N. Patwary and C. Preza, “Image restoration for three-dimensional fluorescence microscopy using an orthonormal basis for efficient representation of depth-variant point-spread functions,” Biomed. Opt. Express 6, 3826–3841 (2015).

[Crossref]

S. V. King, A. Doblas, N. Patwary, G. Saavedra, M. Martínez-Corral, and C. Preza, “Spatial light modulator phase mask implementation of wavefront encoded 3D computational-optical microscopy,” Appl. Opt. 54, 8587–8595 (2015).

[Crossref]

A. Doblas, S. V. King, N. Patwary, G. Saavedra, M. Martínez-Corral, and C. Preza, “Investigation of the SQUBIC phase mask design for depth-invariant widefield microscopy point-spread function engineering,” Proc. SPIE 8949, 894914 (2014).

[Crossref]

G. Saavedra, I. Escobar, R. Martínez-Cuenca, E. Sánchez-Ortiga, and M. Martínez-Corra, “Reduction of spherical-aberration impact in microscopy by wavefront coding,” Opt. Express 17, 13810–13818 (2009).

[Crossref]

M. Bertero, P. Boccacci, G. Desiderà, and G. Vicidomini, “Image deblurring with Poisson data: from cells to galaxies,” Inverse Probl. 25, 123006 (2009).

[Crossref]

O. Haeberlé, “Focusing of light through a stratified medium: a practical approach for computing microscope point spread functions. Part I: conventional microscopy,” Opt. Commun. 216, 55–63 (2003).

[Crossref]

J.-A. Conchello and J. G. McNally, “Fast regularization technique for expectation maximization algorithm for optical sectioning microscopy,” Proc. SPIE 2655, 199–208 (1996).

[Crossref]

D. A. Agard, Y. Hiraoka, P. Sha, and J. W. Sedat, “Fluorescence microscopy in three dimensions,” Methods Cell Biol. 30, 353–377 (1989).

[Crossref]

D. A. Agard, “Optical sectioning microscopy: cellular architecture in three dimensions,” Annu. Rev. Biophys. Bioeng. 13, 191–219 (1984).

[Crossref]

I. J. Good, “Non-parametric roughness penalty for probability densities,” Nat. Phys. Sci. 229, 29–30 (1971).

[Crossref]

M. Arigovindan, J. Shaevitz, J. McGowan, J. W. Sedat, and D. A. Agard, “A parallel product-convolution approach for representing the depth varying point spread functions in 3D widefield microscopy based on principal component analysis,” Opt. Express 18, 6461–6476 (2010).

[Crossref]

D. A. Agard, Y. Hiraoka, P. Sha, and J. W. Sedat, “Fluorescence microscopy in three dimensions,” Methods Cell Biol. 30, 353–377 (1989).

[Crossref]

D. A. Agard, “Optical sectioning microscopy: cellular architecture in three dimensions,” Annu. Rev. Biophys. Bioeng. 13, 191–219 (1984).

[Crossref]

J. R. Swedlow, J. W. Sedat, and D. A. Agard, “Deconvolution in optical microscopy,” in Deconvolution of Images and Spectra (Academic, 1997), Chap. 9.

S. Ben Hadj, L. Blanc-Féraud, G. Aubert, and G. Engler, “Blind restoration of confocal microscopy images in presence of a depth-variant blur and Poisson noise,” in Proceedings of IEEE International Conference on Acoustics, Speech and Signal Processing (IEEE, 2013), pp. 915–919.

S. Bäumer, Handbook of Plastic Optics (Wiley, 2011).

S. Ben Hadj, L. Blanc-Féraud, G. Aubert, and G. Engler, “Blind restoration of confocal microscopy images in presence of a depth-variant blur and Poisson noise,” in Proceedings of IEEE International Conference on Acoustics, Speech and Signal Processing (IEEE, 2013), pp. 915–919.

M. Bertero, P. Boccacci, G. Desiderà, and G. Vicidomini, “Image deblurring with Poisson data: from cells to galaxies,” Inverse Probl. 25, 123006 (2009).

[Crossref]

S. Ben Hadj, L. Blanc-Féraud, G. Aubert, and G. Engler, “Blind restoration of confocal microscopy images in presence of a depth-variant blur and Poisson noise,” in Proceedings of IEEE International Conference on Acoustics, Speech and Signal Processing (IEEE, 2013), pp. 915–919.

