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@INPROCEEDINGS{Kedo:1048413,
      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-2025-04624},
      year         = {2025},
      abstract     = {The hippocampal formation (HF) plays a pivotal role in
                      different aspects of memory, with its subdivisions having
                      various functional implications. 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 with its subdivisions being
                      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 (subiculum).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. 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 [5]. The annotations of each
                      structure were non-linearly transformed to the sections of
                      the 3D reconstructed BigBrain space at 20-micron isotropic
                      resolution [6], and was further visualized using the
                      Neuroglancer.We have identified 12 cytoarchitectonic
                      structures of HF in the BigBrain and analyzed their
                      macroanatomy (Fig. 1). Fasciola cinerea (FD in its
                      mediocaudal extension) was larger in the left hemisphere,
                      while it was minuscule on the right (Fig.1A). Left ProS
                      extended onto dorsomedial surface of the parahippocampal
                      gyrus (PHG), while the right ProS almost does not appear on
                      the surface (Fig.1B). Caudally, PreS occupied medial surface
                      of the PHG. TrS abutted on PreS ventrally. Caudal TrS
                      bordered the temporo-parieto-occipital proisocortex
                      laterally (Fig.1A), while rostral TrS abutted upon area 35.
                      PaS replaced TrS rostrally. The detailed mapping of HF
                      reflected a transition from the allocortex (ProS and Sub) to
                      the periallocortex (PreS, PaS) within the subicular complex
                      that traditionally was considered as a cytoarchitectonic
                      unit. Rostrally, both hemispheres had three Digitationes
                      hippocampi respectively (Fig.1C). The high-resolution (20
                      μm) whole-brain histological references of HF were
                      generated on the basis of the BigBrain. They will be
                      publicly available on the EBRAINS platform and integrated
                      with the BigBrain model, extending maps of the piriform
                      cortex [7] to represent two hubs of limbic system [8].1.
                      Wisse L.E.M. et al. (2017) Hippocampus, 27(1): p. 3-11.2.
                      Yushkevich P.A. et al. (2015), Neuroimage, 111: p. 526-41.3.
                      DeKraker J. et al. (2020), Neuroimage, 206: p. 116328.4.
                      Palomero-Gallagher N. et al. (2020), Brain Struct Funct,
                      225(3): p. 881-907.5. Schiffer C. et al. (2021), Neuroimage,
                      240: p. 118327.6. Amunts K. et al. (2013), Science,
                      340(6139): p. 1472-5.7. Kedo O. et al. (2024), Anatomia,
                      3(2): p. 68–92.8. Catani M. et al. (2013), Neurosci
                      Biobehav Rev, 2013. 37(8): p. 1724-37.},
      month         = {Oct},
      date          = {2025-10-27},
      organization  = {9th BigBrain Workshop -HIBALL Closing
                       Symposium, Berlin (Germany), 27 Oct
                       2025 - 29 Oct 2025},
      subtyp        = {After Call},
      cin          = {INM-1},
      cid          = {I:(DE-Juel1)INM-1-20090406},
      pnm          = {5251 - