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Research ArticleMethods/New Tools, Novel Tools and Methods

Realistic Numerical and Analytical Modeling of Light Scattering in Brain Tissue for Optogenetic Applications

Guy Yona, Nizan Meitav, Itamar Kahn and Shy Shoham
eNeuro 4 January 2016, 3 (1) ENEURO.0059-15.2015; DOI: https://doi.org/10.1523/ENEURO.0059-15.2015
Guy Yona
1Autonomous Systems Program (TASP)
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Nizan Meitav
2Faculty of Biomedical Engineering
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Itamar Kahn
3Rappaport Faculty of Medicine and Institute, Technion - Israel Institute of Technology, Haifa, 31096, Israel
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  • ORCID record for Itamar Kahn
Shy Shoham
2Faculty of Biomedical Engineering
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  • Figure 1.
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    Figure 1.

    Graphical depiction of the BSF calculation process: the distribution of the scattered photons ksc(z,ρ,τ) is a product of the spatial distribution h(z,ρ,τ) and the temporal dispersion distribution G(z,τ) (Eq. 1). The time-dependent distribution is integrated over time to obtain the intensity values ksc(z,ρ), and added to the distribution of the unscattered photons kusc(z,ρ) for the total distribution k(z,ρ) (Eq. 4), called the BSF. Note that the equations also include absorption effects that were omitted from the figure for simplicity.

  • Figure 2.
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    Figure 2.

    a, Simulation procedure: the 1st stage is the calculation of a 3D pencil-beam response, the 2nd stage is the angular convolution of the pencil beam response, and the 3rd stage is a spatial convolution with the fiber tip area. b, Simulation outcomes of the various simulation steps. For better visualization, all of the figures are in log scale. c, Illustration of the experimental setup cross-section.

  • Figure. 3.
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    Figure. 3.

    Comparisons of MC and BSF methods for two different tissue-scattering parameter settings: µs =168.6 cm−1 (top; from Al-Juboori et al. 2013) and µs =120 cm−1 (bottom; from Yaroslavsky et al. 2002). a, Contour maps of the light distribution in the tissue, created using the MC method. b, Contours created using the BSF method. The iso-intensity lines are at 50, 20, 5, and 1% of maximum. c, Light transmission curves along the z-axis.

  • Figure. 4.
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    Figure. 4.

    Transmission of light along the z-axis, comparing published experimental results (red dotted curves) with BSF method (blue curves). a, Best-fit curves to measured data from Aravanis et al. (2007). b, Experimental data from Al-Juboori et al. (2013) measured from the peduncopontine tegmental nucleus; the optical parameters used for the BSF curve are explained in the text.

  • Figure. 5.
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    Figure. 5.

    Experimental results: light transmission in a mouse cortex along the z-axis (a) and the radial axis (b) at 300 μm (blue) and 600 μm (red). The solid lines are the best fit of the BSF model. c, Surface plot of the simulated light distribution in the slice, obtained with BSF model using the experimentally estimated parameters (µs = 211 cm−1, g = 0.86), with overlaid experimental measurements (colors matched to a and b). Light transmission is in log scale. d, Contour map of the simulated light distribution.

Tables

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    Table 1.

    Brain tissue optical parameters

    SourceBrain sampleWavelength, nmScattering coefficient, cm−1Anisotropy factor
    Our experimentAdult mouse cortex, (5 months old)4732110.86
    Aravanis et al. (2007)Mouse cortex47360.70.885
    Al-Juboori et al. (2013)Mouse subcortical, (6–8 weeks old)453168.6—
    Azimipour et al. (2014)Rat cortex532∼170∼0.9
    Yaroslavsky et al. (2002)Human gray matter4801200.88
    • View popup
    Table 2.

    The illuminated tissue volumes for various commercial optical fibers

    Fiber propertiesVolume illuminated (10−3 Embedded Image mm3), %
    NADiameter, µm>50>20>5>1
    0.1250.020.040.090.20
    0.22500.060.140.340.79
    0.221050.290.681.483.28
    0.222001.072.565.5313.7
    0.223653.628.7119.561.7
    0.372001.052.525.5214.3
    0.392001.052.515.5014.4
    0.393002.395.7512.738.1
    0.394004.3010.423.379.4
    0.484004.7610.323.179.0
    • Threshold is in percentage of maximal illumination.

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Realistic Numerical and Analytical Modeling of Light Scattering in Brain Tissue for Optogenetic Applications
Guy Yona, Nizan Meitav, Itamar Kahn, Shy Shoham
eNeuro 4 January 2016, 3 (1) ENEURO.0059-15.2015; DOI: 10.1523/ENEURO.0059-15.2015

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Realistic Numerical and Analytical Modeling of Light Scattering in Brain Tissue for Optogenetic Applications
Guy Yona, Nizan Meitav, Itamar Kahn, Shy Shoham
eNeuro 4 January 2016, 3 (1) ENEURO.0059-15.2015; DOI: 10.1523/ENEURO.0059-15.2015
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Keywords

  • beam-spread function
  • light scattering
  • Monte Carlo
  • optogenetics

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