M. Bertero, P. Boccacci, G. Desiderà, and G. Vicidomini, “Image deblurring with Poisson data: from cells to galaxies,” Inverse Probl. 25, 123006 (2009).

[Crossref]

Z. Wang, A. C. Bovik, H. R. Sheikh, and E. P. Simoncelli, “Image quality assessment: from error visibility to structural similarity,” IEEE Trans. Image Process. 13, 600–612 (2004).

[Crossref]

M. Bertero, P. Boccacci, G. Desiderà, and G. Vicidomini, “Image deblurring with Poisson data: from cells to galaxies,” Inverse Probl. 25, 123006 (2009).

[Crossref]

S. V. King, A. Doblas, N. Patwary, G. Saavedra, M. Martínez-Corral, and C. Preza, “Spatial light modulator phase mask implementation of wavefront encoded 3D computational-optical microscopy,” Appl. Opt. 54, 8587–8595 (2015).

[Crossref]

A. Doblas, S. V. King, N. Patwary, G. Saavedra, M. Martínez-Corral, and C. Preza, “Investigation of the SQUBIC phase mask design for depth-invariant widefield microscopy point-spread function engineering,” Proc. SPIE 8949, 894914 (2014).

[Crossref]

S. Ben Hadj, L. Blanc-Féraud, G. Aubert, and G. Engler, “Blind restoration of confocal microscopy images in presence of a depth-variant blur and Poisson noise,” in Proceedings of IEEE International Conference on Acoustics, Speech and Signal Processing (IEEE, 2013), pp. 915–919.

S. Ghosh and C. Preza, “Three-dimensional block-based restoration integrated with wide-field fluorescence microscopy for the investigation of thick specimens with spatially variant refractive index,” J. Biomed. Opt. 21, 046010 (2016).

[Crossref]

I. J. Good, “Non-parametric roughness penalty for probability densities,” Nat. Phys. Sci. 229, 29–30 (1971).

[Crossref]

O. Haeberlé, “Focusing of light through a stratified medium: a practical approach for computing microscope point spread functions. Part I: conventional microscopy,” Opt. Commun. 216, 55–63 (2003).

[Crossref]

D. A. Agard, Y. Hiraoka, P. Sha, and J. W. Sedat, “Fluorescence microscopy in three dimensions,” Methods Cell Biol. 30, 353–377 (1989).

[Crossref]

N. Patwary, S. V. King, G. Saavedra, and C. Preza, “Reducing effects of aberration in 3D fluorescence imaging using wavefront coding with a radially symmetric phase mask,” Opt. Express 24, 12905–12921 (2016).

[Crossref]

S. V. King, A. Doblas, N. Patwary, G. Saavedra, M. Martínez-Corral, and C. Preza, “Spatial light modulator phase mask implementation of wavefront encoded 3D computational-optical microscopy,” Appl. Opt. 54, 8587–8595 (2015).

[Crossref]

A. Doblas, S. V. King, N. Patwary, G. Saavedra, M. Martínez-Corral, and C. Preza, “Investigation of the SQUBIC phase mask design for depth-invariant widefield microscopy point-spread function engineering,” Proc. SPIE 8949, 894914 (2014).

[Crossref]

N. Patwary, S. V. King, H. Shabani, and C. Preza, “Experimental implementation of wavefront encoding in 3D widefield fluorescence microscopy using a fabricated phase mask designed to reduce system depth variability,” in Classical Optics 2014, OSA Technical Digest (online) (2016), paper CW2D-3.

S. V. King, A. Doblas, N. Patwary, G. Saavedra, M. Martínez-Corral, and C. Preza, “Spatial light modulator phase mask implementation of wavefront encoded 3D computational-optical microscopy,” Appl. Opt. 54, 8587–8595 (2015).

[Crossref]

A. Doblas, S. V. King, N. Patwary, G. Saavedra, M. Martínez-Corral, and C. Preza, “Investigation of the SQUBIC phase mask design for depth-invariant widefield microscopy point-spread function engineering,” Proc. SPIE 8949, 894914 (2014).

