Abstract

Light sheet microscopy (LSM) has emerged as an optical-imaging method for high spatiotemporal volumetric imaging of relatively transparent samples. While this capability has allowed the technique to be highly impactful in fields such as developmental biology, applications involving highly scattering thick tissues have been largely unexplored. Herein, we employ Monte Carlo simulations to explore the use of LSM for imaging turbid media. In particular, due to its similarity to dual-axis confocal (DAC) microscopy, we compare LSM performance to point-scanned (PS-DAC) and line-scanned (LS-DAC) dual-axis confocal microscopy techniques that have been previously shown to produce high-quality images at round-trip optical lengths of ~9 – 10 and ~3 – 4 respectively. The results of this study indicate that LSM using widefield collection (WF-LSM) provides comparable performance to LS-DAC in thick tissues, due to the fact that they both utilize an illumination beam focused in one dimension (i.e. a line or sheet). On the other hand, LSM using confocal line detection (CL-LSM) is more analogous to PS-DAC microscopy, in which the illumination beam is focused in two dimensions to a point. The imaging depth of LSM is only slightly inferior to DAC (~2 – 3 and ~6 – 7 optical lengths for WF-LSM and CL-LSM respectively) due to the use of a lower numerical aperture (NA) illumination beam for extended imaging along the illumination axis. Therefore, we conclude that the ability to image deeply is dictated most by the confocality of the microscope technique. In addition, we find that imaging resolution is mostly dependent on the collection NA, and is relatively invariant to imaging depth in a homogeneous scattering medium. Our results indicate that superficial imaging of highly scattering tissues using light sheet microscopy is possible.

© 2016 Optical Society of America

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References

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2016 (1)

2015 (6)

2014 (7)

A. Elmaklizi, J. Schäfer, and A. Kienle, “Simulating the scanning of a focused beam through scattering media using a numerical solution of Maxwell’s equations,” J. Biomed. Opt. 19(7), 071404 (2014).
[Crossref] [PubMed]

T. Vettenburg, H. I. Dalgarno, J. Nylk, C. Coll-Lladó, D. E. Ferrier, T. Čižmár, F. J. Gunn-Moore, and K. Dholakia, “Light-sheet microscopy using an Airy beam,” Nat. Methods 11(5), 541–544 (2014).
[Crossref] [PubMed]

L. Gao, L. Zhu, C. Li, and L. V. Wang, “Nonlinear light-sheet fluorescence microscopy by photobleaching imprinting,” J. R. Soc. Interface 11(93), 20130851 (2014).
[Crossref] [PubMed]

A. R. Gardner, C. K. Hayakawa, and V. Venugopalan, “Coupled forward-adjoint Monte Carlo simulation of spatial-angular light fields to determine optical sensitivity in turbid media,” J. Biomed. Opt. 19(6), 065003 (2014).
[Crossref] [PubMed]

P. N. Hedde, M. Stakic, and E. Gratton, “Rapid measurement of molecular transport and interaction inside living cells using single plane illumination,” Sci. Rep. 4, 7048 (2014).
[Crossref] [PubMed]

P. Arce, J. I. Lagares, L. Harkness, D. Perez-Astudillo, M. Canadas, P. Rato, M. de Prado, Y. Abreu, G. de Lorenzo, M. Kolstein, and A. Diaz, “GAMOS: A framework to do GEANT4 simulations in different physics fields with an user-friendly interface,” Nucl Instrum Meth A 735, 304–313 (2014).
[Crossref]

D. Wang, D. Meza, Y. Wang, L. Gao, and J. T. C. Liu, “Sheet-scanned dual-axis confocal microscopy using Richardson-Lucy deconvolution,” Opt. Lett. 39(18), 5431–5434 (2014).
[Crossref] [PubMed]

2013 (8)

S. L. Jacques, “Optical properties of biological tissues: a review,” Phys. Med. Biol. 58(11), R37–R61 (2013).
[Crossref] [PubMed]

Y. Chen and J. T. C. Liu, “Optimizing the performance of dual-axis confocal microscopes via Monte-Carlo scattering simulations and diffraction theory,” J. Biomed. Opt. 18(6), 066006 (2013).
[Crossref] [PubMed]

D. Wang, Y. Chen, Y. Wang, and J. T. C. Liu, “Comparison of line-scanned and point-scanned dual-axis confocal microscope performance,” Opt. Lett. 38(24), 5280–5283 (2013).
[Crossref] [PubMed]

A. K. Glaser, S. C. Kanick, R. Zhang, P. Arce, and B. W. Pogue, “A GAMOS plug-in for GEANT4 based Monte Carlo simulation of radiation-induced light transport in biological media,” Biomed. Opt. Express 4(5), 741–759 (2013).
[Crossref] [PubMed]

Z. Lavagnino, F. C. Zanacchi, E. Ronzitti, and A. Diaspro, “Two-photon excitation selective plane illumination microscopy (2PE-SPIM) of highly scattering samples: characterization and application,” Opt. Express 21(5), 5998–6008 (2013).
[Crossref] [PubMed]

F. Cella Zanacchi, Z. Lavagnino, M. Faretta, L. Furia, and A. Diaspro, “Light-sheet confined super-resolution using two-photon photoactivation,” PLoS One 8(7), e67667 (2013).
[Crossref] [PubMed]

F. O. Fahrbach, V. Gurchenkov, K. Alessandri, P. Nassoy, and A. Rohrbach, “Light-sheet microscopy in thick media using scanned Bessel beams and two-photon fluorescence excitation,” Opt. Express 21(11), 13824–13839 (2013).
[Crossref] [PubMed]

I. R. Capoğlu, A. Taflove, and V. Backman, “Computation of tightly-focused laser beams in the FDTD method,” Opt. Express 21(1), 87–101 (2013).
[Crossref] [PubMed]

2012 (6)

2011 (8)

P. J. Keller, A. D. Schmidt, J. Wittbrodt, and E. H. Stelzer, “Digital scanned laser light-sheet fluorescence microscopy (DSLM) of zebrafish and Drosophila embryonic development,” Cold Spring Harb. Protoc. 2011(10), 1235–1243 (2011).
[Crossref] [PubMed]

J. T. C. Liu, N. O. Loewke, M. J. Mandella, R. M. Levenson, J. M. Crawford, and C. H. Contag, “Point-of-care pathology with miniature microscopes,” Anal. Cell Pathol. (Amst.) 34(3), 81–98 (2011).
[Crossref] [PubMed]

J. Mertz, “Optical sectioning microscopy with planar or structured illumination,” Nat. Methods 8(10), 811–819 (2011).
[Crossref] [PubMed]

P. A. Santi, “Light sheet fluorescence microscopy: a review,” J. Histochem. Cytochem. 59(2), 129–138 (2011).
[Crossref] [PubMed]

M. Weber and J. Huisken, “Light sheet microscopy for real-time developmental biology,” Curr. Opin. Genet. Dev. 21(5), 566–572 (2011).
[Crossref] [PubMed]

Y. Wu, A. Ghitani, R. Christensen, A. Santella, Z. Du, G. Rondeau, Z. Bao, D. Colón-Ramos, and H. Shroff, “Inverted selective plane illumination microscopy (iSPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans,” Proc. Natl. Acad. Sci. U.S.A. 108(43), 17708–17713 (2011).
[Crossref] [PubMed]

