Abstract
We present a method for modeling image formation in optical projection tomographic microscopy (OPTM) using high numerical aperture (NA) condensers and objectives. Similar to techniques used in computed tomography, OPTM produces threedimensional, reconstructed images of single cells from twodimensional projections. The model is capable of simulating axial scanning of a microscope objective to produce projections, which are reconstructed using filtered backprojection. Simulation of optical scattering in transmission optical microscopy is designed to analyze all aspects of OPTM image formation, such as degree of specimen staining, refractiveindex matching, and objective scanning. In this preliminary work, a set of simulations is performed to examine the effect of changing the condenser NA, objective scan range, and complex refractive index on the final reconstruction of a microshell with an outer radius of 1.5 μm and an inner radius of 0.9 μm. The model lays the groundwork for optimizing OPTM imaging parameters and triaging efforts to further improve the overall system design. As the model is expanded in the future, it will be used to simulate a more realistic cell, which could lead to even greater impact.
© 2012 Optical Society of America
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References
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 Publication
 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, “Threedimensional imaging of single isolated cell nuclei using optical projection tomography,” Opt. Express 13, 4210–4223 (2005).
[Crossref]  I. T. Young, “Quantitative microscopy,” IEEE Eng. Med. Biol. 15, 59–66 (1996).
[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] 
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 finitedifference timedomain method,” Opt. Lett. 36, 1596–1598 (2011).
[Crossref]  C. Smithpeter, A. K. Dunn, R. Drezek, T. Collier, and R. RichardsKortum, “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] 
N. Nakajima, “Phase retrieval from a highnumericalaperture intensity distribution by use of an aperturearray filter,” J. Opt. Soc. Am. A 26, 2172–2180 (2009).
[Crossref]  M. Totzeck, “Numerical simulation of highNA quantitative polarization microscopy and corresponding nearfields,” Optik 112, 399–406 (2001).
[Crossref] 
F. Slimani, G. Grehan, G. Gouesbet, and D. Allano, “Nearfield Lorenz–Mie theory and its application to microholography,” Appl. Opt. 23, 4140–4148 (1984).
[Crossref]  G. Gouesbet, “Generalized Lorenz–Mie theory and applications,” Part. Part. Syst. Charact. 11, 22–34 (1994).
[Crossref] 
P. Török, P. R. T. Munro, and E. E. Kriezis, “Rigorous near to farfield transformation for vectorial diffraction calculations and its numerical implementation,” J. Opt. Soc. Am. A 23, 713–722 (2006).
[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 FiniteDifference TimeDomain Method (Artech House, 2005).

R. L. Coe and E. J. Seibel, “Improved nearfield calculations using vectorial diffraction integrals in the finitedifference timedomain method,” J. Opt. Soc. Am. A 28, 1776–1783 (2011).
[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, “High numerical aperture vectorial imaging in coherent optical microscopes,” Opt. Express 16, 507–523 (2008).
[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 threedimensional fullvector solutions of Maxwell’s equations at the nanometer scale,” Prog. Opt.57, 1–91 (2012).
[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]  J. P. Berenger, “A perfectly matched layer for the absorption of electromagnetic waves,” J. Comput. Phys. 114, 185–200 (1994).
[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]  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]  T. Martin, “An improved near to farzone transformation for the finitedifference timedomain 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 neartofarfield transformations,” IEEE Trans. Antennas Propag. 55, 3204–3211 (2007).
[Crossref]  T. Martin, “On the FDTD neartofarfield transformations for weakly scattering objects,” IEEE Trans. Antennas Propag. 58, 2794–2795 (2010).
[Crossref]  A. C. Kak and M. Slaney, Principles of Computerized Tomographic Imaging (IEEE, 1988).
 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 highaperture glycerol immersion objective lens and its application to 3Dfluorescence microscopy,” J. Microsc. 206, 146–151 (2002).
[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. 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 selfassembled microlensing rotational probe,” Appl. Phys. Lett. 74, 144–146 (1999).
[Crossref]  J. J. Schwartz, S. Stavrakis, and S. R. Quake, “Colloidal lenses allow hightemperature singlemolecule imaging and improve fluorophore photostability,” Nat. Nanotechnol. 5, 127–132 (2009).
