Abstract

Light sheet fluorescence microscopy has become one of the most widely used techniques for three-dimensional imaging due to its high speed and low phototoxicity. Further improvements in 3D microscopy require limiting the light exposure of the sample and increasing the volumetric acquisition rate. We hereby present an imaging technique that allows volumetric reconstruction of the fluorescent sample using spatial modulation on a selective illumination volume. We demonstrate that this can be implemented using an incoherent LED source, avoiding shadowing artifacts, typical of light sheet microscopy. Furthermore, we show that spatial modulation allows the use of Compressive Sensing, reducing the number of modulation patterns to be acquired. We present results on zebrafish embryos which prove that selective spatial modulation can be used to reconstruct relatively large volumes without any mechanical movement. The technique yields an accurate reconstruction of the sample anatomy even at significant compression ratios, achieving higher volumetric acquisition rate and reducing photodamage biological samples.

© 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

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References

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2018 (6)

O. E. Olarte, J. Andilla, E. J. Gualda, and P. Loza-Alvarez, “Light-sheet microscopy: a tutorial,” Adv. Opt. Photonics 10(1), 111 (2018).
[Crossref]

T. V. Truong, D. B. Holland, S. Madaan, A. Andreev, J. V. Troll, D. E. S. Koo, K. Keomanee-Dizon, M. McFall-Ngai, and S. E. Fraser, “Selective volume illumination microscopy offers synchronous volumetric imaging with high contrast,” bioRxiv Ill, 403303 (2018).

J. Mayer, A. Robert-Moreno, J. Sharpe, and J. Swoger, “Attenuation artifacts in light sheet fluorescence microscopy corrected by OPTiSPIM,” Light: Sci. Appl. 7(1), 70 (2018).
[Crossref]

A. K. Glaser, Y. Chen, C. Yin, L. Wei, L. A. Barner, N. P. Reder, and J. T. C. Liu, “Multidirectional digital scanned light-sheet microscopy enables uniform fluorescence excitation and contrast-enhanced imaging,” Sci. Rep. 8(1), 13878 (2018).
[Crossref]

C. Garbellotto and J. M. Taylor, “Multi-purpose SLM-light-sheet microscope,” Biomed. Opt. Express 9(11), 5419 (2018).
[Crossref]

R. M. Power and J. Huisken, “Adaptable, illumination patterning light sheet microscopy,” Sci. Rep. 8(1), 9615 (2018).
[Crossref]

2017 (3)

2016 (5)

E. McLeod and A. Ozcan, “Unconventional methods of imaging: computational microscopy and compact implementations,” Rep. Prog. Phys. 79(7), 076001 (2016).
[Crossref]

A. Candeo, I. Sana, E. Ferrari, L. Maiuri, C. D’Andrea, G. Valentini, and A. Bassi, “Virtual unfolding of light sheet fluorescence microscopy dataset for quantitative analysis of the mouse intestine,” J. Biomed. Opt. 21(5), 056001 (2016).
[Crossref]

N. C. Pégard, H.-Y. Liu, N. Antipa, M. Gerlock, H. Adesnik, and L. Waller, “Compressive light-field microscopy for 3D neural activity recording,” Optica 3(5), 517 (2016).
[Crossref]

F. Soldevila, P. Clemente, E. Tajahuerce, N. Uribe-Patarroyo, P. Andrés, and J. Lancis, “Computational imaging with a balanced detector,” Sci. Rep. 6(1), 29181 (2016).
[Crossref]

N. Huynh, E. Zhang, M. Betcke, S. Arridge, P. Beard, and B. Cox, “Single-pixel optical camera for video rate ultrasonic imaging,” Optica 3(1), 26 (2016).
[Crossref]

2015 (4)

L. Gao, “Extend the field of view of selective plan illumination microscopy by tiling the excitation light sheet,” Opt. Express 23(5), 6102 (2015).
[Crossref]

K. M. Dean, P. Roudot, E. S. Welf, G. Danuser, and R. Fiolka, “Deconvolution-free Subcellular Imaging with Axially Swept Light Sheet Microscopy,” Biophys. J. 108(12), 2807–2815 (2015).
[Crossref]

O. E. Olarte, J. Andilla, D. Artigas, and P. Loza-Alvarez, “Decoupled illumination detection in light sheet microscopy for fast volumetric imaging,” Optica 2(8), 702 (2015).
[Crossref]

R. Tomer, M. Lovett-Barron, I. Kauvar, A. Andalman, V. M. Burns, S. Sankaran, L. Grosenick, M. Broxton, S. Yang, and K. Deisseroth, “SPED Light Sheet Microscopy: Fast Mapping of Biological System Structure and Function,” Cell 163(7), 1796–1806 (2015).
[Crossref]

2014 (3)

B. Judkewitz and C. Yang, “Axial standing-wave illumination frequency-domain imaging (SWIF),” Opt. Express 22(9), 11001 (2014).
[Crossref]

E. J. Candes and M. B. Wakin, “An Introduction to Compressive Sensing,” IEEE Signal Process. Mag. 25(2), 1–118 (2014).

L. Gao, J. Liang, C. Li, and L. V. Wang, “Single-shot compressed ultrafast photography at one hundred billion frames per second,” Nature 516(7529), 74–77 (2014).
[Crossref]

2013 (3)

2012 (1)