[Crossref]

J.-A. Conchello and J. G. McNally, “Fast regularization technique for expectation maximization algorithm for optical sectioning microscopy,” Proc. SPIE 2655, 199–208 (1996).

[Crossref]

N. Patwary, S. V. King, G. Saavedra, and C. Preza, “Reducing effects of aberration in 3D fluorescence imaging using wavefront coding with a radially symmetric phase mask,” Opt. Express 24, 12905–12921 (2016).

[Crossref]

N. Patwary and C. Preza, “Image restoration for three-dimensional fluorescence microscopy using an orthonormal basis for efficient representation of depth-variant point-spread functions,” Biomed. Opt. Express 6, 3826–3841 (2015).

[Crossref]

S. V. King, A. Doblas, N. Patwary, G. Saavedra, M. Martínez-Corral, and C. Preza, “Spatial light modulator phase mask implementation of wavefront encoded 3D computational-optical microscopy,” Appl. Opt. 54, 8587–8595 (2015).

[Crossref]

A. Doblas, S. V. King, N. Patwary, G. Saavedra, M. Martínez-Corral, and C. Preza, “Investigation of the SQUBIC phase mask design for depth-invariant widefield microscopy point-spread function engineering,” Proc. SPIE 8949, 894914 (2014).

[Crossref]

N. Patwary, S. V. King, H. Shabani, and C. Preza, “Experimental implementation of wavefront encoding in 3D widefield fluorescence microscopy using a fabricated phase mask designed to reduce system depth variability,” in Classical Optics 2014, OSA Technical Digest (online) (2016), paper CW2D-3.

N. Patwary, S. V. King, G. Saavedra, and C. Preza, “Reducing effects of aberration in 3D fluorescence imaging using wavefront coding with a radially symmetric phase mask,” Opt. Express 24, 12905–12921 (2016).

[Crossref]

S. Ghosh and C. Preza, “Three-dimensional block-based restoration integrated with wide-field fluorescence microscopy for the investigation of thick specimens with spatially variant refractive index,” J. Biomed. Opt. 21, 046010 (2016).

[Crossref]

S. V. King, A. Doblas, N. Patwary, G. Saavedra, M. Martínez-Corral, and C. Preza, “Spatial light modulator phase mask implementation of wavefront encoded 3D computational-optical microscopy,” Appl. Opt. 54, 8587–8595 (2015).

[Crossref]

N. Patwary and C. Preza, “Image restoration for three-dimensional fluorescence microscopy using an orthonormal basis for efficient representation of depth-variant point-spread functions,” Biomed. Opt. Express 6, 3826–3841 (2015).

[Crossref]

A. Doblas, S. V. King, N. Patwary, G. Saavedra, M. Martínez-Corral, and C. Preza, “Investigation of the SQUBIC phase mask design for depth-invariant widefield microscopy point-spread function engineering,” Proc. SPIE 8949, 894914 (2014).

[Crossref]

S. Yuan and C. Preza, “Point-spread function engineering to reduce the impact of spherical aberration on 3D computational fluorescence microscopy imaging,” Opt. Express 19, 23298–23314 (2011).

[Crossref]

C. Preza and J.-A. Conchello, “Depth-variant maximum-likelihood restoration for three-dimensional fluorescence microscopy,” J. Opt. Soc. Am. A 21, 1593–1601 (2004).

[Crossref]

N. Patwary, S. V. King, H. Shabani, and C. Preza, “Experimental implementation of wavefront encoding in 3D widefield fluorescence microscopy using a fabricated phase mask designed to reduce system depth variability,” in Classical Optics 2014, OSA Technical Digest (online) (2016), paper CW2D-3.

N. Patwary, S. V. King, G. Saavedra, and C. Preza, “Reducing effects of aberration in 3D fluorescence imaging using wavefront coding with a radially symmetric phase mask,” Opt. Express 24, 12905–12921 (2016).

[Crossref]

S. V. King, A. Doblas, N. Patwary, G. Saavedra, M. Martínez-Corral, and C. Preza, “Spatial light modulator phase mask implementation of wavefront encoded 3D computational-optical microscopy,” Appl. Opt. 54, 8587–8595 (2015).