[Crossref]  W. Choi, C. FangYen, 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. RichardsKortum, “Light scattering from cells: finitedifference timedomain simulations and goniometric measurements,” Appl. Opt. 38, 3651–3661 (1999).
[Crossref] 
R. Drezek, A. Dunn, and R. RichardsKortum, “A pulsed finitedifference timedomain (FDTD) method for calculating light scattering from biological cells over broad wavelength ranges,” Opt. Express 6, 147–157 (2000).
[Crossref] 
H. Subramanian, P. Pradhan, Y. Liu, I. R. Capoglu, J. D. Rogers, H. K. Roy, R. E. Brand, and V. Backman, “Partialwave microscopic spectroscopy detects subwavelength refractive index fluctuations: an application to cancer diagnosis,” Opt. Lett. 34, 518–520 (2009).
[Crossref]
2012 (1)
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]
2011 (2)
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 finitedifference timedomain method,” Opt. Lett. 36, 1596–1598 (2011).
[Crossref]
R. L. Coe and E. J. Seibel, “Improved nearfield calculations using vectorial diffraction integrals in the finitedifference timedomain method,” J. Opt. Soc. Am. A 28, 1776–1783 (2011).
[Crossref]
2010 (3)
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 neartofarfield 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]
2009 (5)
J. J. Schwartz, S. Stavrakis, and S. R. Quake, “Colloidal lenses allow hightemperature singlemolecule imaging and improve fluorophore photostability,” Nat. Nanotechnol. 5, 127–132 (2009).
[Crossref]
H. Subramanian, P. Pradhan, Y. Liu, I. R. Capoglu, J. D. Rogers, H. K. Roy, R. E. Brand, and V. Backman, “Partialwave microscopic spectroscopy detects subwavelength refractive index fluctuations: an application to cancer diagnosis,” Opt. Lett. 34, 518–520 (2009).
[Crossref]
N. Nakajima, “Phase retrieval from a highnumericalaperture intensity distribution by use of an aperturearray filter,” J. Opt. Soc. Am. A 26, 2172–2180 (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]
2008 (2)
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]
2007 (3)
W. Choi, C. FangYen, 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 neartofarfield 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]
2006 (2)
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 farfield transformation for vectorial diffraction calculations and its numerical implementation,” J. Opt. Soc. Am. A 23, 713–722 (2006).
[Crossref]
2005 (1)
M. Fauver, E. J. Seibel, J. R. Rahn, M. G. Meyer, F. W. Patten, T. Neumann, and A. C. Nelson, “Threedimensional imaging of single isolated cell nuclei using optical projection tomography,” Opt. Express 13, 4210–4223 (2005).
[Crossref]
2003 (1)
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]
2002 (1)
N. Martini, J. Bewersdorf, and S. W. Hell, “A new highaperture glycerol immersion objective lens and its application to 3Dfluorescence microscopy,” J. Microsc. 206, 146–151 (2002).
[Crossref]
2001 (1)
M. Totzeck, “Numerical simulation of highNA quantitative polarization microscopy and corresponding nearfields,” Optik 112, 399–406 (2001).
[Crossref]
2000 (3)
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]
R. Drezek, A. Dunn, and R. RichardsKortum, “A pulsed finitedifference timedomain (FDTD) method for calculating light scattering from biological cells over broad wavelength ranges,” Opt. Express 6, 147–157 (2000).
[Crossref]
1999 (2)
R. Drezek, A. Dunn, and R. RichardsKortum, “Light scattering from cells: finitedifference timedomain simulations and goniometric measurements,” Appl. Opt. 38, 3651–3661 (1999).
[Crossref]
J. P. Brody and S. R. Quake, “A selfassembled microlensing rotational probe,” Appl. Phys. Lett. 74, 144–146 (1999).
[Crossref]
1998 (2)
T. Martin, “An improved near to farzone transformation for the finitedifference timedomain method,” IEEE Trans. Antennas Propag. 46, 1263–1271 (1998).
[Crossref]
C. Smithpeter, A. K. Dunn, R. Drezek, T. Collier, and R. RichardsKortum, “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]
1996 (1)
I. T. Young, “Quantitative microscopy,” IEEE Eng. Med. Biol. 15, 59–66 (1996).
[Crossref]
1994 (2)
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]
1984 (1)
F. Slimani, G. Grehan, G. Gouesbet, and D. Allano, “Nearfield Lorenz–Mie theory and its application to microholography,” Appl. Opt. 23, 4140–4148 (1984).