V. Studer, J. Bobin, M. Chahid, H. S. Mousavi, E. Candes, and M. Dahan, “Compressive fluorescence microscopy for biological and hyperspectral imaging,” Proc. Natl. Acad. Sci. 109(26), E1679–E1687 (2012).
[Crossref]

2011 (1)

A. Bassi, L. Fieramonti, C. D’Andrea, M. Mione, and G. Valentini, “In vivo label-free three-dimensional imaging of zebrafish vasculature with optical projection tomography,” J. Biomed. Opt. 16(10), 100502 (2011).
[Crossref]

2010 (3)

Y. Wu, P. Ye, I. O. Mirza, G. R. Arce, and D. W. Prather, “Experimental demonstration of an Optical-Sectioning Compressive Sensing Microscope (CSM),” Opt. Express 18(24), 24565 (2010).
[Crossref]

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]

U. Leischner, A. Schierloh, W. Zieglgänsberger, and H.-U. Dodt, “Formalin-Induced Fluorescence Reveals Cell Shape and Morphology in Biological Tissue Samples,” PLoS One 5(4), e10391 (2010).
[Crossref]

2008 (2)

M. F. Duarte, M. A. Davenport, D. Takhar, J. N. Laska, T. Sun, K. F. Kelly, and R. G. Baraniuk, “Single-pixel imaging via compressive sampling,” IEEE Signal Process. Mag. 25(2), 83–91 (2008).
[Crossref]

E. J. Candes and M. B. Wakin, “An Introduction To Compressive Sampling,” IEEE Signal Process. Mag. 25(2), 21–30 (2008).
[Crossref]

2007 (3)

R. Baraniuk, “Compressive Sensing [Lecture Notes],” IEEE Signal Process. Mag. 24(4), 118–121 (2007).
[Crossref]

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]

J. Huisken and D. Y. R. Stainier, “Even fluorescence excitation by multidirectional selective plane illumination microscopy (mSPIM),” Opt. Lett. 32(17), 2608 (2007).
[Crossref]

2005 (2)

E. J. Candes and T. Tao, “Decoding by Linear Programming,” IEEE Trans. Inf. Theory 51(12), 4203–4215 (2005).
[Crossref]

M. G. L. Gustafsson, “Nonlinear structured-illumination microscopy: Wide-field fluorescence imaging with theoretically unlimited resolution,” Proc. Natl. Acad. Sci. 102(37), 13081–13086 (2005).
[Crossref]

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]

1997 (1)

1992 (1)

L. I. Rudin, S. Osher, and E. Fatemi, “Nonlinear total variation based noise removal algorithms,” Phys. D (Amsterdam, Neth.) 60(1-4), 259–268 (1992).
[Crossref]

Adesnik, H.

Alessandri, K.

Andalman, A.

R. Tomer, M. Lovett-Barron, I. Kauvar, A. Andalman, V. M. Burns, S. Sankaran, L. Grosenick, M. Broxton, S. Yang, and K. Deisseroth, “SPED Light Sheet Microscopy: Fast Mapping of Biological System Structure and Function,” Cell 163(7), 1796–1806 (2015).
[Crossref]

Andilla, J.

O. E. Olarte, J. Andilla, E. J. Gualda, and P. Loza-Alvarez, “Light-sheet microscopy: a tutorial,” Adv. Opt. Photonics 10(1), 111 (2018).
[Crossref]

O. E. Olarte, J. Andilla, D. Artigas, and P. Loza-Alvarez, “Decoupled illumination detection in light sheet microscopy for fast volumetric imaging,” Optica 2(8), 702 (2015).
[Crossref]

Andreev, A.

T. V. Truong, D. B. Holland, S. Madaan, A. Andreev, J. V. Troll, D. E. S. Koo, K. Keomanee-Dizon, M. McFall-Ngai, and S. E. Fraser, “Selective volume illumination microscopy offers synchronous volumetric imaging with high contrast,” bioRxiv Ill, 403303 (2018).

Andrés, P.

F. Soldevila, P. Clemente, E. Tajahuerce, N. Uribe-Patarroyo, P. Andrés, and J. Lancis, “Computational imaging with a balanced detector,” Sci. Rep. 6(1), 29181 (2016).
[Crossref]

P. Clemente, V. Durán, E. Tajahuerce, P. Andrés, V. Climent, and J. Lancis, “Compressive holography with a single-pixel detector,” Opt. Lett. 38(14), 2524 (2013).
[Crossref]

Antipa, N.

Arce, G. R.

Arridge, S.

Artigas, D.

Bao, Z.

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]

Baraniuk, R.

R. Baraniuk, “Compressive Sensing [Lecture Notes],” IEEE Signal Process. Mag. 24(4), 118–121 (2007).
[Crossref]

Baraniuk, R. G.

M. F. Duarte, M. A. Davenport, D. Takhar, J. N. Laska, T. Sun, K. F. Kelly, and R. G. Baraniuk, “Single-pixel imaging via compressive sampling,” IEEE Signal Process. Mag. 25(2), 83–91 (2008).
[Crossref]

Barner, L. A.

A. K. Glaser, Y. Chen, C. Yin, L. Wei, L. A. Barner, N. P. Reder, and J. T. C. Liu, “Multidirectional digital scanned light-sheet microscopy enables uniform fluorescence excitation and contrast-enhanced imaging,” Sci. Rep. 8(1), 13878 (2018).
[Crossref]

Bassi, A.

