6, 147–157 (2000).

[Crossref]

R. Drezek, A. Dunn, and R. Richards-Kortum, “Light scattering from cells: finite-difference time-domain simulations and goniometric measurements,” Appl. Opt. 38, 3651–3661 (1999).

[Crossref]

C. Smithpeter, A. K. Dunn, R. Drezek, T. Collier, and R. Richards-Kortum, “Near real time confocal microscopy of cultured amelanotic cells: sources of signal, contrast agents and limits of contrast,” J. Biomed. Opt. 3, 429–436 (1998).

[Crossref]

D. J. Robinson and J. B. Schneider, “On the use of the geometric mean in FDTD near-to-far-field transformations,” IEEE Trans. Antennas Propag. 55, 3204–3211 (2007).

[Crossref]

J. A. Roden and S. D. Gedney, “Convolution PML (CPML): an efficient FDTD implementation of the CFS–PML for arbitrary media,” Microw. Opt. Technol. Lett. 27, 334–339 (2000).

[Crossref]

I. R. Çapoglu, C. A. White, J. D. Rogers, H. Subramanian, A. Taflove, and V. Backman, “Numerical simulation of partially coherent broadband optical imaging using the finite-difference time-domain method,” Opt. Lett. 36, 1596–1598 (2011).

[Crossref]

H. Subramanian, P. Pradhan, Y. Liu, I. R. Capoglu, J. D. Rogers, H. K. Roy, R. E. Brand, and V. Backman, “Partial-wave microscopic spectroscopy detects subwavelength refractive index fluctuations: an application to cancer diagnosis,” Opt. Lett. 34, 518–520 (2009).

[Crossref]

I. R. Capoglu, J. D. Rogers, A. Taflove, and V. Backman, “The microscope in a computer: Image synthesis from three-dimensional full-vector solutions of Maxwell’s equations at the nanometer scale,” Prog. Opt.57, 1–91 (2012).

[Crossref]

H. Subramanian, H. K. Roy, P. Pradhan, M. J. Goldberg, J. Muldoon, R. E. Brand, C. Sturgis, T. Hensing, D. Ray, A. Bogojevic, J. Mohammed, J. Chang, and V. Backman, “Nanoscale cellular changes in field carcinogenesis detected by partial wave spectroscopy,” Cancer Res. 69, 5357–5363 (2009).

[Crossref]

H. Subramanian, P. Pradhan, Y. Liu, I. R. Capoglu, J. D. Rogers, H. K. Roy, R. E. Brand, and V. Backman, “Partial-wave microscopic spectroscopy detects subwavelength refractive index fluctuations: an application to cancer diagnosis,” Opt. Lett. 34, 518–520 (2009).

[Crossref]

D. J. Robinson and J. B. Schneider, “On the use of the geometric mean in FDTD near-to-far-field transformations,” IEEE Trans. Antennas Propag. 55, 3204–3211 (2007).

[Crossref]

J. B. Schneider and K. Abdijalilov, “Analytic field propagation TFSF boundary for FDTD problems involving planar interfaces: PECs, TE, and TM,” IEEE Trans. Antennas. Propag. 54, 2531–2542 (2006).

[Crossref]

J. J. Schwartz, S. Stavrakis, and S. R. Quake, “Colloidal lenses allow high-temperature single-molecule imaging and improve fluorophore photostability,” Nat. Nanotechnol. 5, 127–132 (2009).

[Crossref]

Q. Miao, A. P. Reeves, F. W. Patten, and E. J. Seibel, “Multimodal 3D imaging of cells and tissue: bridging the gap between clinical and research microscopy,” Ann. Biomed. Eng. 40, 263–276 (2012).

[Crossref]

R. L. Coe and E. J. Seibel, “Improved near-field calculations using vectorial diffraction integrals in the finite-difference time-domain method,” J. Opt. Soc. Am. A 28, 1776–1783 (2011).

[Crossref]

M. Fauver, E. J. Seibel, J. R. Rahn, M. G. Meyer, F. W. Patten, T. Neumann, and A. C. Nelson, “Three-dimensional imaging of single isolated cell nuclei using optical projection tomography,” Opt. Express 13, 4210–4223 (2005).

[Crossref]

T. H. Chow, W. M. Lee, K. M. Tan, B. K. Ng, and C. J. R. Sheppard, “Resolving interparticle position and optical forces along the axial direction using optical coherence gating,” Appl. Phys. Lett. 97, 231113 (2010).

[Crossref]

A. C. Kak and M. Slaney, Principles of Computerized Tomographic Imaging (IEEE, 1988).

D. Merewether, R. Fisher, and F. W. Smith, “On implementing a numeric Huygen’s source scheme in a finite difference program to illuminate scattering bodies,” IEEE Trans. Nucl. Sci. 27, 1829–1833 (1980).

