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@INPROCEEDINGS{Kedo:1048666,
      author       = {Kedo, Olga and Lothmann, Kimberley and Schiffer, Christian
                      and Mohlberg, Hartmut and Dickscheid, Timo and Amunts,
                      Katrin},
      title        = {{T}he hippocampal formation mapped in the {B}ig{B}rain:
                      {T}he deep-learning supported high-resolution mapping and
                      3{D} reconstruction},
      reportid     = {FZJ-2025-04794},
      year         = {2025},
      abstract     = {The hippocampal formation (HF) plays an important role in
                      memory, with its subdivisions being involved in its differnt
                      functions and neuropathologies. The hippocampus has been
                      parcellated in different ways both in histological and MRI
                      studies [1, 2]. In the BigBrain, 3D rendering of the
                      hippocampus was performed, based on the main hippocampal
                      subdivisions, which were revealed through unfolding and
                      unsupervised clustering of laminar and morphological
                      features [3]. However, this parcellation was not detailed
                      enough, e.g. in the field of the subicular complex.We
                      cytoarchitectonically identified and mapped in 10 postmortem
                      brains and generated probabilistic maps of CA1, CA2, CA3,
                      CA4, Fascia dentata (FD), prosubiculum (ProS), subiculum
                      (Sub), presubiculum (PreS), parasubiculum (PaS),
                      transsubiculum (TrS), hippocampal-amygdaloid transition area
                      (HATA) and entorhinal cortex (EC) [4]. Based on this
                      research, we mapped HF in the BigBrain and generated the 3D
                      maps of HF in the BigBrain template [5].Cytoarchitectonic
                      mapping of 12 structures was performed in at least each 15th
                      serial histological sections in the web-based annotation
                      tool MicroDraw at 1-micron resolution in-plane in the
                      BigBrain. Subsequently, a Deep Learning Workflow was
                      utilized to 3D-reconstruct the structures. Convolutional
                      Neural Networks were trained for image segmentation in the
                      sections lying between those manually mapped using ATLaSUI
                      [6]. The annotations of each structure were non-linearly
                      transformed to the sections of the 3D reconstructed BigBrain
                      space at 20-micron isotropic resolution, and was further
                      visualized using the Neuroglancer.We have identified 12
                      cytoarchitectonic structures of HF in the BigBrain and
                      analyzed their macroanatomy. The volumes of HF in the
                      BigBrain were compared with those from the previous sample
                      of 10 brains.Fasciola cinerea (FD in its mediocaudal
                      extension) was larger in the left hemisphere, while it was
                      minuscule on the right. Left ProS extended onto dorsomedial
                      surface of the parahippocampal gyrus (PHG), while the right
                      ProS almost does not appear on the surface. Caudally, PreS
                      occupied medial surface of the PHG. TrS abutted on PreS
                      ventrally. Caudal TrS bordered the temporo-parieto-occipital
                      proisocortex laterally, while rostral TrS abutted upon area
                      35. PaS replaced TrS rostrally. Rostrally, both hemispheres
                      had three Digitationes hippocampi respectively.The
                      high-resolution (20 μm) whole-brain histological references
                      of HF were generated on the basis of the BigBrain. These
                      maps allow styding and exploring neighborhood relationships
                      between the structures. They will be publicly available on
                      the EBRAINS platform and integrated with the BigBrain model
                      (https://go.fzj.de/bigbrain/). The maps can extend those of
                      the piriform cortex in the BigBrain [7] to represent two
                      hubs of limbic system [8]. Wisse L.E.M. et al. (2017)
                      Hippocampus, 27(1): p. 3-11. Yushkevich P.A. et al. (2015),
                      Neuroimage, 111: p. 526-41. DeKraker J. et al. (2020),
                      Neuroimage, 206: p. 116328. Palomero-Gallagher N. et al.
                      (2020), Brain Struct Funct, 225(3): p. 881-907. Amunts K. et
                      al. (2013), Science, 340(6139): p. 1472-5. Schiffer C. et
                      al. (2021), Neuroimage, 240: p. 118327. Kedo O. et al.
                      (2024), Anatomia, 3(2): p. 68–92. Catani M. et al. (2013),
                      Neurosci Biobehav Rev, 2013. 37(8): p. 1724-37.},
      month         = {Nov},
      date          = {2025-11-28},
      organization  = {INM Retreat 2025, Jülich (Germany),
                       28 Nov 2025 - 28 Nov 2025},
      subtyp        = {After Call},
      cin          = {INM-1},
      cid          = {I:(DE-Juel1)INM-1-20090406},
      pnm          = {5251 - Multilevel Brain Organization and Variability
                      (POF4-525)},
      pid          = {G:(DE-HGF)POF4-5251},
      typ          = {PUB:(DE-HGF)24},
      doi          = {10.34734/FZJ-2025-04794},
      url          = {https://juser.fz-juelich.de/record/1048666},
}