A. Candeo, I. Sana, E. Ferrari, L. Maiuri, C. D’Andrea, G. Valentini, and A. Bassi, “Virtual unfolding of light sheet fluorescence microscopy dataset for quantitative analysis of the mouse intestine,” J. Biomed. Opt. 21(5), 056001 (2016).
[Crossref]

A. Bassi, L. Fieramonti, C. D’Andrea, M. Mione, and G. Valentini, “In vivo label-free three-dimensional imaging of zebrafish vasculature with optical projection tomography,” J. Biomed. Opt. 16(10), 100502 (2011).
[Crossref]

Beard, P.

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]

Betcke, M.

Bobin, J.

V. Studer, J. Bobin, M. Chahid, H. S. Mousavi, E. Candes, and M. Dahan, “Compressive fluorescence microscopy for biological and hyperspectral imaging,” Proc. Natl. Acad. Sci. 109(26), E1679–E1687 (2012).
[Crossref]

Bolus, D.

Brown, J. Q.

Broxton, M.

R. Tomer, M. Lovett-Barron, I. Kauvar, A. Andalman, V. M. Burns, S. Sankaran, L. Grosenick, M. Broxton, S. Yang, and K. Deisseroth, “SPED Light Sheet Microscopy: Fast Mapping of Biological System Structure and Function,” Cell 163(7), 1796–1806 (2015).
[Crossref]

Burns, V. M.

R. Tomer, M. Lovett-Barron, I. Kauvar, A. Andalman, V. M. Burns, S. Sankaran, L. Grosenick, M. Broxton, S. Yang, and K. Deisseroth, “SPED Light Sheet Microscopy: Fast Mapping of Biological System Structure and Function,” Cell 163(7), 1796–1806 (2015).
[Crossref]

Candeo, A.

A. Candeo, I. Sana, E. Ferrari, L. Maiuri, C. D’Andrea, G. Valentini, and A. Bassi, “Virtual unfolding of light sheet fluorescence microscopy dataset for quantitative analysis of the mouse intestine,” J. Biomed. Opt. 21(5), 056001 (2016).
[Crossref]

Candes, E.

V. Studer, J. Bobin, M. Chahid, H. S. Mousavi, E. Candes, and M. Dahan, “Compressive fluorescence microscopy for biological and hyperspectral imaging,” Proc. Natl. Acad. Sci. 109(26), E1679–E1687 (2012).
[Crossref]

Candes, E. J.

E. J. Candes and M. B. Wakin, “An Introduction to Compressive Sensing,” IEEE Signal Process. Mag. 25(2), 1–118 (2014).

E. J. Candes and M. B. Wakin, “An Introduction To Compressive Sampling,” IEEE Signal Process. Mag. 25(2), 21–30 (2008).
[Crossref]

E. J. Candes and T. Tao, “Decoding by Linear Programming,” IEEE Trans. Inf. Theory 51(12), 4203–4215 (2005).
[Crossref]

Chahid, M.

V. Studer, J. Bobin, M. Chahid, H. S. Mousavi, E. Candes, and M. Dahan, “Compressive fluorescence microscopy for biological and hyperspectral imaging,” Proc. Natl. Acad. Sci. 109(26), E1679–E1687 (2012).
[Crossref]

Chang, B.-J.

B.-J. Chang, V. D. Perez Meza, and E. H. K. Stelzer, “csiLSFM combines light-sheet fluorescence microscopy and coherent structured illumination for a lateral resolution below 100 nm,” Proc. Natl. Acad. Sci. 114(19), 4869–4874 (2017).
[Crossref]

Chen, Y.

A. K. Glaser, Y. Chen, C. Yin, L. Wei, L. A. Barner, N. P. Reder, and J. T. C. Liu, “Multidirectional digital scanned light-sheet microscopy enables uniform fluorescence excitation and contrast-enhanced imaging,” Sci. Rep. 8(1), 13878 (2018).
[Crossref]

Clemente, P.

F. Soldevila, P. Clemente, E. Tajahuerce, N. Uribe-Patarroyo, P. Andrés, and J. Lancis, “Computational imaging with a balanced detector,” Sci. Rep. 6(1), 29181 (2016).
[Crossref]

P. Clemente, V. Durán, E. Tajahuerce, P. Andrés, V. Climent, and J. Lancis, “Compressive holography with a single-pixel detector,” Opt. Lett. 38(14), 2524 (2013).
[Crossref]

Climent, V.

Cox, B.

D’Andrea, C.

A. Candeo, I. Sana, E. Ferrari, L. Maiuri, C. D’Andrea, G. Valentini, and A. Bassi, “Virtual unfolding of light sheet fluorescence microscopy dataset for quantitative analysis of the mouse intestine,” J. Biomed. Opt. 21(5), 056001 (2016).
[Crossref]

A. Bassi, L. Fieramonti, C. D’Andrea, M. Mione, and G. Valentini, “In vivo label-free three-dimensional imaging of zebrafish vasculature with optical projection tomography,” J. Biomed. Opt. 16(10), 100502 (2011).
[Crossref]

Dahan, M.

V. Studer, J. Bobin, M. Chahid, H. S. Mousavi, E. Candes, and M. Dahan, “Compressive fluorescence microscopy for biological and hyperspectral imaging,” Proc. Natl. Acad. Sci. 109(26), E1679–E1687 (2012).
[Crossref]

Danuser, G.