[Crossref]

C. Smithpeter, A. K. Dunn, R. Drezek, T. Collier, and R. Richards-Kortum, “Near real time confocal microscopy of cultured amelanotic cells: sources of signal, contrast agents and limits of contrast,” J. Biomed. Opt. 3, 429–436 (1998).

[Crossref]

J. J. Schwartz, S. Stavrakis, and S. R. Quake, “Colloidal lenses allow high-temperature single-molecule imaging and improve fluorophore photostability,” Nat. Nanotechnol. 5, 127–132 (2009).

[Crossref]

H. Subramanian, H. K. Roy, P. Pradhan, M. J. Goldberg, J. Muldoon, R. E. Brand, C. Sturgis, T. Hensing, D. Ray, A. Bogojevic, J. Mohammed, J. Chang, and V. Backman, “Nanoscale cellular changes in field carcinogenesis detected by partial wave spectroscopy,” Cancer Res. 69, 5357–5363 (2009).

[Crossref]

I. R. Çapoglu, C. A. White, J. D. Rogers, H. Subramanian, A. Taflove, and V. Backman, “Numerical simulation of partially coherent broadband optical imaging using the finite-difference time-domain method,” Opt. Lett. 36, 1596–1598 (2011).

[Crossref]

H. Subramanian, P. Pradhan, Y. Liu, I. R. Capoglu, J. D. Rogers, H. K. Roy, R. E. Brand, and V. Backman, “Partial-wave microscopic spectroscopy detects subwavelength refractive index fluctuations: an application to cancer diagnosis,” Opt. Lett. 34, 518–520 (2009).

[Crossref]

H. Subramanian, H. K. Roy, P. Pradhan, M. J. Goldberg, J. Muldoon, R. E. Brand, C. Sturgis, T. Hensing, D. Ray, A. Bogojevic, J. Mohammed, J. Chang, and V. Backman, “Nanoscale cellular changes in field carcinogenesis detected by partial wave spectroscopy,” Cancer Res. 69, 5357–5363 (2009).

[Crossref]

I. R. Çapoglu, C. A. White, J. D. Rogers, H. Subramanian, A. Taflove, and V. Backman, “Numerical simulation of partially coherent broadband optical imaging using the finite-difference time-domain method,” Opt. Lett. 36, 1596–1598 (2011).

[Crossref]

I. R. Çapoglu, A. Taflove, and V. Backman, “Generation of an incident focused light pulse in FDTD,” Opt. Express 16, 19208–19220 (2008).

[Crossref]

A. Taflove and S. C. Hagness,Computational Electrodynamics: The Finite-Difference Time-Domain Method (Artech House, 2005).

I. R. Capoglu, J. D. Rogers, A. Taflove, and V. Backman, “The microscope in a computer: Image synthesis from three-dimensional full-vector solutions of Maxwell’s equations at the nanometer scale,” Prog. Opt.57, 1–91 (2012).

[Crossref]

T. H. Chow, W. M. Lee, K. M. Tan, B. K. Ng, and C. J. R. Sheppard, “Resolving interparticle position and optical forces along the axial direction using optical coherence gating,” Appl. Phys. Lett. 97, 231113 (2010).

[Crossref]

P. Török, P. R. T. Munro, and E. E. Kriezis, “High numerical aperture vectorial imaging in coherent optical microscopes,” Opt. Express 16, 507–523 (2008).

[Crossref]

P. R. T. Munro and P. Török, “Calculation of the image of an arbitrary vectorial electromagnetic field,” Opt. Express 15, 9293–9307 (2007).

[Crossref]

P. Török, P. R. T. Munro, and E. E. Kriezis, “Rigorous near- to far-field transformation for vectorial diffraction calculations and its numerical implementation,” J. Opt. Soc. Am. A 23, 713–722 (2006).

[Crossref]

M. Totzeck, “Numerical simulation of high-NA quantitative polarization microscopy and corresponding near-fields,” Optik 112, 399–406 (2001).

[Crossref]

B. Richards and E. Wolf, “Electromagnetic diffraction in optical systems. II. Structure of the image field in an aplanatic system,” Proc. R. Soc. A 253, 358–379 (1959).

[Crossref]

M. Born and E. Wolf, Principles of Optics: Electromagnetic Theory of Propagation, Interference and Diffraction of Light (Pergamon, 1980).

X. Ma, J. Q. Lu, R. S. Brock, K. M. Jacobs, P. Yang, and X.-H. Hu, “Determination of complex refractive index of polystyrene microspheres from 370 to 1610 nm,” Phys. Med. Biol. 48, 4165–4172 (2003).