J. Chen and X. Intes, “Comparison of Monte Carlo methods for fluorescence molecular tomography-computational efficiency,” Med. Phys. 38(10), 5788–5798 (2011).
[Crossref] [PubMed]

T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8(5), 417–423 (2011).
[Crossref] [PubMed]

2010 (3)

P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. K. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods 7(8), 637–642 (2010).
[Crossref] [PubMed]

Q. Fang, “Mesh-based Monte Carlo method using fast ray-tracing in Plücker coordinates,” Biomed. Opt. Express 1(1), 165–175 (2010).
[Crossref] [PubMed]

J. T. C. Liu, M. J. Mandella, N. O. Loewke, H. Haeberle, H. Ra, W. Piyawattanametha, O. Solgaard, G. S. Kino, and C. H. Contag, “Micromirror-scanned dual-axis confocal microscope utilizing a gradient-index relay lens for image guidance during brain surgery,” J. Biomed. Opt. 15(2), 026029 (2010).
[Crossref] [PubMed]

2009 (2)

2008 (1)

J. T. C. Liu, M. J. Mandella, J. M. Crawford, C. H. Contag, T. D. Wang, and G. S. Kino, “Efficient rejection of scattered light enables deep optical sectioning in turbid media with low-numerical-aperture optics in a dual-axis confocal architecture,” J. Biomed. Opt. 13(3), 034020 (2008).
[Crossref] [PubMed]

2007 (2)

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

J. A. Buytaert and J. J. Dirckx, “Design and quantitative resolution measurements of an optical virtual sectioning three-dimensional imaging technique for biomedical specimens, featuring two-micrometer slicing resolution,” J. Biomed. Opt. 12(1), 014039 (2007).
[Crossref] [PubMed]

2006 (1)

2004 (1)

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

2003 (1)

2000 (1)

P. K. Milsom, “A ray-optic, Monte Carlo, description of a Gaussian beam waist - applied to reverse saturable absorption,” Appl. Phys. B 70(4), 593–599 (2000).
[Crossref]

1999 (1)

1997 (1)

1995 (2)

L. Wang, S. L. Jacques, and L. Zheng, “MCML--Monte Carlo modeling of light transport in multi-layered tissues,” Comput. Methods Programs Biomed. 47(2), 131–146 (1995).
[Crossref] [PubMed]

E. H. K. Stelzer, S. Lindek, S. Albrecht, R. Pick, G. Ritter, N. J. Salmon, and R. Stricker, “A New Tool for the Observation of Embryos and Other Large Specimens - Confocal Theta-Fluorescence Microscopy,” J Microsc-Oxford 179(1), 1–10 (1995).
[Crossref]

Abdellah, M.

M. Abdellah, A. Bilgili, S. Eilemann, H. Markram, and F. Schürmann, “Physically-based in silico light sheet microscopy for visualizing fluorescent brain models,” BMC Bioinformatics 16(Suppl 11), S8 (2015).
[Crossref] [PubMed]

Abeytunge, S.

Abreu, Y.

P. Arce, J. I. Lagares, L. Harkness, D. Perez-Astudillo, M. Canadas, P. Rato, M. de Prado, Y. Abreu, G. de Lorenzo, M. Kolstein, and A. Diaz, “GAMOS: A framework to do GEANT4 simulations in different physics fields with an user-friendly interface,” Nucl Instrum Meth A 735, 304–313 (2014).
[Crossref]

Albrecht, S.

E. H. K. Stelzer, S. Lindek, S. Albrecht, R. Pick, G. Ritter, N. J. Salmon, and R. Stricker, “A New Tool for the Observation of Embryos and Other Large Specimens - Confocal Theta-Fluorescence Microscopy,” J Microsc-Oxford 179(1), 1–10 (1995).
[Crossref]

Alessandri, K.

Arce, P.

P. Arce, J. I. Lagares, L. Harkness, D. Perez-Astudillo, M. Canadas, P. Rato, M. de Prado, Y. Abreu, G. de Lorenzo, M. Kolstein, and A. Diaz, “GAMOS: A framework to do GEANT4 simulations in different physics fields with an user-friendly interface,” Nucl Instrum Meth A 735, 304–313 (2014).
[Crossref]

A. K. Glaser, S. C. Kanick, R. Zhang, P. Arce, and B. W. Pogue, “A GAMOS plug-in for GEANT4 based Monte Carlo simulation of radiation-induced light transport in biological media,” Biomed. Opt. Express 4(5), 741–759 (2013).
[Crossref] [PubMed]

Backman, V.

Bao, Z.

Y. Wu, A. Ghitani, R. Christensen, A. Santella, Z. Du, G. Rondeau, Z. Bao, D. Colón-Ramos, and H. Shroff, “Inverted selective plane illumination microscopy (iSPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans,” Proc. Natl. Acad. Sci. U.S.A. 108(43), 17708–17713 (2011).
[Crossref] [PubMed]

P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. K. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods 7(8), 637–642 (2010).
[Crossref] [PubMed]

Baumgart, E.

Becker, K.

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Betzig, E.

T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8(5), 417–423 (2011).
[Crossref] [PubMed]

Bilgili, A.

M. Abdellah, A. Bilgili, S. Eilemann, H. Markram, and F. Schürmann, “Physically-based in silico light sheet microscopy for visualizing fluorescent brain models,” BMC Bioinformatics 16(Suppl 11), S8 (2015).
[Crossref] [PubMed]

Bixler, J. N.

Boas, D. A.

Brandes, A.

A. Elmaklizi, D. Reitzle, A. Brandes, and A. Kienle, “Penetration depth of focused beams in highly scattering media investigated with a numerical solution of Maxwell’s equations in two dimensions,” J. Biomed. Opt. 20(6), 065007 (2015).
[Crossref] [PubMed]

Bria, A.

Buytaert, J. A.

J. A. Buytaert and J. J. Dirckx, “Design and quantitative resolution measurements of an optical virtual sectioning three-dimensional imaging technique for biomedical specimens, featuring two-micrometer slicing resolution,” J. Biomed. Opt. 12(1), 014039 (2007).
[Crossref] [PubMed]

Campion, M.

E. Mei, P. A. Fomitchov, R. Graves, and M. Campion, “A line scanning confocal fluorescent microscope using a CMOS rolling shutter as an adjustable aperture,” J. Microsc. 247(3), 269–276 (2012).
[Crossref] [PubMed]

Canadas, M.

P. Arce, J. I. Lagares, L. Harkness, D. Perez-Astudillo, M. Canadas, P. Rato, M. de Prado, Y. Abreu, G. de Lorenzo, M. Kolstein, and A. Diaz, “GAMOS: A framework to do GEANT4 simulations in different physics fields with an user-friendly interface,” Nucl Instrum Meth A 735, 304–313 (2014).
[Crossref]

Capoglu, I. R.

Cella Zanacchi, F.

F. Cella Zanacchi, Z. Lavagnino, M. Faretta, L. Furia, and A. Diaspro, “Light-sheet confined super-resolution using two-photon photoactivation,” PLoS One 8(7), e67667 (2013).
[Crossref] [PubMed]

Chen, J.

J. Chen and X. Intes, “Comparison of Monte Carlo methods for fluorescence molecular tomography-computational efficiency,” Med. Phys. 38(10), 5788–5798 (2011).
[Crossref] [PubMed]

Chen, L. W. Y.

Chen, Y.

Cheong, W. F.

Christensen, R.