K. M. Dean, P. Roudot, E. S. Welf, G. Danuser, and R. Fiolka, “Deconvolution-free Subcellular Imaging with Axially Swept Light Sheet Microscopy,” Biophys. J. 108(12), 2807–2815 (2015).
[Crossref]

Darzacq, X.

Davenport, M. A.

M. F. Duarte, M. A. Davenport, D. Takhar, J. N. Laska, T. Sun, K. F. Kelly, and R. G. Baraniuk, “Single-pixel imaging via compressive sampling,” IEEE Signal Process. Mag. 25(2), 83–91 (2008).
[Crossref]

Dean, K. M.

K. M. Dean, P. Roudot, E. S. Welf, G. Danuser, and R. Fiolka, “Deconvolution-free Subcellular Imaging with Axially Swept Light Sheet Microscopy,” Biophys. J. 108(12), 2807–2815 (2015).
[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).
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R. Tomer, M. Lovett-Barron, I. Kauvar, A. Andalman, V. M. Burns, S. Sankaran, L. Grosenick, M. Broxton, S. Yang, and K. Deisseroth, “SPED Light Sheet Microscopy: Fast Mapping of Biological System Structure and Function,” Cell 163(7), 1796–1806 (2015).
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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).
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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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U. Leischner, A. Schierloh, W. Zieglgänsberger, and H.-U. Dodt, “Formalin-Induced Fluorescence Reveals Cell Shape and Morphology in Biological Tissue Samples,” PLoS One 5(4), e10391 (2010).
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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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M. F. Duarte, M. A. Davenport, D. Takhar, J. N. Laska, T. Sun, K. F. Kelly, and R. G. Baraniuk, “Single-pixel imaging via compressive sampling,” IEEE Signal Process. Mag. 25(2), 83–91 (2008).
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Eder, 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]

Fahrbach, F. O.

Fatemi, E.

L. I. Rudin, S. Osher, and E. Fatemi, “Nonlinear total variation based noise removal algorithms,” Phys. D (Amsterdam, Neth.) 60(1-4), 259–268 (1992).
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A. Candeo, I. Sana, E. Ferrari, L. Maiuri, C. D’Andrea, G. Valentini, and A. Bassi, “Virtual unfolding of light sheet fluorescence microscopy dataset for quantitative analysis of the mouse intestine,” J. Biomed. Opt. 21(5), 056001 (2016).
[Crossref]

Fieramonti, L.

A. Bassi, L. Fieramonti, C. D’Andrea, M. Mione, and G. Valentini, “In vivo label-free three-dimensional imaging of zebrafish vasculature with optical projection tomography,” J. Biomed. Opt. 16(10), 100502 (2011).
[Crossref]

Fiolka, R.

K. M. Dean, P. Roudot, E. S. Welf, G. Danuser, and R. Fiolka, “Deconvolution-free Subcellular Imaging with Axially Swept Light Sheet Microscopy,” Biophys. J. 108(12), 2807–2815 (2015).
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Fraser, S. E.

T. V. Truong, D. B. Holland, S. Madaan, A. Andreev, J. V. Troll, D. E. S. Koo, K. Keomanee-Dizon, M. McFall-Ngai, and S. E. Fraser, “Selective volume illumination microscopy offers synchronous volumetric imaging with high contrast,” bioRxiv Ill, 403303 (2018).

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L. Gao, “Extend the field of view of selective plan illumination microscopy by tiling the excitation light sheet,” Opt. Express 23(5), 6102 (2015).
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L. Gao, J. Liang, C. Li, and L. V. Wang, “Single-shot compressed ultrafast photography at one hundred billion frames per second,” Nature 516(7529), 74–77 (2014).
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Gerlock, M.

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A. K. Glaser, Y. Chen, C. Yin, L. Wei, L. A. Barner, N. P. Reder, and J. T. C. Liu, “Multidirectional digital scanned light-sheet microscopy enables uniform fluorescence excitation and contrast-enhanced imaging,” Sci. Rep. 8(1), 13878 (2018).
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R. Tomer, M. Lovett-Barron, I. Kauvar, A. Andalman, V. M. Burns, S. Sankaran, L. Grosenick, M. Broxton, S. Yang, and K. Deisseroth, “SPED Light Sheet Microscopy: Fast Mapping of Biological System Structure and Function,” Cell 163(7), 1796–1806 (2015).
[Crossref]

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O. E. Olarte, J. Andilla, E. J. Gualda, and P. Loza-Alvarez, “Light-sheet microscopy: a tutorial,” Adv. Opt. Photonics 10(1), 111 (2018).
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M. Harwit and N. J. A. Sloane, Hadamard Transform Optics (Elsevier, 1979).

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T. V. Truong, D. B. Holland, S. Madaan, A. Andreev, J. V. Troll, D. E. S. Koo, K. Keomanee-Dizon, M. McFall-Ngai, and S. E. Fraser, “Selective volume illumination microscopy offers synchronous volumetric imaging with high contrast,” bioRxiv Ill, 403303 (2018).

Hu, B.

Huang, G.

G. Huang, H. Jiang, K. Matthews, and P. Wilford, “Lensless imaging by compressive sensing,” in 2013 IEEE International Conference on Image Processing (IEEE, 2013), pp. 2101–2105.

Huisken, J.

