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@INPROCEEDINGS{MoralesGregorio:902920,
      author       = {Morales-Gregorio, Aitor and Bakker, Rembrandt and van
                      Albada, Sacha},
      title        = {3{D} reconstruction and analysis of the macaque brain from
                      histological slices},
      reportid     = {FZJ-2021-04674},
      year         = {2021},
      abstract     = {Given the usefulness of the BigBrain high resolution
                      histological volume, it would be very valuable to have a
                      similar public domain resource for the macaque. Isotropic
                      high resolution data to build such a resource is not
                      currently available, but as an initial step we present a
                      histological volume based on the NIH Blueprint Non-Human
                      Primate (NHP) Atlas [1], acquired by the Allen Institute and
                      funded by the NIH. Our contribution is to take the set of
                      Nissl stained slices (50 μm thick, 250 μm apart) and to
                      create a smooth volume by calculating the optimal alignment.
                      We used open tools [2, 3] for processing, modernized the
                      code of the poSSum three-dimensional reconstruction toolbox
                      [4] and extended the deformable registration method thereof,
                      using the an MRI-based macaque atlas [5] as a reference
                      template. We will use the reconstructed volume to estimate
                      neuron densities across all cortical areas used in the
                      core-nets.org macaque connectivity database [6]. Besides
                      adding to the body of knowledge on the cytoarchitecture [7]
                      and geometry of the macaque cortex, this work will provide
                      tools to further analyze histological data and support
                      large-scale dynamical modeling studies.[1] NIH Blueprint NHP
                      Atlas, www.blueprintnhpatlas.org[2] Bakker et al.
                      Neuroinformatics, 2015[3] Microdraw, microdraw.pasteur.fr[4]
                      Majka et al. Journal of Comparative Neurology, 2016[5]
                      Calabrese et al. NeuroImage, 2015[6] Markov et al. Cerebral
                      Cortex, 2012[7] Beul and Hilgetag. NeuroImage, 2019},
      month         = {Sep},
      date          = {2021-09-21},
      organization  = {5th BigBrain Workshop, Virtual
                       (Germany), 21 Sep 2021 - 23 Sep 2021},
      subtyp        = {After Call},
      cin          = {INM-6 / IAS-6 / INM-10},
      cid          = {I:(DE-Juel1)INM-6-20090406 / I:(DE-Juel1)IAS-6-20130828 /
                      I:(DE-Juel1)INM-10-20170113},
      pnm          = {5231 - Neuroscientific Foundations (POF4-523) / HBP SGA3 -
                      Human Brain Project Specific Grant Agreement 3 (945539) /
                      DFG project 347572269 - Heterogenität von Zytoarchitektur,
                      Chemoarchitektur und Konnektivität in einem großskaligen
                      Computermodell der menschlichen Großhirnrinde (347572269)},
      pid          = {G:(DE-HGF)POF4-5231 / G:(EU-Grant)945539 /
                      G:(GEPRIS)347572269},
      typ          = {PUB:(DE-HGF)6},
      url          = {https://juser.fz-juelich.de/record/902920},
}