[Crossref]

K. Yee, “Numerical solution of initial boundary value problems involving Maxwell’s equations in isotropic media,” IEEE Trans. Antennas Propag. 14, 302–307 (1966).

[Crossref]

I. T. Young, “Quantitative microscopy,” IEEE Eng. Med. Biol. 15, 59–66 (1996).

[Crossref]

Q. Miao, A. P. Reeves, F. W. Patten, and E. J. Seibel, “Multimodal 3D imaging of cells and tissue: bridging the gap between clinical and research microscopy,” Ann. Biomed. Eng. 40, 263–276 (2012).

[Crossref]

N. N. Boustany, S. A. Boppart, and V. Backman, “Microscopic imaging and spectroscopy with scattered light,” Annu. Rev. Biomed. Eng. 12, 285–314 (2010).

[Crossref]

F. Slimani, G. Grehan, G. Gouesbet, and D. Allano, “Near-field Lorenz–Mie theory and its application to microholography,” Appl. Opt. 23, 4140–4148 (1984).

[Crossref]

R. Drezek, A. Dunn, and R. Richards-Kortum, “Light scattering from cells: finite-difference time-domain simulations and goniometric measurements,” Appl. Opt. 38, 3651–3661 (1999).

[Crossref]

T. H. Chow, W. M. Lee, K. M. Tan, B. K. Ng, and C. J. R. Sheppard, “Resolving interparticle position and optical forces along the axial direction using optical coherence gating,” Appl. Phys. Lett. 97, 231113 (2010).

[Crossref]

J. P. Brody and S. R. Quake, “A self-assembled microlensing rotational probe,” Appl. Phys. Lett. 74, 144–146 (1999).

[Crossref]

H. Subramanian, H. K. Roy, P. Pradhan, M. J. Goldberg, J. Muldoon, R. E. Brand, C. Sturgis, T. Hensing, D. Ray, A. Bogojevic, J. Mohammed, J. Chang, and V. Backman, “Nanoscale cellular changes in field carcinogenesis detected by partial wave spectroscopy,” Cancer Res. 69, 5357–5363 (2009).

[Crossref]

I. T. Young, “Quantitative microscopy,” IEEE Eng. Med. Biol. 15, 59–66 (1996).

[Crossref]

K. Yee, “Numerical solution of initial boundary value problems involving Maxwell’s equations in isotropic media,” IEEE Trans. Antennas Propag. 14, 302–307 (1966).

[Crossref]

T. Martin, “An improved near- to far-zone transformation for the finite-difference time-domain method,” IEEE Trans. Antennas Propag. 46, 1263–1271 (1998).

[Crossref]

D. J. Robinson and J. B. Schneider, “On the use of the geometric mean in FDTD near-to-far-field transformations,” IEEE Trans. Antennas Propag. 55, 3204–3211 (2007).

[Crossref]

T. Martin, “On the FDTD near-to-far-field transformations for weakly scattering objects,” IEEE Trans. Antennas Propag. 58, 2794–2795 (2010).

[Crossref]

J. B. Schneider and K. Abdijalilov, “Analytic field propagation TFSF boundary for FDTD problems involving planar interfaces: PECs, TE, and TM,” IEEE Trans. Antennas. Propag. 54, 2531–2542 (2006).

[Crossref]

D. Merewether, R. Fisher, and F. W. Smith, “On implementing a numeric Huygen’s source scheme in a finite difference program to illuminate scattering bodies,” IEEE Trans. Nucl. Sci. 27, 1829–1833 (1980).

[Crossref]

C. Smithpeter, A. K. Dunn, R. Drezek, T. Collier, and R. Richards-Kortum, “Near real time confocal microscopy of cultured amelanotic cells: sources of signal, contrast agents and limits of contrast,” J. Biomed. Opt. 3, 429–436 (1998).

[Crossref]

J. P. Berenger, “A perfectly matched layer for the absorption of electromagnetic waves,” J. Comput. Phys. 114, 185–200 (1994).

[Crossref]

M. G. L. Gustafsson, “Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy,” J. Microsc. 198, 82–87 (2000).

[Crossref]

N. Martini, J. Bewersdorf, and S. W. Hell, “A new high-aperture glycerol immersion objective lens and its application to 3D-fluorescence microscopy,” J. Microsc. 206, 146–151 (2002).

[Crossref]

P. Török, P. R. T. Munro, and E. E. Kriezis, “Rigorous near- to far-field transformation for vectorial diffraction calculations and its numerical implementation,” J. Opt. Soc. Am. A 23, 713–722 (2006).