R. M. Power and J. Huisken, “Adaptable, illumination patterning light sheet microscopy,” Sci. Rep. 8(1), 9615 (2018).
[Crossref]

J. Huisken and D. Y. R. Stainier, “Even fluorescence excitation by multidirectional selective plane illumination microscopy (mSPIM),” Opt. Lett. 32(17), 2608 (2007).
[Crossref]

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]

Huynh, N.

Jährling, N.

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]

Jiang, H.

C. Li, W. Yin, H. Jiang, and Y. Zhang, “An efficient augmented Lagrangian method with applications to total variation minimization,” Comput. Optim. Appl. 56(3), 507–530 (2013).
[Crossref]

G. Huang, H. Jiang, K. Matthews, and P. Wilford, “Lensless imaging by compressive sensing,” in 2013 IEEE International Conference on Image Processing (IEEE, 2013), pp. 2101–2105.

Judkewitz, B.

Juškaitis, R.

Kauvar, I.

R. Tomer, M. Lovett-Barron, I. Kauvar, A. Andalman, V. M. Burns, S. Sankaran, L. Grosenick, M. Broxton, S. Yang, and K. Deisseroth, “SPED Light Sheet Microscopy: Fast Mapping of Biological System Structure and Function,” Cell 163(7), 1796–1806 (2015).
[Crossref]

Keller, P. J.

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]

Kelly, K. F.

M. F. Duarte, M. A. Davenport, D. Takhar, J. N. Laska, T. Sun, K. F. Kelly, and R. G. Baraniuk, “Single-pixel imaging via compressive sampling,” IEEE Signal Process. Mag. 25(2), 83–91 (2008).
[Crossref]

Keomanee-Dizon, K.

T. V. Truong, D. B. Holland, S. Madaan, A. Andreev, J. V. Troll, D. E. S. Koo, K. Keomanee-Dizon, M. McFall-Ngai, and S. E. Fraser, “Selective volume illumination microscopy offers synchronous volumetric imaging with high contrast,” bioRxiv Ill, 403303 (2018).

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).
[Crossref]

Koo, D. E. S.

T. V. Truong, D. B. Holland, S. Madaan, A. Andreev, J. V. Troll, D. E. S. Koo, K. Keomanee-Dizon, M. McFall-Ngai, and S. E. Fraser, “Selective volume illumination microscopy offers synchronous volumetric imaging with high contrast,” bioRxiv Ill, 403303 (2018).

Lancis, J.

F. Soldevila, P. Clemente, E. Tajahuerce, N. Uribe-Patarroyo, P. Andrés, and J. Lancis, “Computational imaging with a balanced detector,” Sci. Rep. 6(1), 29181 (2016).
[Crossref]

P. Clemente, V. Durán, E. Tajahuerce, P. Andrés, V. Climent, and J. Lancis, “Compressive holography with a single-pixel detector,” Opt. Lett. 38(14), 2524 (2013).
[Crossref]

Laska, J. N.

M. F. Duarte, M. A. Davenport, D. Takhar, J. N. Laska, T. Sun, K. F. Kelly, and R. G. Baraniuk, “Single-pixel imaging via compressive sampling,” IEEE Signal Process. Mag. 25(2), 83–91 (2008).
[Crossref]

Leischner, U.

U. Leischner, A. Schierloh, W. Zieglgänsberger, and H.-U. Dodt, “Formalin-Induced Fluorescence Reveals Cell Shape and Morphology in Biological Tissue Samples,” PLoS One 5(4), e10391 (2010).
[Crossref]

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]

Li, C.

L. Gao, J. Liang, C. Li, and L. V. Wang, “Single-shot compressed ultrafast photography at one hundred billion frames per second,” Nature 516(7529), 74–77 (2014).
[Crossref]

C. Li, W. Yin, H. Jiang, and Y. Zhang, “An efficient augmented Lagrangian method with applications to total variation minimization,” Comput. Optim. Appl. 56(3), 507–530 (2013).
[Crossref]

Liang, J.

L. Gao, J. Liang, C. Li, and L. V. Wang, “Single-shot compressed ultrafast photography at one hundred billion frames per second,” Nature 516(7529), 74–77 (2014).
[Crossref]

Liu, H.-Y.

Liu, J. T. C.

A. K. Glaser, Y. Chen, C. Yin, L. Wei, L. A. Barner, N. P. Reder, and J. T. C. Liu, “Multidirectional digital scanned light-sheet microscopy enables uniform fluorescence excitation and contrast-enhanced imaging,” Sci. Rep. 8(1), 13878 (2018).
[Crossref]

Lovett-Barron, M.

R. Tomer, M. Lovett-Barron, I. Kauvar, A. Andalman, V. M. Burns, S. Sankaran, L. Grosenick, M. Broxton, S. Yang, and K. Deisseroth, “SPED Light Sheet Microscopy: Fast Mapping of Biological System Structure and Function,” Cell 163(7), 1796–1806 (2015).
[Crossref]

Loza-Alvarez, P.

O. E. Olarte, J. Andilla, E. J. Gualda, and P. Loza-Alvarez, “Light-sheet microscopy: a tutorial,” Adv. Opt. Photonics 10(1), 111 (2018).
[Crossref]

O. E. Olarte, J. Andilla, D. Artigas, and P. Loza-Alvarez, “Decoupled illumination detection in light sheet microscopy for fast volumetric imaging,” Optica 2(8), 702 (2015).
[Crossref]

Madaan, S.