[Crossref]
1980 (1)
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]
1966 (1)
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]
1959 (1)
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]
Abdijalilov, K.
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]
Allano, D.
F. Slimani, G. Grehan, G. Gouesbet, and D. Allano, “Nearfield Lorenz–Mie theory and its application to microholography,” Appl. Opt. 23, 4140–4148 (1984).
[Crossref]
Backman, V.
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 finitedifference timedomain 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, P. Pradhan, Y. Liu, I. R. Capoglu, J. D. Rogers, H. K. Roy, R. E. Brand, and V. Backman, “Partialwave 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, 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 threedimensional fullvector solutions of Maxwell’s equations at the nanometer scale,” Prog. Opt.57, 1–91 (2012).
[Crossref]
Badizadegan, K.
W. Choi, C. FangYen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods 4, 717–719 (2007).
[Crossref]
Berenger, J. P.
J. P. Berenger, “A perfectly matched layer for the absorption of electromagnetic waves,” J. Comput. Phys. 114, 185–200 (1994).
[Crossref]
Bewersdorf, J.
N. Martini, J. Bewersdorf, and S. W. Hell, “A new highaperture glycerol immersion objective lens and its application to 3Dfluorescence microscopy,” J. Microsc. 206, 146–151 (2002).
[Crossref]
Bogojevic, A.
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]
Boppart, S. A.
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]
Born, M.
M. Born and E. Wolf, Principles of Optics: Electromagnetic Theory of Propagation, Interference and Diffraction of Light (Pergamon, 1980).
Boustany, N. N.
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]
Brand, R. E.
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, “Partialwave microscopic spectroscopy detects subwavelength refractive index fluctuations: an application to cancer diagnosis,” Opt. Lett. 34, 518–520 (2009).
[Crossref]
Brock, R. S.
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]
Brody, J. P.
J. P. Brody and S. R. Quake, “A selfassembled microlensing rotational probe,” Appl. Phys. Lett. 74, 144–146 (1999).
[Crossref]
Capoglu, I. R.
H. Subramanian, P. Pradhan, Y. Liu, I. R. Capoglu, J. D. Rogers, H. K. Roy, R. E. Brand, and V. Backman, “Partialwave 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 threedimensional fullvector solutions of Maxwell’s equations at the nanometer scale,” Prog. Opt.57, 1–91 (2012).
[Crossref]
Çapoglu, I. R.
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 finitedifference timedomain 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]
Chang, J.
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]
Choi, W.
W. Choi, C. FangYen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods 4, 717–719 (2007).
[Crossref]
Chow, T. H.
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]
Coe, R. L.
R. L. Coe and E. J. Seibel, “Improved nearfield calculations using vectorial diffraction integrals in the finitedifference timedomain method,” J. Opt. Soc. Am. A 28, 1776–1783 (2011).
[Crossref]
Collier, T.
C. Smithpeter, A. K. Dunn, R. Drezek, T. Collier, and R. RichardsKortum, “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]
Dasari, R. R.
W. Choi, C. FangYen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods 4, 717–719 (2007).
[Crossref]
Drezek, R.
R. Drezek, A. Dunn, and R. RichardsKortum, “A pulsed finitedifference timedomain (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. RichardsKortum, “Light scattering from cells: finitedifference timedomain simulations and goniometric measurements,” Appl. Opt. 38, 3651–3661 (1999).
[Crossref]
C. Smithpeter, A. K. Dunn, R. Drezek, T. Collier, and R. RichardsKortum, “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]
Dunn, A.
R. Drezek, A. Dunn, and R. RichardsKortum, “A pulsed finitedifference timedomain (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. RichardsKortum, “Light scattering from cells: finitedifference timedomain simulations and goniometric measurements,” Appl. Opt. 38, 3651–3661 (1999).
[Crossref]
Dunn, A. K.
C. Smithpeter, A. K. Dunn, R. Drezek, T. Collier, and R. RichardsKortum, “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]
FangYen, C.
W. Choi, C. FangYen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods 4, 717–719 (2007).
[Crossref]
Fauver, M.
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, “Threedimensional imaging of single isolated cell nuclei using optical projection tomography,” Opt. Express 13, 4210–4223 (2005).