Y. Wu, A. Ghitani, R. Christensen, A. Santella, Z. Du, G. Rondeau, Z. Bao, D. Colón-Ramos, and H. Shroff, “Inverted selective plane illumination microscopy (iSPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans,” Proc. Natl. Acad. Sci. U.S.A. 108(43), 17708–17713 (2011).
[Crossref] [PubMed]

Cižmár, T.

T. Vettenburg, H. I. Dalgarno, J. Nylk, C. Coll-Lladó, D. E. Ferrier, T. Čižmár, F. J. Gunn-Moore, and K. Dholakia, “Light-sheet microscopy using an Airy beam,” Nat. Methods 11(5), 541–544 (2014).
[Crossref] [PubMed]

Coll-Lladó, C.

T. Vettenburg, H. I. Dalgarno, J. Nylk, C. Coll-Lladó, D. E. Ferrier, T. Čižmár, F. J. Gunn-Moore, and K. Dholakia, “Light-sheet microscopy using an Airy beam,” Nat. Methods 11(5), 541–544 (2014).
[Crossref] [PubMed]

Colón-Ramos, D.

Y. Wu, A. Ghitani, R. Christensen, A. Santella, Z. Du, G. Rondeau, Z. Bao, D. Colón-Ramos, and H. Shroff, “Inverted selective plane illumination microscopy (iSPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans,” Proc. Natl. Acad. Sci. U.S.A. 108(43), 17708–17713 (2011).
[Crossref] [PubMed]

Contag, C. H.

J. T. C. Liu, N. O. Loewke, M. J. Mandella, R. M. Levenson, J. M. Crawford, and C. H. Contag, “Point-of-care pathology with miniature microscopes,” Anal. Cell Pathol. (Amst.) 34(3), 81–98 (2011).
[Crossref] [PubMed]

J. T. C. Liu, M. J. Mandella, N. O. Loewke, H. Haeberle, H. Ra, W. Piyawattanametha, O. Solgaard, G. S. Kino, and C. H. Contag, “Micromirror-scanned dual-axis confocal microscope utilizing a gradient-index relay lens for image guidance during brain surgery,” J. Biomed. Opt. 15(2), 026029 (2010).
[Crossref] [PubMed]

J. T. C. Liu, M. J. Mandella, J. M. Crawford, C. H. Contag, T. D. Wang, and G. S. Kino, “Efficient rejection of scattered light enables deep optical sectioning in turbid media with low-numerical-aperture optics in a dual-axis confocal architecture,” J. Biomed. Opt. 13(3), 034020 (2008).
[Crossref] [PubMed]

T. D. Wang, M. J. Mandella, C. H. Contag, and G. S. Kino, “Dual-axis confocal microscope for high-resolution in vivo imaging,” Opt. Lett. 28(6), 414–416 (2003).
[Crossref] [PubMed]

Crawford, J. M.

J. T. C. Liu, N. O. Loewke, M. J. Mandella, R. M. Levenson, J. M. Crawford, and C. H. Contag, “Point-of-care pathology with miniature microscopes,” Anal. Cell Pathol. (Amst.) 34(3), 81–98 (2011).
[Crossref] [PubMed]

J. T. C. Liu, M. J. Mandella, J. M. Crawford, C. H. Contag, T. D. Wang, and G. S. Kino, “Efficient rejection of scattered light enables deep optical sectioning in turbid media with low-numerical-aperture optics in a dual-axis confocal architecture,” J. Biomed. Opt. 13(3), 034020 (2008).
[Crossref] [PubMed]

Crilly, R. J.

Dalgarno, H. I.

T. Vettenburg, H. I. Dalgarno, J. Nylk, C. Coll-Lladó, D. E. Ferrier, T. Čižmár, F. J. Gunn-Moore, and K. Dholakia, “Light-sheet microscopy using an Airy beam,” Nat. Methods 11(5), 541–544 (2014).
[Crossref] [PubMed]

Davidson, M. W.

T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8(5), 417–423 (2011).
[Crossref] [PubMed]

de Lorenzo, G.

P. Arce, J. I. Lagares, L. Harkness, D. Perez-Astudillo, M. Canadas, P. Rato, M. de Prado, Y. Abreu, G. de Lorenzo, M. Kolstein, and A. Diaz, “GAMOS: A framework to do GEANT4 simulations in different physics fields with an user-friendly interface,” Nucl Instrum Meth A 735, 304–313 (2014).
[Crossref]

de Prado, M.

P. Arce, J. I. Lagares, L. Harkness, D. Perez-Astudillo, M. Canadas, P. Rato, M. de Prado, Y. Abreu, G. de Lorenzo, M. Kolstein, and A. Diaz, “GAMOS: A framework to do GEANT4 simulations in different physics fields with an user-friendly interface,” Nucl Instrum Meth A 735, 304–313 (2014).
[Crossref]

Deininger, K.

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Del Bene, F.

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Deussing, J. M.

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Dholakia, K.

T. Vettenburg, H. I. Dalgarno, J. Nylk, C. Coll-Lladó, D. E. Ferrier, T. Čižmár, F. J. Gunn-Moore, and K. Dholakia, “Light-sheet microscopy using an Airy beam,” Nat. Methods 11(5), 541–544 (2014).
[Crossref] [PubMed]

Diaspro, A.

Diaz, A.

P. Arce, J. I. Lagares, L. Harkness, D. Perez-Astudillo, M. Canadas, P. Rato, M. de Prado, Y. Abreu, G. de Lorenzo, M. Kolstein, and A. Diaz, “GAMOS: A framework to do GEANT4 simulations in different physics fields with an user-friendly interface,” Nucl Instrum Meth A 735, 304–313 (2014).
[Crossref]

Dirckx, J. J.

J. A. Buytaert and J. J. Dirckx, “Design and quantitative resolution measurements of an optical virtual sectioning three-dimensional imaging technique for biomedical specimens, featuring two-micrometer slicing resolution,” J. Biomed. Opt. 12(1), 014039 (2007).
[Crossref] [PubMed]

Dodt, H. U.

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Dong, Z.

Du, Z.

Y. Wu, A. Ghitani, R. Christensen, A. Santella, Z. Du, G. Rondeau, Z. Bao, D. Colón-Ramos, and H. Shroff, “Inverted selective plane illumination microscopy (iSPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans,” Proc. Natl. Acad. Sci. U.S.A. 108(43), 17708–17713 (2011).
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H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Eilemann, S.

M. Abdellah, A. Bilgili, S. Eilemann, H. Markram, and F. Schürmann, “Physically-based in silico light sheet microscopy for visualizing fluorescent brain models,” BMC Bioinformatics 16(Suppl 11), S8 (2015).
[Crossref] [PubMed]

Elmaklizi, A.

A. Elmaklizi, D. Reitzle, A. Brandes, and A. Kienle, “Penetration depth of focused beams in highly scattering media investigated with a numerical solution of Maxwell’s equations in two dimensions,” J. Biomed. Opt. 20(6), 065007 (2015).
[Crossref] [PubMed]

A. Elmaklizi, J. Schäfer, and A. Kienle, “Simulating the scanning of a focused beam through scattering media using a numerical solution of Maxwell’s equations,” J. Biomed. Opt. 19(7), 071404 (2014).
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Engelbrecht, C. J.

Fahrbach, F. O.

Fang, Q.

Faretta, M.

F. Cella Zanacchi, Z. Lavagnino, M. Faretta, L. Furia, and A. Diaspro, “Light-sheet confined super-resolution using two-photon photoactivation,” PLoS One 8(7), e67667 (2013).
[Crossref] [PubMed]

Ferrier, D. E.