T. V. Truong, D. B. Holland, S. Madaan, A. Andreev, J. V. Troll, D. E. S. Koo, K. Keomanee-Dizon, M. McFall-Ngai, and S. E. Fraser, “Selective volume illumination microscopy offers synchronous volumetric imaging with high contrast,” bioRxiv Ill, 403303 (2018).

Maiuri, L.

A. Candeo, I. Sana, E. Ferrari, L. Maiuri, C. D’Andrea, G. Valentini, and A. Bassi, “Virtual unfolding of light sheet fluorescence microscopy dataset for quantitative analysis of the mouse intestine,” J. Biomed. Opt. 21(5), 056001 (2016).
[Crossref]

Matthews, K.

G. Huang, H. Jiang, K. Matthews, and P. Wilford, “Lensless imaging by compressive sensing,” in 2013 IEEE International Conference on Image Processing (IEEE, 2013), pp. 2101–2105.

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]

Mayer, J.

J. Mayer, A. Robert-Moreno, J. Sharpe, and J. Swoger, “Attenuation artifacts in light sheet fluorescence microscopy corrected by OPTiSPIM,” Light: Sci. Appl. 7(1), 70 (2018).
[Crossref]

McFall-Ngai, M.

T. V. Truong, D. B. Holland, S. Madaan, A. Andreev, J. V. Troll, D. E. S. Koo, K. Keomanee-Dizon, M. McFall-Ngai, and S. E. Fraser, “Selective volume illumination microscopy offers synchronous volumetric imaging with high contrast,” bioRxiv Ill, 403303 (2018).

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E. McLeod and A. Ozcan, “Unconventional methods of imaging: computational microscopy and compact implementations,” Rep. Prog. Phys. 79(7), 076001 (2016).
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Mione, M.

A. Bassi, L. Fieramonti, C. D’Andrea, M. Mione, and G. Valentini, “In vivo label-free three-dimensional imaging of zebrafish vasculature with optical projection tomography,” J. Biomed. Opt. 16(10), 100502 (2011).
[Crossref]

Mir, M.

Mirza, I. O.

Mousavi, H. S.

V. Studer, J. Bobin, M. Chahid, H. S. Mousavi, E. Candes, and M. Dahan, “Compressive fluorescence microscopy for biological and hyperspectral imaging,” Proc. Natl. Acad. Sci. 109(26), E1679–E1687 (2012).
[Crossref]

Nassoy, P.

Neil, M. A. A.

Olarte, O. E.

O. E. Olarte, J. Andilla, E. J. Gualda, and P. Loza-Alvarez, “Light-sheet microscopy: a tutorial,” Adv. Opt. Photonics 10(1), 111 (2018).
[Crossref]

O. E. Olarte, J. Andilla, D. Artigas, and P. Loza-Alvarez, “Decoupled illumination detection in light sheet microscopy for fast volumetric imaging,” Optica 2(8), 702 (2015).
[Crossref]

Osher, S.

L. I. Rudin, S. Osher, and E. Fatemi, “Nonlinear total variation based noise removal algorithms,” Phys. D (Amsterdam, Neth.) 60(1-4), 259–268 (1992).
[Crossref]

Ozcan, A.

E. McLeod and A. Ozcan, “Unconventional methods of imaging: computational microscopy and compact implementations,” Rep. Prog. Phys. 79(7), 076001 (2016).
[Crossref]

Pégard, N. C.

Perez Meza, V. D.

B.-J. Chang, V. D. Perez Meza, and E. H. K. Stelzer, “csiLSFM combines light-sheet fluorescence microscopy and coherent structured illumination for a lateral resolution below 100 nm,” Proc. Natl. Acad. Sci. 114(19), 4869–4874 (2017).
[Crossref]

Power, R. M.

R. M. Power and J. Huisken, “Adaptable, illumination patterning light sheet microscopy,” Sci. Rep. 8(1), 9615 (2018).
[Crossref]

Prather, D. W.

Reder, N. P.

A. K. Glaser, Y. Chen, C. Yin, L. Wei, L. A. Barner, N. P. Reder, and J. T. C. Liu, “Multidirectional digital scanned light-sheet microscopy enables uniform fluorescence excitation and contrast-enhanced imaging,” Sci. Rep. 8(1), 13878 (2018).
[Crossref]

Robert-Moreno, A.

J. Mayer, A. Robert-Moreno, J. Sharpe, and J. Swoger, “Attenuation artifacts in light sheet fluorescence microscopy corrected by OPTiSPIM,” Light: Sci. Appl. 7(1), 70 (2018).
[Crossref]

Rohrbach, A.

Roudot, P.

K. M. Dean, P. Roudot, E. S. Welf, G. Danuser, and R. Fiolka, “Deconvolution-free Subcellular Imaging with Axially Swept Light Sheet Microscopy,” Biophys. J. 108(12), 2807–2815 (2015).
[Crossref]

Rudin, L. I.

L. I. Rudin, S. Osher, and E. Fatemi, “Nonlinear total variation based noise removal algorithms,” Phys. D (Amsterdam, Neth.) 60(1-4), 259–268 (1992).
[Crossref]

Sana, I.

A. Candeo, I. Sana, E. Ferrari, L. Maiuri, C. D’Andrea, G. Valentini, and A. Bassi, “Virtual unfolding of light sheet fluorescence microscopy dataset for quantitative analysis of the mouse intestine,” J. Biomed. Opt. 21(5), 056001 (2016).
[Crossref]

Sankaran, S.