[Crossref]

A. Doblas, S. V. King, N. Patwary, G. Saavedra, M. Martínez-Corral, and C. Preza, “Investigation of the SQUBIC phase mask design for depth-invariant widefield microscopy point-spread function engineering,” Proc. SPIE 8949, 894914 (2014).

[Crossref]

G. Saavedra, I. Escobar, R. Martínez-Cuenca, E. Sánchez-Ortiga, and M. Martínez-Corra, “Reduction of spherical-aberration impact in microscopy by wavefront coding,” Opt. Express 17, 13810–13818 (2009).

[Crossref]

B. E. A. Saleh and M. C. Teich, Fundamentals of Photonics (Wiley, 1991).

M. Arigovindan, J. Shaevitz, J. McGowan, J. W. Sedat, and D. A. Agard, “A parallel product-convolution approach for representing the depth varying point spread functions in 3D widefield microscopy based on principal component analysis,” Opt. Express 18, 6461–6476 (2010).

[Crossref]

D. A. Agard, Y. Hiraoka, P. Sha, and J. W. Sedat, “Fluorescence microscopy in three dimensions,” Methods Cell Biol. 30, 353–377 (1989).

[Crossref]

J. R. Swedlow, J. W. Sedat, and D. A. Agard, “Deconvolution in optical microscopy,” in Deconvolution of Images and Spectra (Academic, 1997), Chap. 9.

D. A. Agard, Y. Hiraoka, P. Sha, and J. W. Sedat, “Fluorescence microscopy in three dimensions,” Methods Cell Biol. 30, 353–377 (1989).

[Crossref]

N. Patwary, S. V. King, H. Shabani, and C. Preza, “Experimental implementation of wavefront encoding in 3D widefield fluorescence microscopy using a fabricated phase mask designed to reduce system depth variability,” in Classical Optics 2014, OSA Technical Digest (online) (2016), paper CW2D-3.

Z. Wang, A. C. Bovik, H. R. Sheikh, and E. P. Simoncelli, “Image quality assessment: from error visibility to structural similarity,” IEEE Trans. Image Process. 13, 600–612 (2004).

[Crossref]

Z. Wang, A. C. Bovik, H. R. Sheikh, and E. P. Simoncelli, “Image quality assessment: from error visibility to structural similarity,” IEEE Trans. Image Process. 13, 600–612 (2004).

[Crossref]

J. R. Swedlow, J. W. Sedat, and D. A. Agard, “Deconvolution in optical microscopy,” in Deconvolution of Images and Spectra (Academic, 1997), Chap. 9.

B. E. A. Saleh and M. C. Teich, Fundamentals of Photonics (Wiley, 1991).

M. Bertero, P. Boccacci, G. Desiderà, and G. Vicidomini, “Image deblurring with Poisson data: from cells to galaxies,” Inverse Probl. 25, 123006 (2009).

[Crossref]

Z. Wang, A. C. Bovik, H. R. Sheikh, and E. P. Simoncelli, “Image quality assessment: from error visibility to structural similarity,” IEEE Trans. Image Process. 13, 600–612 (2004).

[Crossref]

D. A. Agard, “Optical sectioning microscopy: cellular architecture in three dimensions,” Annu. Rev. Biophys. Bioeng. 13, 191–219 (1984).

[Crossref]

E. R. Dowski and W. T. Cathey, “Extended depth of field through wave-front coding,” Appl. Opt. 34, 1859–1866 (1995).

[Crossref]

S. V. King, A. Doblas, N. Patwary, G. Saavedra, M. Martínez-Corral, and C. Preza, “Spatial light modulator phase mask implementation of wavefront encoded 3D computational-optical microscopy,” Appl. Opt. 54, 8587–8595 (2015).

[Crossref]

Z. Wang, A. C. Bovik, H. R. Sheikh, and E. P. Simoncelli, “Image quality assessment: from error visibility to structural similarity,” IEEE Trans. Image Process. 13, 600–612 (2004).

[Crossref]

M. Bertero, P. Boccacci, G. Desiderà, and G. Vicidomini, “Image deblurring with Poisson data: from cells to galaxies,” Inverse Probl. 25, 123006 (2009).

[Crossref]

S. Ghosh and C. Preza, “Three-dimensional block-based restoration integrated with wide-field fluorescence microscopy for the investigation of thick specimens with spatially variant refractive index,” J. Biomed. Opt. 21, 046010 (2016).