T. Vettenburg, H. I. Dalgarno, J. Nylk, C. Coll-Lladó, D. E. Ferrier, T. Čižmár, F. J. Gunn-Moore, and K. Dholakia, “Light-sheet microscopy using an Airy beam,” Nat. Methods 11(5), 541–544 (2014).
[Crossref] [PubMed]

Fomitchov, P. A.

E. Mei, P. A. Fomitchov, R. Graves, and M. Campion, “A line scanning confocal fluorescent microscope using a CMOS rolling shutter as an adjustable aperture,” J. Microsc. 247(3), 269–276 (2012).
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Fu, L.

Furia, L.

F. Cella Zanacchi, Z. Lavagnino, M. Faretta, L. Furia, and A. Diaspro, “Light-sheet confined super-resolution using two-photon photoactivation,” PLoS One 8(7), e67667 (2013).
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T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8(5), 417–423 (2011).
[Crossref] [PubMed]

Galbraith, J. A.

T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8(5), 417–423 (2011).
[Crossref] [PubMed]

Gao, L.

L. Gao, L. Zhu, C. Li, and L. V. Wang, “Nonlinear light-sheet fluorescence microscopy by photobleaching imprinting,” J. R. Soc. Interface 11(93), 20130851 (2014).
[Crossref] [PubMed]

D. Wang, D. Meza, Y. Wang, L. Gao, and J. T. C. Liu, “Sheet-scanned dual-axis confocal microscopy using Richardson-Lucy deconvolution,” Opt. Lett. 39(18), 5431–5434 (2014).
[Crossref] [PubMed]

T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8(5), 417–423 (2011).
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A. R. Gardner, C. K. Hayakawa, and V. Venugopalan, “Coupled forward-adjoint Monte Carlo simulation of spatial-angular light fields to determine optical sensitivity in turbid media,” J. Biomed. Opt. 19(6), 065003 (2014).
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Y. Wu, A. Ghitani, R. Christensen, A. Santella, Z. Du, G. Rondeau, Z. Bao, D. Colón-Ramos, and H. Shroff, “Inverted selective plane illumination microscopy (iSPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans,” Proc. Natl. Acad. Sci. U.S.A. 108(43), 17708–17713 (2011).
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Glazowski, C.

Gong, H.

Gratton, E.

P. N. Hedde, M. Stakic, and E. Gratton, “Rapid measurement of molecular transport and interaction inside living cells using single plane illumination,” Sci. Rep. 4, 7048 (2014).
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Graves, R.

E. Mei, P. A. Fomitchov, R. Graves, and M. Campion, “A line scanning confocal fluorescent microscope using a CMOS rolling shutter as an adjustable aperture,” J. Microsc. 247(3), 269–276 (2012).
[Crossref] [PubMed]

Gunn-Moore, F. J.

T. Vettenburg, H. I. Dalgarno, J. Nylk, C. Coll-Lladó, D. E. Ferrier, T. Čižmár, F. J. Gunn-Moore, and K. Dholakia, “Light-sheet microscopy using an Airy beam,” Nat. Methods 11(5), 541–544 (2014).
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Gurchenkov, V.

Haeberle, H.

J. T. C. Liu, M. J. Mandella, N. O. Loewke, H. Haeberle, H. Ra, W. Piyawattanametha, O. Solgaard, G. S. Kino, and C. H. Contag, “Micromirror-scanned dual-axis confocal microscope utilizing a gradient-index relay lens for image guidance during brain surgery,” J. Biomed. Opt. 15(2), 026029 (2010).
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P. Arce, J. I. Lagares, L. Harkness, D. Perez-Astudillo, M. Canadas, P. Rato, M. de Prado, Y. Abreu, G. de Lorenzo, M. Kolstein, and A. Diaz, “GAMOS: A framework to do GEANT4 simulations in different physics fields with an user-friendly interface,” Nucl Instrum Meth A 735, 304–313 (2014).
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A. R. Gardner, C. K. Hayakawa, and V. Venugopalan, “Coupled forward-adjoint Monte Carlo simulation of spatial-angular light fields to determine optical sensitivity in turbid media,” J. Biomed. Opt. 19(6), 065003 (2014).
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P. N. Hedde, M. Stakic, and E. Gratton, “Rapid measurement of molecular transport and interaction inside living cells using single plane illumination,” Sci. Rep. 4, 7048 (2014).
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M. Weber and J. Huisken, “Light sheet microscopy for real-time developmental biology,” Curr. Opin. Genet. Dev. 21(5), 566–572 (2011).
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J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
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Intes, X.

J. Chen and X. Intes, “Comparison of Monte Carlo methods for fluorescence molecular tomography-computational efficiency,” Med. Phys. 38(10), 5788–5798 (2011).
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S. L. Jacques, “Optical properties of biological tissues: a review,” Phys. Med. Biol. 58(11), R37–R61 (2013).
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H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
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Kamiyama, D.

Kanick, S. C.

Keller, P. J.

P. J. Keller, A. D. Schmidt, J. Wittbrodt, and E. H. Stelzer, “Digital scanned laser light-sheet fluorescence microscopy (DSLM) of zebrafish and Drosophila embryonic development,” Cold Spring Harb. Protoc. 2011(10), 1235–1243 (2011).
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P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. K. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods 7(8), 637–642 (2010).
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Khairy, K.

P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. K. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods 7(8), 637–642 (2010).
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Kienle, A.

A. Elmaklizi, D. Reitzle, A. Brandes, and A. Kienle, “Penetration depth of focused beams in highly scattering media investigated with a numerical solution of Maxwell’s equations in two dimensions,” J. Biomed. Opt. 20(6), 065007 (2015).
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A. Elmaklizi, J. Schäfer, and A. Kienle, “Simulating the scanning of a focused beam through scattering media using a numerical solution of Maxwell’s equations,” J. Biomed. Opt. 19(7), 071404 (2014).
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J. T. C. Liu, M. J. Mandella, N. O. Loewke, H. Haeberle, H. Ra, W. Piyawattanametha, O. Solgaard, G. S. Kino, and C. H. Contag, “Micromirror-scanned dual-axis confocal microscope utilizing a gradient-index relay lens for image guidance during brain surgery,” J. Biomed. Opt. 15(2), 026029 (2010).
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J. T. C. Liu, M. J. Mandella, J. M. Crawford, C. H. Contag, T. D. Wang, and G. S. Kino, “Efficient rejection of scattered light enables deep optical sectioning in turbid media with low-numerical-aperture optics in a dual-axis confocal architecture,” J. Biomed. Opt. 13(3), 034020 (2008).
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T. D. Wang, M. J. Mandella, C. H. Contag, and G. S. Kino, “Dual-axis confocal microscope for high-resolution in vivo imaging,” Opt. Lett. 28(6), 414–416 (2003).
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P. Arce, J. I. Lagares, L. Harkness, D. Perez-Astudillo, M. Canadas, P. Rato, M. de Prado, Y. Abreu, G. de Lorenzo, M. Kolstein, and A. Diaz, “GAMOS: A framework to do GEANT4 simulations in different physics fields with an user-friendly interface,” Nucl Instrum Meth A 735, 304–313 (2014).
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Lagares, J. I.