R. Tomer, M. Lovett-Barron, I. Kauvar, A. Andalman, V. M. Burns, S. Sankaran, L. Grosenick, M. Broxton, S. Yang, and K. Deisseroth, “SPED Light Sheet Microscopy: Fast Mapping of Biological System Structure and Function,” Cell 163(7), 1796–1806 (2015).
[Crossref]

Santella, A.

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]

Schierloh, A.

U. Leischner, A. Schierloh, W. Zieglgänsberger, and H.-U. Dodt, “Formalin-Induced Fluorescence Reveals Cell Shape and Morphology in Biological Tissue Samples,” PLoS One 5(4), e10391 (2010).
[Crossref]

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]

Schmidt, A. D.

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]

Sharpe, J.

J. Mayer, A. Robert-Moreno, J. Sharpe, and J. Swoger, “Attenuation artifacts in light sheet fluorescence microscopy corrected by OPTiSPIM,” Light: Sci. Appl. 7(1), 70 (2018).
[Crossref]

Sloane, N. J. A.

M. Harwit and N. J. A. Sloane, Hadamard Transform Optics (Elsevier, 1979).

Soldevila, F.

F. Soldevila, P. Clemente, E. Tajahuerce, N. Uribe-Patarroyo, P. Andrés, and J. Lancis, “Computational imaging with a balanced detector,” Sci. Rep. 6(1), 29181 (2016).
[Crossref]

Stainier, D. Y. R.

Stelzer, E. H. K.

B.-J. Chang, V. D. Perez Meza, and E. H. K. Stelzer, “csiLSFM combines light-sheet fluorescence microscopy and coherent structured illumination for a lateral resolution below 100 nm,” Proc. Natl. Acad. Sci. 114(19), 4869–4874 (2017).
[Crossref]

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]

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]

Studer, V.

V. Studer, J. Bobin, M. Chahid, H. S. Mousavi, E. Candes, and M. Dahan, “Compressive fluorescence microscopy for biological and hyperspectral imaging,” Proc. Natl. Acad. Sci. 109(26), E1679–E1687 (2012).
[Crossref]

Sun, T.

M. F. Duarte, M. A. Davenport, D. Takhar, J. N. Laska, T. Sun, K. F. Kelly, and R. G. Baraniuk, “Single-pixel imaging via compressive sampling,” IEEE Signal Process. Mag. 25(2), 83–91 (2008).
[Crossref]

Swoger, J.

J. Mayer, A. Robert-Moreno, J. Sharpe, and J. Swoger, “Attenuation artifacts in light sheet fluorescence microscopy corrected by OPTiSPIM,” Light: Sci. Appl. 7(1), 70 (2018).
[Crossref]

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]

Tajahuerce, E.

F. Soldevila, P. Clemente, E. Tajahuerce, N. Uribe-Patarroyo, P. Andrés, and J. Lancis, “Computational imaging with a balanced detector,” Sci. Rep. 6(1), 29181 (2016).
[Crossref]

P. Clemente, V. Durán, E. Tajahuerce, P. Andrés, V. Climent, and J. Lancis, “Compressive holography with a single-pixel detector,” Opt. Lett. 38(14), 2524 (2013).
[Crossref]

Takhar, D.

M. F. Duarte, M. A. Davenport, D. Takhar, J. N. Laska, T. Sun, K. F. Kelly, and R. G. Baraniuk, “Single-pixel imaging via compressive sampling,” IEEE Signal Process. Mag. 25(2), 83–91 (2008).
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E. J. Candes and T. Tao, “Decoding by Linear Programming,” IEEE Trans. Inf. Theory 51(12), 4203–4215 (2005).
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Tomer, R.

R. Tomer, M. Lovett-Barron, I. Kauvar, A. Andalman, V. M. Burns, S. Sankaran, L. Grosenick, M. Broxton, S. Yang, and K. Deisseroth, “SPED Light Sheet Microscopy: Fast Mapping of Biological System Structure and Function,” Cell 163(7), 1796–1806 (2015).
[Crossref]

Troll, J. V.

T. V. Truong, D. B. Holland, S. Madaan, A. Andreev, J. V. Troll, D. E. S. Koo, K. Keomanee-Dizon, M. McFall-Ngai, and S. E. Fraser, “Selective volume illumination microscopy offers synchronous volumetric imaging with high contrast,” bioRxiv Ill, 403303 (2018).

Truong, T. V.

T. V. Truong, D. B. Holland, S. Madaan, A. Andreev, J. V. Troll, D. E. S. Koo, K. Keomanee-Dizon, M. McFall-Ngai, and S. E. Fraser, “Selective volume illumination microscopy offers synchronous volumetric imaging with high contrast,” bioRxiv Ill, 403303 (2018).

Uribe-Patarroyo, N.

F. Soldevila, P. Clemente, E. Tajahuerce, N. Uribe-Patarroyo, P. Andrés, and J. Lancis, “Computational imaging with a balanced detector,” Sci. Rep. 6(1), 29181 (2016).
[Crossref]

Valentini, G.