[Crossref]

J.-A. Conchello, “Superresolution and convergence properties of the expectation-maximization algorithm for maximum-likelihood deconvolution of incoherent images,” J. Opt. Soc. Am. A 15, 2609–2619 (1998).

[Crossref]

S. F. Gibson and F. Lanni, “Experimental test of an analytical model of aberration in an oil-immersion objective lens used in three-dimensional light microscopy,” J. Opt. Soc. Am. A 9, 154–166 (1992).

[Crossref]

D. L. Snyder, A. M. Hammoud, and R. L. White, “Image recovery from data acquired with a charge-coupled-device camera,” J. Opt. Soc. Am. A 10, 1014–1023 (1993).

[Crossref]

C. Preza and J.-A. Conchello, “Depth-variant maximum-likelihood restoration for three-dimensional fluorescence microscopy,” J. Opt. Soc. Am. A 21, 1593–1601 (2004).

[Crossref]

D. A. Agard, Y. Hiraoka, P. Sha, and J. W. Sedat, “Fluorescence microscopy in three dimensions,” Methods Cell Biol. 30, 353–377 (1989).

[Crossref]

I. J. Good, “Non-parametric roughness penalty for probability densities,” Nat. Phys. Sci. 229, 29–30 (1971).

[Crossref]

O. Haeberlé, “Focusing of light through a stratified medium: a practical approach for computing microscope point spread functions. Part I: conventional microscopy,” Opt. Commun. 216, 55–63 (2003).

[Crossref]

G. Saavedra, I. Escobar, R. Martínez-Cuenca, E. Sánchez-Ortiga, and M. Martínez-Corra, “Reduction of spherical-aberration impact in microscopy by wavefront coding,” Opt. Express 17, 13810–13818 (2009).

[Crossref]

M. Arigovindan, J. Shaevitz, J. McGowan, J. W. Sedat, and D. A. Agard, “A parallel product-convolution approach for representing the depth varying point spread functions in 3D widefield microscopy based on principal component analysis,” Opt. Express 18, 6461–6476 (2010).

[Crossref]

S. Yuan and C. Preza, “Point-spread function engineering to reduce the impact of spherical aberration on 3D computational fluorescence microscopy imaging,” Opt. Express 19, 23298–23314 (2011).

[Crossref]

N. Patwary, S. V. King, G. Saavedra, and C. Preza, “Reducing effects of aberration in 3D fluorescence imaging using wavefront coding with a radially symmetric phase mask,” Opt. Express 24, 12905–12921 (2016).

[Crossref]

J.-A. Conchello and J. G. McNally, “Fast regularization technique for expectation maximization algorithm for optical sectioning microscopy,” Proc. SPIE 2655, 199–208 (1996).

[Crossref]

A. Doblas, S. V. King, N. Patwary, G. Saavedra, M. Martínez-Corral, and C. Preza, “Investigation of the SQUBIC phase mask design for depth-invariant widefield microscopy point-spread function engineering,” Proc. SPIE 8949, 894914 (2014).

[Crossref]

Computational Imaging Research Laboratory, Computational Optical Sectioning Microscopy Open Source (COSMOS) software package; http://cirl.memphis.edu/COSMOS .

J. R. Swedlow, J. W. Sedat, and D. A. Agard, “Deconvolution in optical microscopy,” in Deconvolution of Images and Spectra (Academic, 1997), Chap. 9.

S. Ben Hadj, L. Blanc-Féraud, G. Aubert, and G. Engler, “Blind restoration of confocal microscopy images in presence of a depth-variant blur and Poisson noise,” in Proceedings of IEEE International Conference on Acoustics, Speech and Signal Processing (IEEE, 2013), pp. 915–919.

N. Patwary, S. V. King, H. Shabani, and C. Preza, “Experimental implementation of wavefront encoding in 3D widefield fluorescence microscopy using a fabricated phase mask designed to reduce system depth variability,” in Classical Optics 2014, OSA Technical Digest (online) (2016), paper CW2D-3.

S. Bäumer, Handbook of Plastic Optics (Wiley, 2011).

B. E. A. Saleh and M. C. Teich, Fundamentals of Photonics (Wiley, 1991).