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@ARTICLE{Menzel:859427,
      author       = {Menzel, Miriam and Axer, Markus and De Raedt, Hans and
                      Costantini, Irene and Silvestri, Ludovico and Pavone,
                      Francesco S. and Amunts, Katrin and Michielsen, Kristel},
      title        = {{F}inite-{D}ifference {T}ime-{D}omain simulations of
                      transmission microscopy enable a better interpretation of
                      3{D} nerve fiber architectures in the brain},
      reportid     = {FZJ-2019-00285},
      year         = {2018},
      note         = {15 pages, 6 figures (main part); 18 pages, 13 figures, 2
                      tables (supplementary information)
                      https://arxiv.org/abs/1806.07157},
      abstract     = {Transmission microscopy measurements of histological brain
                      sections provide usually only 2D (in-plane) information
                      about the spatial nerve fibre architecture. To access the
                      third dimension (out-of-plane orientation) of the nerve
                      fibres, more advanced techniques are required, such as
                      Three-dimensional Polarized Light Imaging (3D-PLI) which
                      uses birefringence measurements to derive the 3D fibre
                      orientations. Here, we show that the
                      polarization-independent transmitted light intensity
                      (transmittance) already contains 3D information: we
                      demonstrate in experimental studies of multiple species
                      (rodent, monkey, human) that the transmittance decreases
                      significantly (by more than 50 $\%)$ with increasing
                      out-of-plane angle of the nerve fibres. Using
                      finite-difference time-domain simulations, we demonstrate
                      that this decrease is mainly caused by
                      polarization-independent light scattering in combination
                      with the finite numerical aperture of the imaging system,
                      and that the transmittance does not depend on the crossing
                      angle between in-plane fibres. This allows to use the
                      transmittance e.g. to distinguish between in-plane crossing
                      and out-of-plane nerve fibres in 3D-PLI measurements.},
      cin          = {INM-1 / JSC},
      cid          = {I:(DE-Juel1)INM-1-20090406 / I:(DE-Juel1)JSC-20090406},
      pnm          = {574 - Theory, modelling and simulation (POF3-574) / 571 -
                      Connectivity and Activity (POF3-571) / 511 - Computational
                      Science and Mathematical Methods (POF3-511) / SMHB -
                      Supercomputing and Modelling for the Human Brain
                      (HGF-SMHB-2013-2017) / HBP SGA2 - Human Brain Project
                      Specific Grant Agreement 2 (785907) / HBP SGA1 - Human Brain
                      Project Specific Grant Agreement 1 (720270)},
      pid          = {G:(DE-HGF)POF3-574 / G:(DE-HGF)POF3-571 /
                      G:(DE-HGF)POF3-511 / G:(DE-Juel1)HGF-SMHB-2013-2017 /
                      G:(EU-Grant)785907 / G:(EU-Grant)720270},
      typ          = {PUB:(DE-HGF)25},
      eprint       = {1806.07157},
      howpublished = {arXiv:1806.07157},
      archivePrefix = {arXiv},
      SLACcitation = {$\%\%CITATION$ = $arXiv:1806.07157;\%\%$},
      url          = {https://juser.fz-juelich.de/record/859427},
}