P. Arce, J. I. Lagares, L. Harkness, D. Perez-Astudillo, M. Canadas, P. Rato, M. de Prado, Y. Abreu, G. de Lorenzo, M. Kolstein, and A. Diaz, “GAMOS: A framework to do GEANT4 simulations in different physics fields with an user-friendly interface,” Nucl Instrum Meth A 735, 304–313 (2014).
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H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
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J. T. C. Liu, N. O. Loewke, M. J. Mandella, R. M. Levenson, J. M. Crawford, and C. H. Contag, “Point-of-care pathology with miniature microscopes,” Anal. Cell Pathol. (Amst.) 34(3), 81–98 (2011).
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L. Gao, L. Zhu, C. Li, and L. V. Wang, “Nonlinear light-sheet fluorescence microscopy by photobleaching imprinting,” J. R. Soc. Interface 11(93), 20130851 (2014).
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[Crossref] [PubMed]

J. T. C. Liu, M. J. Mandella, N. O. Loewke, H. Haeberle, H. Ra, W. Piyawattanametha, O. Solgaard, G. S. Kino, and C. H. Contag, “Micromirror-scanned dual-axis confocal microscope utilizing a gradient-index relay lens for image guidance during brain surgery,” J. Biomed. Opt. 15(2), 026029 (2010).
[Crossref] [PubMed]

J. T. C. Liu, M. J. Mandella, J. M. Crawford, C. H. Contag, T. D. Wang, and G. S. Kino, “Efficient rejection of scattered light enables deep optical sectioning in turbid media with low-numerical-aperture optics in a dual-axis confocal architecture,” J. Biomed. Opt. 13(3), 034020 (2008).
[Crossref] [PubMed]

Loewke, N. O.

J. T. C. Liu, N. O. Loewke, M. J. Mandella, R. M. Levenson, J. M. Crawford, and C. H. Contag, “Point-of-care pathology with miniature microscopes,” Anal. Cell Pathol. (Amst.) 34(3), 81–98 (2011).
[Crossref] [PubMed]

J. T. C. Liu, M. J. Mandella, N. O. Loewke, H. Haeberle, H. Ra, W. Piyawattanametha, O. Solgaard, G. S. Kino, and C. H. Contag, “Micromirror-scanned dual-axis confocal microscope utilizing a gradient-index relay lens for image guidance during brain surgery,” J. Biomed. Opt. 15(2), 026029 (2010).
[Crossref] [PubMed]

Luo, Q.

Mandella, M. J.

C. Yin, A. K. Glaser, S. Y. Leigh, L. W. Y. Chen, P. C. S. Pillai, M. C. Rosenberg, S. Abeytunge, G. Peterson, C. Glazowski, N. Sanai, M. J. Mandella, M. Rajadhyaksha, and J. T. C. Liu, “Miniature in vivo MEMS-based line-scanned dual-axis confocal microscope for point-of-care pathology,” Biomed. Opt. Express 7(2), 251–263 (2016).
[Crossref]

J. T. C. Liu, N. O. Loewke, M. J. Mandella, R. M. Levenson, J. M. Crawford, and C. H. Contag, “Point-of-care pathology with miniature microscopes,” Anal. Cell Pathol. (Amst.) 34(3), 81–98 (2011).
[Crossref] [PubMed]

J. T. C. Liu, M. J. Mandella, N. O. Loewke, H. Haeberle, H. Ra, W. Piyawattanametha, O. Solgaard, G. S. Kino, and C. H. Contag, “Micromirror-scanned dual-axis confocal microscope utilizing a gradient-index relay lens for image guidance during brain surgery,” J. Biomed. Opt. 15(2), 026029 (2010).
[Crossref] [PubMed]

J. T. C. Liu, M. J. Mandella, J. M. Crawford, C. H. Contag, T. D. Wang, and G. S. Kino, “Efficient rejection of scattered light enables deep optical sectioning in turbid media with low-numerical-aperture optics in a dual-axis confocal architecture,” J. Biomed. Opt. 13(3), 034020 (2008).
[Crossref] [PubMed]

T. D. Wang, M. J. Mandella, C. H. Contag, and G. S. Kino, “Dual-axis confocal microscope for high-resolution in vivo imaging,” Opt. Lett. 28(6), 414–416 (2003).
[Crossref] [PubMed]

Markram, H.

M. Abdellah, A. Bilgili, S. Eilemann, H. Markram, and F. Schürmann, “Physically-based in silico light sheet microscopy for visualizing fluorescent brain models,” BMC Bioinformatics 16(Suppl 11), S8 (2015).
[Crossref] [PubMed]

Mauch, C. P.

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

McGorty, R.

Mei, E.

E. Mei, P. A. Fomitchov, R. Graves, and M. Campion, “A line scanning confocal fluorescent microscope using a CMOS rolling shutter as an adjustable aperture,” J. Microsc. 247(3), 269–276 (2012).
[Crossref] [PubMed]

Mei, L.

Mertz, J.

J. Mertz, “Optical sectioning microscopy with planar or structured illumination,” Nat. Methods 8(10), 811–819 (2011).
[Crossref] [PubMed]

Meza, D.

Milkie, D. E.

T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8(5), 417–423 (2011).
[Crossref] [PubMed]

Milsom, P. K.

P. K. Milsom, “A ray-optic, Monte Carlo, description of a Gaussian beam waist - applied to reverse saturable absorption,” Appl. Phys. B 70(4), 593–599 (2000).
[Crossref]

Nassoy, P.

Nylk, J.

T. Vettenburg, H. I. Dalgarno, J. Nylk, C. Coll-Lladó, D. E. Ferrier, T. Čižmár, F. J. Gunn-Moore, and K. Dholakia, “Light-sheet microscopy using an Airy beam,” Nat. Methods 11(5), 541–544 (2014).
[Crossref] [PubMed]

Pavone, F. S.

Perez-Astudillo, D.

P. Arce, J. I. Lagares, L. Harkness, D. Perez-Astudillo, M. Canadas, P. Rato, M. de Prado, Y. Abreu, G. de Lorenzo, M. Kolstein, and A. Diaz, “GAMOS: A framework to do GEANT4 simulations in different physics fields with an user-friendly interface,” Nucl Instrum Meth A 735, 304–313 (2014).
[Crossref]

Peterson, G.

Pick, R.

E. H. K. Stelzer, S. Lindek, S. Albrecht, R. Pick, G. Ritter, N. J. Salmon, and R. Stricker, “A New Tool for the Observation of Embryos and Other Large Specimens - Confocal Theta-Fluorescence Microscopy,” J Microsc-Oxford 179(1), 1–10 (1995).
[Crossref]

Pillai, P. C. S.

Piyawattanametha, W.

J. T. C. Liu, M. J. Mandella, N. O. Loewke, H. Haeberle, H. Ra, W. Piyawattanametha, O. Solgaard, G. S. Kino, and C. H. Contag, “Micromirror-scanned dual-axis confocal microscope utilizing a gradient-index relay lens for image guidance during brain surgery,” J. Biomed. Opt. 15(2), 026029 (2010).
[Crossref] [PubMed]

Planchon, T. A.

T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8(5), 417–423 (2011).
[Crossref] [PubMed]

Pogue, B. W.

Ra, H.

J. T. C. Liu, M. J. Mandella, N. O. Loewke, H. Haeberle, H. Ra, W. Piyawattanametha, O. Solgaard, G. S. Kino, and C. H. Contag, “Micromirror-scanned dual-axis confocal microscope utilizing a gradient-index relay lens for image guidance during brain surgery,” J. Biomed. Opt. 15(2), 026029 (2010).
[Crossref] [PubMed]

Rajadhyaksha, M.