A. Candeo, I. Sana, E. Ferrari, L. Maiuri, C. D’Andrea, G. Valentini, and A. Bassi, “Virtual unfolding of light sheet fluorescence microscopy dataset for quantitative analysis of the mouse intestine,” J. Biomed. Opt. 21(5), 056001 (2016).
[Crossref]

A. Bassi, L. Fieramonti, C. D’Andrea, M. Mione, and G. Valentini, “In vivo label-free three-dimensional imaging of zebrafish vasculature with optical projection tomography,” J. Biomed. Opt. 16(10), 100502 (2011).
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Waller, L.

Wang, L. V.

L. Gao, J. Liang, C. Li, and L. V. Wang, “Single-shot compressed ultrafast photography at one hundred billion frames per second,” Nature 516(7529), 74–77 (2014).
[Crossref]

Wei, L.

A. K. Glaser, Y. Chen, C. Yin, L. Wei, L. A. Barner, N. P. Reder, and J. T. C. Liu, “Multidirectional digital scanned light-sheet microscopy enables uniform fluorescence excitation and contrast-enhanced imaging,” Sci. Rep. 8(1), 13878 (2018).
[Crossref]

Welf, E. S.

K. M. Dean, P. Roudot, E. S. Welf, G. Danuser, and R. Fiolka, “Deconvolution-free Subcellular Imaging with Axially Swept Light Sheet Microscopy,” Biophys. J. 108(12), 2807–2815 (2015).
[Crossref]

Wilford, P.

G. Huang, H. Jiang, K. Matthews, and P. Wilford, “Lensless imaging by compressive sensing,” in 2013 IEEE International Conference on Image Processing (IEEE, 2013), pp. 2101–2105.

Wilson, T.

Wittbrodt, J.

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Supplementary Material (2)

NameDescription
» Visualization 1       Visualization 1): The video shows the modulation patterns displayed one after the other on the DMD.The modulation occurs along the entire y extension of the LED spot, over a region 64 pixels thick.
» Visualization 2       Visualization 2): 128 Raw images acquired upon patterned modulation of a Tg(kdrl:GFP) Zebrafish

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Figures (7)

Fig. 1.
Fig. 1. (a) Schematic representation of light sheet illumination and detection. (b) Spatial modulation in Selective Volume Illumination. (c) Scheme of the experimental setup. Light from the LED impinges on a Digital Micromirror Device, which spatially modulates light according to a binary pattern (schematically represented in the figure below). Reflected light is collected and refocused over the illumination volume by two objective lenses. The fluorescence signal is collected by a wide field microscope. The coordinate reference system in shown in the top right corner.
Fig. 2.
Fig. 2. Imaging of fluorescent beads for evaluation of the working volume. Scale bar is 100µm. (a) Reconstructed single plane (xy plane) upon acquisition with sm-SVI. (b) Transverse view (xz).of the reconstructed beads sample. The volume where the resolution ±$\sqrt 2 $ δr laterally and ±$\sqrt 2 $ δz axially, is indicated by the red box. (c) Bead intensity profile along x and z in the centre of the measured volume (green arrow). The FWHM is 2.3µm laterally, and 2.9µm axially. (d) Lateral and axial bead intensity profile, at the border of the red box (blue arrow).
Fig. 3.
Fig. 3. Comparison of SPIM and sm-SVI with incoherent illumination. Scale bar is 100µm. (a) Single plane acquired with SPIM of a Tg(α-actin:GFP) zebrafish tail. (b) Reconstructed plane in approximately the same location with sm-SVI.
Fig. 4.
Fig. 4. Reconstruction of a Tg(α-actin:GFP) zebrafish embryos. Scale bars are 100µm. (a) Plane by plane reconstruction at different depth: z = 0, z = 67µm, z = 134µm, from left to right. (b, c) Transverse sections of the sample acquired in frontal and sagittal positions. (d) Frontal Maximum Intensity Projections (e) Sagittal Maximum Intensity projection. (f, g) Details of the regions shown in the green and blue boxes.
Fig. 5.
Fig. 5. sm-SVI acquisition of a Tg(kdrl:GFP) zebrafish embryos. Scale bars are 100µm. (a) Maximum Intensity Projection of 3D reconstruction of the trunk and head region. (b) Detail of the blue box. (c) Single sagittal plane (d) Single frontal plane. The yellow lines indicate the corresponding position in the sagittal and frontal planes.
Fig. 6.
Fig. 6. Compressed volumetric reconstruction in a Tg(kdrl:GFP) zebrafish embryo at different undersampling ratio C. Scale bars are 100µm. Maximum intensity projection (left hand side of each panel) and single frontal plane (right hand side). The yellow line highlights the plane shown on the right-hand side. The red box is a detail of the Maximum Intensity Projection, for each panel. From left to right: reconstruction from complete Scrambled Hadamard measurement set and for compressing ratio of 2, 4, 8.
Fig. 7.
Fig. 7. Compressed volumetric reconstruction quality in a fluorescent beads sample at different compression ratio. Each panel shows a maximum intensity projection. From left to right: reconstruction from complete Scrambled Hadamard measurement set and for compressing ratio of 2, 4, 8. Scale bar is 100µm.

Equations (4)

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ξ ( x ¯ , y ¯ ) = A χ ( x ¯ , y ¯ )
ψ = a r g m i n ψ { 1 2 ∣∣ ξ A W ψ 2 2 + λ R ( ψ ) } , s . t . χ = W ψ ,
R ( x ) =∣∣ T V ( x )
χ = a r g m i n χ { μ 2 ∣∣ ξ A ( χ ) 2 2 + ∣∣ T V ( χ ) 2 } ,

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