[Crossref]

N. Nakajima, “Phase retrieval from a high-numerical-aperture intensity distribution by use of an aperture-array filter,” J. Opt. Soc. Am. A 26, 2172–2180 (2009).

[Crossref]

R. L. Coe and E. J. Seibel, “Improved near-field calculations using vectorial diffraction integrals in the finite-difference time-domain method,” J. Opt. Soc. Am. A 28, 1776–1783 (2011).

[Crossref]

J. A. Roden and S. D. Gedney, “Convolution PML (CPML): an efficient FDTD implementation of the CFS–PML for arbitrary media,” Microw. Opt. Technol. Lett. 27, 334–339 (2000).

[Crossref]

W. Choi, C. Fang-Yen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods 4, 717–719 (2007).

[Crossref]

J. J. Schwartz, S. Stavrakis, and S. R. Quake, “Colloidal lenses allow high-temperature single-molecule imaging and improve fluorophore photostability,” Nat. Nanotechnol. 5, 127–132 (2009).

[Crossref]

P. R. T. Munro and P. Török, “Calculation of the image of an arbitrary vectorial electromagnetic field,” Opt. Express 15, 9293–9307 (2007).

[Crossref]

P. Török, P. R. T. Munro, and E. E. Kriezis, “High numerical aperture vectorial imaging in coherent optical microscopes,” Opt. Express 16, 507–523 (2008).

[Crossref]

I. R. Çapoglu, A. Taflove, and V. Backman, “Generation of an incident focused light pulse in FDTD,” Opt. Express 16, 19208–19220 (2008).

[Crossref]

R. Drezek, A. Dunn, and R. Richards-Kortum, “A pulsed finite-difference time-domain (FDTD) method for calculating light scattering from biological cells over broad wavelength ranges,” Opt. Express 6, 147–157 (2000).

[Crossref]

M. Fauver, E. J. Seibel, J. R. Rahn, M. G. Meyer, F. W. Patten, T. Neumann, and A. C. Nelson, “Three-dimensional imaging of single isolated cell nuclei using optical projection tomography,” Opt. Express 13, 4210–4223 (2005).

[Crossref]

H. Subramanian, P. Pradhan, Y. Liu, I. R. Capoglu, J. D. Rogers, H. K. Roy, R. E. Brand, and V. Backman, “Partial-wave microscopic spectroscopy detects subwavelength refractive index fluctuations: an application to cancer diagnosis,” Opt. Lett. 34, 518–520 (2009).

[Crossref]

I. R. Çapoglu, C. A. White, J. D. Rogers, H. Subramanian, A. Taflove, and V. Backman, “Numerical simulation of partially coherent broadband optical imaging using the finite-difference time-domain method,” Opt. Lett. 36, 1596–1598 (2011).

[Crossref]

M. Totzeck, “Numerical simulation of high-NA quantitative polarization microscopy and corresponding near-fields,” Optik 112, 399–406 (2001).

[Crossref]

G. Gouesbet, “Generalized Lorenz–Mie theory and applications,” Part. Part. Syst. Charact. 11, 22–34 (1994).

[Crossref]

M. G. Meyer, M. Fauver, J. R. Rahn, T. Neumann, and F. W. Patten, “Automated cell analysis in 2D and 3D: a comparative study,” Pattern Recogn. 42, 141–146 (2009).

[Crossref]

X. Ma, J. Q. Lu, R. S. Brock, K. M. Jacobs, P. Yang, and X.-H. Hu, “Determination of complex refractive index of polystyrene microspheres from 370 to 1610 nm,” Phys. Med. Biol. 48, 4165–4172 (2003).

[Crossref]

B. Richards and E. Wolf, “Electromagnetic diffraction in optical systems. II. Structure of the image field in an aplanatic system,” Proc. R. Soc. A 253, 358–379 (1959).

[Crossref]

M. Born and E. Wolf, Principles of Optics: Electromagnetic Theory of Propagation, Interference and Diffraction of Light (Pergamon, 1980).

I. R. Capoglu, J. D. Rogers, A. Taflove, and V. Backman, “The microscope in a computer: Image synthesis from three-dimensional full-vector solutions of Maxwell’s equations at the nanometer scale,” Prog. Opt.57, 1–91 (2012).

[Crossref]

A. Taflove and S. C. Hagness,Computational Electrodynamics: The Finite-Difference Time-Domain Method (Artech House, 2005).

C. Guiffaut and K. Mahdjoubi, “Perfect wideband plane wave injector for FDTD method,” in Proceedings of IEEE Antennas Propagation Society International Symposium (IEEE, 2000), pp. 236–239.

A. C. Kak and M. Slaney, Principles of Computerized Tomographic Imaging (IEEE, 1988).