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@ARTICLE{Schubert:808909,
      author       = {Schubert, Nicole and Axer, Markus and Schober, Martin and
                      Huynh, Anh Minh and Huysegoms, Marcel and
                      Palomero-Gallagher, Nicola and Bjaalie, J. G. and Leergaard,
                      T. B. and Kirlangic, Mehmet Eylem and Amunts, Katrin and
                      Zilles, Karl},
      title        = {3{D} {R}econstructed cyto- muscarinic {M}2 receptor, and
                      fiber archtiecture of the rat brain registered to the
                      {W}axholm {S}pace {A}tlas},
      journal      = {Frontiers in neuroanatomy},
      volume       = {10},
      issn         = {1662-5129},
      address      = {Lausanne},
      publisher    = {Frontiers Research Foundation},
      reportid     = {FZJ-2016-02439},
      pages        = {51},
      year         = {2016},
      abstract     = {High-resolution multiscale and multimodal 3D models of the
                      brain are essential tools to understand its complex
                      structural and functional organization. Neuroimaging
                      techniques addressing different aspects of brain
                      organization should be integrated in a reference space to
                      enable topographically correct alignment and subsequent
                      analysis of the various datasets and their modalities. The
                      Waxholm Space
                      (http://software.incf.org/software/waxholm-space) is a
                      publicly available 3D coordinate-based standard reference
                      space for the mapping and registration of neuroanatomical
                      data in rodent brains. This paper provides a newly developed
                      pipeline combining imaging and reconstruction steps with a
                      novel registration strategy to integrate new neuroimaging
                      modalities into the Waxholm Space atlas. As a proof of
                      principle, we incorporated large scale high-resolution
                      cyto-, muscarinic M2 receptor, and fiber architectonic
                      images of rat brains into the 3D digital MRI based atlas of
                      the Sprague Dawley rat in Waxholm Space. We describe the
                      whole workflow, from image acquisition to reconstruction and
                      registration of these three modalities into the Waxholm
                      Space rat atlas. The registration of the brain sections into
                      the atlas is performed by using both linear and non-linear
                      transformations. The validity of the procedure is
                      qualitatively demonstrated by visual inspection, and a
                      quantitative evaluation is performed by measurement of the
                      concordance between representative atlas-delineated regions
                      and the same regions based on receptor or fiber
                      architectonic data. This novel approach enables for the
                      first time the generation of 3D reconstructed volumes of
                      nerve fibers and fiber tracts, or of muscarinic M2 receptor
                      density distributions, in an entire rat brain. Additionally,
                      our pipeline facilitates the inclusion of further
                      neuroimaging datasets, e.g., 3D reconstructed volumes of
                      histochemical stainings or of the regional distributions of
                      multiple other receptor types, into the Waxholm Space.
                      Thereby, a multiscale and multimodal rat brain model was
                      created in the Waxholm Space atlas of the rat brain. Since
                      the registration of these multimodal high-resolution
                      datasets into the same coordinate system is an indispensable
                      requisite for multi-parameter analyses, this approach
                      enables combined studies on receptor and cell distributions
                      as well as fiber densities in the same anatomical structures
                      at microscopic scales for the first time.},
      cin          = {INM-1},
      ddc          = {610},
      cid          = {I:(DE-Juel1)INM-1-20090406},
      pnm          = {574 - Theory, modelling and simulation (POF3-574) /
                      NIH-R01MH092311 - Postnatal Development of Cortical
                      Receptors and White Matter Tracts in the Vervet
                      (NIH-R01MH092311) / SMHB - Supercomputing and Modelling for
                      the Human Brain (HGF-SMHB-2013-2017) / HBP - The Human Brain
                      Project (604102)},
      pid          = {G:(DE-HGF)POF3-574 / G:(DE-Juel1)NIH-R01MH092311 /
                      G:(DE-Juel1)HGF-SMHB-2013-2017 / G:(EU-Grant)604102},
      typ          = {PUB:(DE-HGF)16},
      UT           = {WOS:000375251500001},
      pubmed       = {pmid:27199682},
      doi          = {10.3389/fnana.2016.00051},
      url          = {https://juser.fz-juelich.de/record/808909},
}