[Crossref]
Feld, M. S.
W. Choi, C. FangYen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods 4, 717–719 (2007).
[Crossref]
Fisher, R.
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]
Gedney, S. D.
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]
Goldberg, M. J.
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).
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G. Gouesbet, “Generalized Lorenz–Mie theory and applications,” Part. Part. Syst. Charact. 11, 22–34 (1994).
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F. Slimani, G. Grehan, G. Gouesbet, and D. Allano, “Nearfield Lorenz–Mie theory and its application to microholography,” Appl. Opt. 23, 4140–4148 (1984).
[Crossref]
Grehan, G.
F. Slimani, G. Grehan, G. Gouesbet, and D. Allano, “Nearfield Lorenz–Mie theory and its application to microholography,” Appl. Opt. 23, 4140–4148 (1984).
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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.
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M. G. L. Gustafsson, “Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy,” J. Microsc. 198, 82–87 (2000).
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Hagness, S. C.
A. Taflove and S. C. Hagness,Computational Electrodynamics: The FiniteDifference TimeDomain Method (Artech House, 2005).
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N. Martini, J. Bewersdorf, and S. W. Hell, “A new highaperture glycerol immersion objective lens and its application to 3Dfluorescence microscopy,” J. Microsc. 206, 146–151 (2002).
[Crossref]
Hensing, T.
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]
Hu, X.H.
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]
Jacobs, K. M.
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).
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Kak, A. C.
A. C. Kak and M. Slaney, Principles of Computerized Tomographic Imaging (IEEE, 1988).
Kriezis, E. E.
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 farfield transformation for vectorial diffraction calculations and its numerical implementation,” J. Opt. Soc. Am. A 23, 713–722 (2006).
[Crossref]
Lee, W. M.
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]
Liu, Y.
H. Subramanian, P. Pradhan, Y. Liu, I. R. Capoglu, J. D. Rogers, H. K. Roy, R. E. Brand, and V. Backman, “Partialwave microscopic spectroscopy detects subwavelength refractive index fluctuations: an application to cancer diagnosis,” Opt. Lett. 34, 518–520 (2009).
[Crossref]
Lu, J. Q.
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]
Lue, N.
W. Choi, C. FangYen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods 4, 717–719 (2007).
[Crossref]
Ma, X.
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]
Mahdjoubi, K.
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.
Martin, T.
T. Martin, “On the FDTD neartofarfield transformations for weakly scattering objects,” IEEE Trans. Antennas Propag. 58, 2794–2795 (2010).
[Crossref]
T. Martin, “An improved near to farzone transformation for the finitedifference timedomain method,” IEEE Trans. Antennas Propag. 46, 1263–1271 (1998).
[Crossref]
Martini, N.
N. Martini, J. Bewersdorf, and S. W. Hell, “A new highaperture glycerol immersion objective lens and its application to 3Dfluorescence microscopy,” J. Microsc. 206, 146–151 (2002).
[Crossref]
Merewether, D.
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]
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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).
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M. Fauver, E. J. Seibel, J. R. Rahn, M. G. Meyer, F. W. Patten, T. Neumann, and A. C. Nelson, “Threedimensional imaging of single isolated cell nuclei using optical projection tomography,” Opt. Express 13, 4210–4223 (2005).
[Crossref]
Miao, Q.
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]
Mohammed, J.
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]
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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]
Munro, P. R. T.
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 farfield transformation for vectorial diffraction calculations and its numerical implementation,” J. Opt. Soc. Am. A 23, 713–722 (2006).
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M. Fauver, E. J. Seibel, J. R. Rahn, M. G. Meyer, F. W. Patten, T. Neumann, and A. C. Nelson, “Threedimensional imaging of single isolated cell nuclei using optical projection tomography,” Opt. Express 13, 4210–4223 (2005).
[Crossref]
Neumann, T.
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, “Threedimensional imaging of single isolated cell nuclei using optical projection tomography,” Opt. Express 13, 4210–4223 (2005).
[Crossref]
Ng, B. K.
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]
Oh, S.
W. Choi, C. FangYen, K. Badizadegan, S. Oh, N. Lue, R. R. Dasari, and M. S. Feld, “Tomographic phase microscopy,” Nat. Methods 4, 717–719 (2007).
[Crossref]
Patten, F. W.