Rato, P.

P. Arce, J. I. Lagares, L. Harkness, D. Perez-Astudillo, M. Canadas, P. Rato, M. de Prado, Y. Abreu, G. de Lorenzo, M. Kolstein, and A. Diaz, “GAMOS: A framework to do GEANT4 simulations in different physics fields with an user-friendly interface,” Nucl Instrum Meth A 735, 304–313 (2014).
[Crossref]

Reitzle, D.

A. Elmaklizi, D. Reitzle, A. Brandes, and A. Kienle, “Penetration depth of focused beams in highly scattering media investigated with a numerical solution of Maxwell’s equations in two dimensions,” J. Biomed. Opt. 20(6), 065007 (2015).
[Crossref] [PubMed]

Ritter, G.

E. H. K. Stelzer, S. Lindek, S. Albrecht, R. Pick, G. Ritter, N. J. Salmon, and R. Stricker, “A New Tool for the Observation of Embryos and Other Large Specimens - Confocal Theta-Fluorescence Microscopy,” J Microsc-Oxford 179(1), 1–10 (1995).
[Crossref]

Rogomentich, F.

Rohrbach, A.

Rondeau, G.

Y. Wu, A. Ghitani, R. Christensen, A. Santella, Z. Du, G. Rondeau, Z. Bao, D. Colón-Ramos, and H. Shroff, “Inverted selective plane illumination microscopy (iSPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans,” Proc. Natl. Acad. Sci. U.S.A. 108(43), 17708–17713 (2011).
[Crossref] [PubMed]

Ronzitti, E.

Rosenberg, M. C.

Sacconi, L.

Salmon, N. J.

E. H. K. Stelzer, S. Lindek, S. Albrecht, R. Pick, G. Ritter, N. J. Salmon, and R. Stricker, “A New Tool for the Observation of Embryos and Other Large Specimens - Confocal Theta-Fluorescence Microscopy,” J Microsc-Oxford 179(1), 1–10 (1995).
[Crossref]

Sanai, N.

Santella, A.

Y. Wu, A. Ghitani, R. Christensen, A. Santella, Z. Du, G. Rondeau, Z. Bao, D. Colón-Ramos, and H. Shroff, “Inverted selective plane illumination microscopy (iSPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans,” Proc. Natl. Acad. Sci. U.S.A. 108(43), 17708–17713 (2011).
[Crossref] [PubMed]

P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. K. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods 7(8), 637–642 (2010).
[Crossref] [PubMed]

Santi, P. A.

P. A. Santi, “Light sheet fluorescence microscopy: a review,” J. Histochem. Cytochem. 59(2), 129–138 (2011).
[Crossref] [PubMed]

Schäfer, J.

A. Elmaklizi, J. Schäfer, and A. Kienle, “Simulating the scanning of a focused beam through scattering media using a numerical solution of Maxwell’s equations,” J. Biomed. Opt. 19(7), 071404 (2014).
[Crossref] [PubMed]

Schierloh, A.

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Schmidt, A. D.

P. J. Keller, A. D. Schmidt, J. Wittbrodt, and E. H. Stelzer, “Digital scanned laser light-sheet fluorescence microscopy (DSLM) of zebrafish and Drosophila embryonic development,” Cold Spring Harb. Protoc. 2011(10), 1235–1243 (2011).
[Crossref] [PubMed]

P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. K. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods 7(8), 637–642 (2010).
[Crossref] [PubMed]

Schürmann, F.

M. Abdellah, A. Bilgili, S. Eilemann, H. Markram, and F. Schürmann, “Physically-based in silico light sheet microscopy for visualizing fluorescent brain models,” BMC Bioinformatics 16(Suppl 11), S8 (2015).
[Crossref] [PubMed]

Scully, M. O.

Shroff, H.

Y. Wu, A. Ghitani, R. Christensen, A. Santella, Z. Du, G. Rondeau, Z. Bao, D. Colón-Ramos, and H. Shroff, “Inverted selective plane illumination microscopy (iSPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans,” Proc. Natl. Acad. Sci. U.S.A. 108(43), 17708–17713 (2011).
[Crossref] [PubMed]

Silvestri, L.

Solgaard, O.

J. T. C. Liu, M. J. Mandella, N. O. Loewke, H. Haeberle, H. Ra, W. Piyawattanametha, O. Solgaard, G. S. Kino, and C. H. Contag, “Micromirror-scanned dual-axis confocal microscope utilizing a gradient-index relay lens for image guidance during brain surgery,” J. Biomed. Opt. 15(2), 026029 (2010).
[Crossref] [PubMed]

Spears, J. R.

Stakic, M.

P. N. Hedde, M. Stakic, and E. Gratton, “Rapid measurement of molecular transport and interaction inside living cells using single plane illumination,” Sci. Rep. 4, 7048 (2014).
[Crossref] [PubMed]

Stelzer, E. H.

P. J. Keller, A. D. Schmidt, J. Wittbrodt, and E. H. Stelzer, “Digital scanned laser light-sheet fluorescence microscopy (DSLM) of zebrafish and Drosophila embryonic development,” Cold Spring Harb. Protoc. 2011(10), 1235–1243 (2011).
[Crossref] [PubMed]

C. J. Engelbrecht and E. H. Stelzer, “Resolution enhancement in a light-sheet-based microscope (SPIM),” Opt. Lett. 31(10), 1477–1479 (2006).
[Crossref] [PubMed]

Stelzer, E. H. K.

P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. K. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods 7(8), 637–642 (2010).
[Crossref] [PubMed]

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

E. H. K. Stelzer, S. Lindek, S. Albrecht, R. Pick, G. Ritter, N. J. Salmon, and R. Stricker, “A New Tool for the Observation of Embryos and Other Large Specimens - Confocal Theta-Fluorescence Microscopy,” J Microsc-Oxford 179(1), 1–10 (1995).
[Crossref]

Stricker, R.

E. H. K. Stelzer, S. Lindek, S. Albrecht, R. Pick, G. Ritter, N. J. Salmon, and R. Stricker, “A New Tool for the Observation of Embryos and Other Large Specimens - Confocal Theta-Fluorescence Microscopy,” J Microsc-Oxford 179(1), 1–10 (1995).
[Crossref]

Swoger, J.

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Taflove, A.

Thomas, R. J.

Venugopalan, V.

A. R. Gardner, C. K. Hayakawa, and V. Venugopalan, “Coupled forward-adjoint Monte Carlo simulation of spatial-angular light fields to determine optical sensitivity in turbid media,” J. Biomed. Opt. 19(6), 065003 (2014).
[Crossref] [PubMed]

Vettenburg, T.

T. Vettenburg, H. I. Dalgarno, J. Nylk, C. Coll-Lladó, D. E. Ferrier, T. Čižmár, F. J. Gunn-Moore, and K. Dholakia, “Light-sheet microscopy using an Airy beam,” Nat. Methods 11(5), 541–544 (2014).
[Crossref] [PubMed]

Wang, D.

Wang, L.

L. Wang, S. L. Jacques, and L. Zheng, “MCML--Monte Carlo modeling of light transport in multi-layered tissues,” Comput. Methods Programs Biomed. 47(2), 131–146 (1995).
[Crossref] [PubMed]

Wang, L. V.

