% IMPORTANT: The following is UTF-8 encoded.  This means that in the presence
% of non-ASCII characters, it will not work with BibTeX 0.99 or older.
% Instead, you should use an up-to-date BibTeX implementation like “bibtex8” or
% “biber”.

@MISC{Dickscheid:1048778,
      author       = {Dickscheid, Timo and Bludau, Sebastian},
      title        = {{W}orking with quantitative cortical cell densities using
                      siibra},
      reportid     = {FZJ-2025-04893},
      year         = {2025},
      abstract     = {The regional microstructure of cortical brain areas, along
                      with their connectivity to other regions, is linked to their
                      functional profile. Consequently, microstructure varies
                      significantly between different brain region. Along with
                      modern image analysis methods, the BigBrain provides a
                      unique resource for quantifying microstructure in terms of
                      numbers, densities, and distributions of cell bodies at
                      different locations in the brain. In this tutorial, we
                      demonstrate how the siibra toolsuite can be used to access
                      micrometer resolution BigBrain image data and extract
                      cortical image patches for custom regions of interest. We
                      will show how locations can be specified or sampled in
                      interactive and scripted workflows, and demonstrate how
                      state of the art AI models can be used to extract and
                      quantify cell instances from extracted image patches in a
                      reproducible fashion. We will present a dataset of
                      layer-specific cell densities for areas defined in the
                      Julich-Brain cytoarchitectonic atlas, which has been created
                      on the basis of these ideas and is available through
                      siibra.},
      month         = {Oct},
      date          = {2025-10-27},
      organization  = {9th BigBrain Workshop - HIBALL Closing
                       Symposium, Berlin (Germany), 27 Oct
                       2025 - 27 Oct 2025},
      subtyp        = {Invited},
      cin          = {INM-1},
      cid          = {I:(DE-Juel1)INM-1-20090406},
      pnm          = {5254 - Neuroscientific Data Analytics and AI (POF4-525) /
                      5251 - Multilevel Brain Organization and Variability
                      (POF4-525) / HIBALL - Helmholtz International BigBrain
                      Analytics and Learning Laboratory (HIBALL) (InterLabs-0015)
                      / EBRAINS 2.0 - EBRAINS 2.0: A Research Infrastructure to
                      Advance Neuroscience and Brain Health (101147319)},
      pid          = {G:(DE-HGF)POF4-5254 / G:(DE-HGF)POF4-5251 /
                      G:(DE-HGF)InterLabs-0015 / G:(EU-Grant)101147319},
      typ          = {PUB:(DE-HGF)17},
      url          = {https://juser.fz-juelich.de/record/1048778},
}