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, “Threedimensional imaging of single isolated cell nuclei using optical projection tomography,” Opt. Express 13, 4210–4223 (2005).
[Crossref]
Pradhan, P.
H. Subramanian, P. Pradhan, Y. Liu, I. R. Capoglu, J. D. Rogers, H. K. Roy, R. E. Brand, and V. Backman, “Partialwave 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]
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J. J. Schwartz, S. Stavrakis, and S. R. Quake, “Colloidal lenses allow hightemperature singlemolecule imaging and improve fluorophore photostability,” Nat. Nanotechnol. 5, 127–132 (2009).
[Crossref]
J. P. Brody and S. R. Quake, “A selfassembled microlensing rotational probe,” Appl. Phys. Lett. 74, 144–146 (1999).
[Crossref]
Rahn, J. R.
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, “Threedimensional imaging of single isolated cell nuclei using optical projection tomography,” Opt. Express 13, 4210–4223 (2005).
[Crossref]
Ray, D.
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]
Reeves, A. P.
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]
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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).
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R. Drezek, A. Dunn, and R. RichardsKortum, “A pulsed finitedifference timedomain (FDTD) method for calculating light scattering from biological cells over broad wavelength ranges,” Opt. Express 6, 147–157 (2000).
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R. Drezek, A. Dunn, and R. RichardsKortum, “Light scattering from cells: finitedifference timedomain simulations and goniometric measurements,” Appl. Opt. 38, 3651–3661 (1999).
[Crossref]
C. Smithpeter, A. K. Dunn, R. Drezek, T. Collier, and R. RichardsKortum, “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]
Robinson, D. J.
D. J. Robinson and J. B. Schneider, “On the use of the geometric mean in FDTD neartofarfield transformations,” IEEE Trans. Antennas Propag. 55, 3204–3211 (2007).
[Crossref]
Roden, J. A.
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]
Rogers, J. D.
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 finitedifference timedomain 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, “Partialwave 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 threedimensional fullvector solutions of Maxwell’s equations at the nanometer scale,” Prog. Opt.57, 1–91 (2012).
[Crossref]
Roy, H. K.
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, “Partialwave microscopic spectroscopy detects subwavelength refractive index fluctuations: an application to cancer diagnosis,” Opt. Lett. 34, 518–520 (2009).
[Crossref]
Schneider, J. B.
D. J. Robinson and J. B. Schneider, “On the use of the geometric mean in FDTD neartofarfield 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]
Schwartz, J. J.
J. J. Schwartz, S. Stavrakis, and S. R. Quake, “Colloidal lenses allow hightemperature singlemolecule imaging and improve fluorophore photostability,” Nat. Nanotechnol. 5, 127–132 (2009).
[Crossref]
Seibel, E. J.
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).
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M. Fauver, E. J. Seibel, J. R. Rahn, M. G. Meyer, F. W. Patten, T. Neumann, and A. C. Nelson, “Threedimensional imaging of single isolated cell nuclei using optical projection tomography,” Opt. Express 13, 4210–4223 (2005).
[Crossref]
Sheppard, C. J. R.
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]
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A. C. Kak and M. Slaney, Principles of Computerized Tomographic Imaging (IEEE, 1988).
Slimani, F.
F. Slimani, G. Grehan, G. Gouesbet, and D. Allano, “Nearfield Lorenz–Mie theory and its application to microholography,” Appl. Opt. 23, 4140–4148 (1984).
[Crossref]
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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]
Smithpeter, C.
C. Smithpeter, A. K. Dunn, R. Drezek, T. Collier, and R. RichardsKortum, “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]
Stavrakis, S.
J. J. Schwartz, S. Stavrakis, and S. R. Quake, “Colloidal lenses allow hightemperature singlemolecule imaging and improve fluorophore photostability,” Nat. Nanotechnol. 5, 127–132 (2009).
[Crossref]
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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]
Subramanian, H.
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 finitedifference timedomain 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, “Partialwave 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]
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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 finitedifference timedomain method,” Opt. Lett. 36, 1596–1598 (2011).
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I. R. Çapoglu, A. Taflove, and V. Backman, “Generation of an incident focused light pulse in FDTD,” Opt. Express 16, 19208–19220 (2008).
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A. Taflove and S. C. Hagness,Computational Electrodynamics: The FiniteDifference TimeDomain Method (Artech House, 2005).