L. Gao, L. Zhu, C. Li, and L. V. Wang, “Nonlinear light-sheet fluorescence microscopy by photobleaching imprinting,” J. R. Soc. Interface 11(93), 20130851 (2014).
[Crossref] [PubMed]

Wang, T. D.

J. T. C. Liu, M. J. Mandella, J. M. Crawford, C. H. Contag, T. D. Wang, and G. S. Kino, “Efficient rejection of scattered light enables deep optical sectioning in turbid media with low-numerical-aperture optics in a dual-axis confocal architecture,” J. Biomed. Opt. 13(3), 034020 (2008).
[Crossref] [PubMed]

T. D. Wang, M. J. Mandella, C. H. Contag, and G. S. Kino, “Dual-axis confocal microscope for high-resolution in vivo imaging,” Opt. Lett. 28(6), 414–416 (2003).
[Crossref] [PubMed]

Wang, Y.

Webb, R. H.

Weber, M.

M. Weber and J. Huisken, “Light sheet microscopy for real-time developmental biology,” Curr. Opin. Genet. Dev. 21(5), 566–572 (2011).
[Crossref] [PubMed]

Wilson, B.

Wittbrodt, J.

P. J. Keller, A. D. Schmidt, J. Wittbrodt, and E. H. Stelzer, “Digital scanned laser light-sheet fluorescence microscopy (DSLM) of zebrafish and Drosophila embryonic development,” Cold Spring Harb. Protoc. 2011(10), 1235–1243 (2011).
[Crossref] [PubMed]

P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. K. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods 7(8), 637–642 (2010).
[Crossref] [PubMed]

J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science 305(5686), 1007–1009 (2004).
[Crossref] [PubMed]

Wu, Y.

Y. Wu, A. Ghitani, R. Christensen, A. Santella, Z. Du, G. Rondeau, Z. Bao, D. Colón-Ramos, and H. Shroff, “Inverted selective plane illumination microscopy (iSPIM) enables coupled cell identity lineaging and neurodevelopmental imaging in Caenorhabditis elegans,” Proc. Natl. Acad. Sci. U.S.A. 108(43), 17708–17713 (2011).
[Crossref] [PubMed]

Xia, F.

Yakovlev, V. V.

Yang, Z.

Yin, C.

Zanacchi, F. C.

Zhang, R.

Zheng, L.

L. Wang, S. L. Jacques, and L. Zheng, “MCML--Monte Carlo modeling of light transport in multi-layered tissues,” Comput. Methods Programs Biomed. 47(2), 131–146 (1995).
[Crossref] [PubMed]

Zhu, L.

L. Gao, L. Zhu, C. Li, and L. V. Wang, “Nonlinear light-sheet fluorescence microscopy by photobleaching imprinting,” J. R. Soc. Interface 11(93), 20130851 (2014).
[Crossref] [PubMed]

Zieglgänsberger, W.

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

Zollars, B.

Anal. Cell Pathol. (Amst.) (1)

J. T. C. Liu, N. O. Loewke, M. J. Mandella, R. M. Levenson, J. M. Crawford, and C. H. Contag, “Point-of-care pathology with miniature microscopes,” Anal. Cell Pathol. (Amst.) 34(3), 81–98 (2011).
[Crossref] [PubMed]

Appl. Opt. (2)

Appl. Phys. B (1)

P. K. Milsom, “A ray-optic, Monte Carlo, description of a Gaussian beam waist - applied to reverse saturable absorption,” Appl. Phys. B 70(4), 593–599 (2000).
[Crossref]

Biomed. Opt. Express (6)

BMC Bioinformatics (1)

M. Abdellah, A. Bilgili, S. Eilemann, H. Markram, and F. Schürmann, “Physically-based in silico light sheet microscopy for visualizing fluorescent brain models,” BMC Bioinformatics 16(Suppl 11), S8 (2015).
[Crossref] [PubMed]

Cold Spring Harb. Protoc. (1)

P. J. Keller, A. D. Schmidt, J. Wittbrodt, and E. H. Stelzer, “Digital scanned laser light-sheet fluorescence microscopy (DSLM) of zebrafish and Drosophila embryonic development,” Cold Spring Harb. Protoc. 2011(10), 1235–1243 (2011).
[Crossref] [PubMed]

Comput. Methods Programs Biomed. (1)

L. Wang, S. L. Jacques, and L. Zheng, “MCML--Monte Carlo modeling of light transport in multi-layered tissues,” Comput. Methods Programs Biomed. 47(2), 131–146 (1995).
[Crossref] [PubMed]

Curr. Opin. Genet. Dev. (1)

M. Weber and J. Huisken, “Light sheet microscopy for real-time developmental biology,” Curr. Opin. Genet. Dev. 21(5), 566–572 (2011).
[Crossref] [PubMed]

J Microsc-Oxford (1)

E. H. K. Stelzer, S. Lindek, S. Albrecht, R. Pick, G. Ritter, N. J. Salmon, and R. Stricker, “A New Tool for the Observation of Embryos and Other Large Specimens - Confocal Theta-Fluorescence Microscopy,” J Microsc-Oxford 179(1), 1–10 (1995).
[Crossref]

J. Biomed. Opt. (7)

J. T. C. Liu, M. J. Mandella, J. M. Crawford, C. H. Contag, T. D. Wang, and G. S. Kino, “Efficient rejection of scattered light enables deep optical sectioning in turbid media with low-numerical-aperture optics in a dual-axis confocal architecture,” J. Biomed. Opt. 13(3), 034020 (2008).
[Crossref] [PubMed]

J. T. C. Liu, M. J. Mandella, N. O. Loewke, H. Haeberle, H. Ra, W. Piyawattanametha, O. Solgaard, G. S. Kino, and C. H. Contag, “Micromirror-scanned dual-axis confocal microscope utilizing a gradient-index relay lens for image guidance during brain surgery,” J. Biomed. Opt. 15(2), 026029 (2010).
[Crossref] [PubMed]

J. A. Buytaert and J. J. Dirckx, “Design and quantitative resolution measurements of an optical virtual sectioning three-dimensional imaging technique for biomedical specimens, featuring two-micrometer slicing resolution,” J. Biomed. Opt. 12(1), 014039 (2007).
[Crossref] [PubMed]

Y. Chen and J. T. C. Liu, “Optimizing the performance of dual-axis confocal microscopes via Monte-Carlo scattering simulations and diffraction theory,” J. Biomed. Opt. 18(6), 066006 (2013).
[Crossref] [PubMed]

A. Elmaklizi, J. Schäfer, and A. Kienle, “Simulating the scanning of a focused beam through scattering media using a numerical solution of Maxwell’s equations,” J. Biomed. Opt. 19(7), 071404 (2014).
[Crossref] [PubMed]

A. Elmaklizi, D. Reitzle, A. Brandes, and A. Kienle, “Penetration depth of focused beams in highly scattering media investigated with a numerical solution of Maxwell’s equations in two dimensions,” J. Biomed. Opt. 20(6), 065007 (2015).
[Crossref] [PubMed]

A. R. Gardner, C. K. Hayakawa, and V. Venugopalan, “Coupled forward-adjoint Monte Carlo simulation of spatial-angular light fields to determine optical sensitivity in turbid media,” J. Biomed. Opt. 19(6), 065003 (2014).
[Crossref] [PubMed]

J. Histochem. Cytochem. (1)

P. A. Santi, “Light sheet fluorescence microscopy: a review,” J. Histochem. Cytochem. 59(2), 129–138 (2011).
[Crossref] [PubMed]