I. R. Capoglu, J. D. Rogers, A. Taflove, and V. Backman, “The microscope in a computer: Image synthesis from threedimensional fullvector solutions of Maxwell’s equations at the nanometer scale,” Prog. Opt.57, 1–91 (2012).
[Crossref]
Tan, K. M.
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]
Török, P.
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 farfield transformation for vectorial diffraction calculations and its numerical implementation,” J. Opt. Soc. Am. A 23, 713–722 (2006).
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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 finitedifference timedomain method,” Opt. Lett. 36, 1596–1598 (2011).
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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).
Yang, P.
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]
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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]
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I. T. Young, “Quantitative microscopy,” IEEE Eng. Med. Biol. 15, 59–66 (1996).
[Crossref]
Ann. Biomed. Eng. (1)
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]
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Appl. Opt. (2)
F. Slimani, G. Grehan, G. Gouesbet, and D. Allano, “Nearfield Lorenz–Mie theory and its application to microholography,” Appl. Opt. 23, 4140–4148 (1984).
[Crossref]
R. Drezek, A. Dunn, and R. RichardsKortum, “Light scattering from cells: finitedifference timedomain simulations and goniometric measurements,” Appl. Opt. 38, 3651–3661 (1999).
[Crossref]
Appl. Phys. Lett. (2)
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 selfassembled microlensing rotational probe,” Appl. Phys. Lett. 74, 144–146 (1999).
[Crossref]
Cancer Res. (1)
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]
IEEE Eng. Med. Biol. (1)
I. T. Young, “Quantitative microscopy,” IEEE Eng. Med. Biol. 15, 59–66 (1996).
[Crossref]
IEEE Trans. Antennas Propag. (4)
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 farzone transformation for the finitedifference timedomain 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 neartofarfield transformations,” IEEE Trans. Antennas Propag. 55, 3204–3211 (2007).
[Crossref]
T. Martin, “On the FDTD neartofarfield transformations for weakly scattering objects,” IEEE Trans. Antennas Propag. 58, 2794–2795 (2010).
[Crossref]
IEEE Trans. Antennas. Propag. (1)
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]
IEEE Trans. Nucl. Sci. (1)
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. Biomed. Opt. (1)
C. Smithpeter, A. K. Dunn, R. Drezek, T. Collier, and R. RichardsKortum, “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).
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[Crossref]
J. Microsc. (2)
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]
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Figures (8)
Diagram of the imageformation process utilized in OPTM where projections are produced by scanning the objective to optically integrate through the cell. Projections are acquired from desired angles by rotating the microcapillary between the condenser and objective.
Diagram of the image formation model for a highNA brightfield, transmission microscope. The model consists of four main parts: illumination, numerical method, resampling, and image formation.
Representation of axially scanning the objective in comparison to the condenser illumination. Three different positions of the objective (on the right with red focal circles) are shown in relation to the condenser (on the left with black focal crosses) and the resampled infinite plane (vertical line). These diagrams show that the nearfield scattered light produced by the object would be the same on the resampled infinite plane irrespective of the objective position. The only difference is the distance between the infinite plane and the focus of the objective (i.e., distance between red cross and infinite plane) meaning only the final image formation portion of the algorithm has to be repeated to axially scan through the object.
Diagram of the process to simulate an OPTM projection using visual forloops. The illumination is defined for the desired illumination source and NA, which is incorporated in a numerical method to determine the nearfield scattering from a cell. The nearfield scattering is resampled for a particular frequency and used to compute an image at every desired focal plane. The nearfield scattering is then resampled for another desired frequency and images are computed for all of the same focal planes. This entire process is performed for every scanning position to illuminate the entire cell. Each of these images is finally integrated to produce a single projection. Projections are acquired for each rotation of the cell and these projections are reconstructed into a threedimensional image in a final postprocessing step (not shown).
Axial cross section for varying NAs of scattered light with a constant microshell RI of
Axial cross sections produced using the 0.5 NA condenser (top row) and the 1.3 NA condenser (bottom row) for microshells with complex refractive indices of
Crosssectional reconstruction plot (left) for varying NA for 0.5, 0.9, and 1.3 with a constant microshell RI of
Crosssectional reconstructions produced with a condenser whose NA is 1.3. The projection consists of axial scanning from
Equations (17)
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