J. Microsc. (1)

E. Mei, P. A. Fomitchov, R. Graves, and M. Campion, “A line scanning confocal fluorescent microscope using a CMOS rolling shutter as an adjustable aperture,” J. Microsc. 247(3), 269–276 (2012).
[Crossref] [PubMed]

J. R. Soc. Interface (1)

L. Gao, L. Zhu, C. Li, and L. V. Wang, “Nonlinear light-sheet fluorescence microscopy by photobleaching imprinting,” J. R. Soc. Interface 11(93), 20130851 (2014).
[Crossref] [PubMed]

Med. Phys. (1)

J. Chen and X. Intes, “Comparison of Monte Carlo methods for fluorescence molecular tomography-computational efficiency,” Med. Phys. 38(10), 5788–5798 (2011).
[Crossref] [PubMed]

Nat. Commun. (1)

F. O. Fahrbach and A. Rohrbach, “Propagation stability of self-reconstructing Bessel beams enables contrast-enhanced imaging in thick media,” Nat. Commun. 3, 632 (2012).
[Crossref] [PubMed]

Nat. Methods (5)

T. Vettenburg, H. I. Dalgarno, J. Nylk, C. Coll-Lladó, D. E. Ferrier, T. Čižmár, F. J. Gunn-Moore, and K. Dholakia, “Light-sheet microscopy using an Airy beam,” Nat. Methods 11(5), 541–544 (2014).
[Crossref] [PubMed]

J. Mertz, “Optical sectioning microscopy with planar or structured illumination,” Nat. Methods 8(10), 811–819 (2011).
[Crossref] [PubMed]

H. U. Dodt, U. Leischner, A. Schierloh, N. Jährling, C. P. Mauch, K. Deininger, J. M. Deussing, M. Eder, W. Zieglgänsberger, and K. Becker, “Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain,” Nat. Methods 4(4), 331–336 (2007).
[Crossref] [PubMed]

P. J. Keller, A. D. Schmidt, A. Santella, K. Khairy, Z. Bao, J. Wittbrodt, and E. H. K. Stelzer, “Fast, high-contrast imaging of animal development with scanned light sheet-based structured-illumination microscopy,” Nat. Methods 7(8), 637–642 (2010).
[Crossref] [PubMed]

T. A. Planchon, L. Gao, D. E. Milkie, M. W. Davidson, J. A. Galbraith, C. G. Galbraith, and E. Betzig, “Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination,” Nat. Methods 8(5), 417–423 (2011).
[Crossref] [PubMed]

Nucl Instrum Meth A (1)

P. Arce, J. I. Lagares, L. Harkness, D. Perez-Astudillo, M. Canadas, P. Rato, M. de Prado, Y. Abreu, G. de Lorenzo, M. Kolstein, and A. Diaz, “GAMOS: A framework to do GEANT4 simulations in different physics fields with an user-friendly interface,” Nucl Instrum Meth A 735, 304–313 (2014).
[Crossref]

Opt. Express (8)

L. Silvestri, A. Bria, L. Sacconi, G. Iannello, and F. S. Pavone, “Confocal light sheet microscopy: micron-scale neuroanatomy of the entire mouse brain,” Opt. Express 20(18), 20582–20598 (2012).
[Crossref] [PubMed]

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Figures (7)

Fig. 1
Fig. 1 The illumination, collection, focal volume, and detector configurations for the PS-DAC, LS-DAC, WF-LSM, and CL-LSM microscope geometries. In (a), the PS-DAC geometry uses a moderate numerical aperture to illuminate a single point within the tissue, and a similar collection NA to image that point to a pinhole detector. In (b), the LS-DAC geometry uses a moderate illumination NA focused to a line, rather than a point within the tissue volume. This focal line is then imaged onto a linear detector array. In (c), the WF-LSM geometry uses a low illumination NA to provide a sheet of illumination (a low-NA line focus) within the tissue volume, which is imaged with a higher NA onto a two-dimensional (2D) image sensor. In (d), the CL-LSM geometry is shown, in which an illumination sheet identical to that in (c) is created over time by scanning a low-NA point-focused illumination beam, which is synchronized with the rolling shutter (line-by-line acquisition) of a 2D image sensor.
Fig. 2
Fig. 2 The general microscope geometry for the DAC and LSM methods is shown. The illumination beam (blue) enters the tissue from the left, at an angle θ from the normal, along the illumination coordinate axes denoted by xi, yi, and zi. Similarly, light is collected (green) to the right at an angle θ from the normal, along the collection coordinate axes xc, yc, and zc. The effective focal volume is shown for illustrative purposes (yellow). The numerical aperture of each optical path is given by NAi and NAc respectively, which dictates the corresponding beam waists, wo,i and wo,c and Rayleigh ranges zR,i and zR,c. Both beams are focused at a depth, zf, into tissue with scattering coefficient μs, and scattering anisotropy, g. The coordinate axes of the tissue are given by x, y, and z.
Fig. 3
Fig. 3 In (a) and (b), the illumination beam thickness, 2wo and depth of focus, 2zR are plotted for the PS-DAC, LS-DAC, WF-LSM, and CL-LSM microscope geometries, respectively.
Fig. 4
Fig. 4 In (a), using a ray-optics model that accurately simulates Gaussian beam profiles, the irradiance profile is simulated at the focal plane of a beam with NAx = NAy = 0.10 at λ = 500 nm, along with plots of the x and y line profiles through the focus. The measured beam waists, wo,x = wo,y = 1.60 μm, are in close agreement to the expected beam waist of 1.59 μm. In (b), the principle of the adjoint method is shown, where the PSF, Si,c is calculated by multiplying the illumination fluence, Si, by the reversed collection fluence, Sc.
Fig. 5
Fig. 5 In (a), the PSFs, Si,c(x,y,z,L), are shown for the WF-LSM geometry. Each is self-normalized and displayed on a dB scale (10log10) down to −30 dB (10−3). In (b), the corresponding x, y, and z line profiles through the focus are plotted for each optical length, L. The corresponding axial scans Si,c(z,L) are shown in (c). In (d), the contrast (SBR) of the PS-DAC, LS-DAC, WF-LSM, and CL-LSM are plotted as a function of optical length. The scale bar in (a) represents 20 μm.
Fig. 6
Fig. 6 For each microscopy method, x-y sections of a fluorescent bead phantom, convolved with the appropriate PSF, are shown in (a), self normalized to a maximum value of 1.0. In (b) and (c), the calculated contrast of the images is plotted, as well as the decay in the peak signal of the PSFs as a function of optical length. The scale bar in (a) represents 20 μm.
Fig. 7
Fig. 7 Image contrast values as a function of optical length in the fluorescent bead phantom are plotted for: (a) WF-LSM as a function of NAi for a fixed NAc = 0.30, (b) WF-LSM as a function of NAc for a fixed NAi = 0.03, (c) CL-LSM as a function of NAi for a fixed NAc = 0.30, (b) CL-LSM as a function of NAc for a fixed NAi = 0.03. For (a-b), the dashed line represents the performance of LS-DAC where NAi = NAc = 0.20, and in (c-d) the dashed line represents the performance of PS-DAC where NAi = NAc = 0.20.

Tables (2)

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Table 1 Summary of simulation parameters used for each microscope geometry at λ = 500 nm

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Table 2 Summary of the FWHM values as a function of NAi and NAc for WF-LSM for the x (top), y (middle), and z (bottom) directions

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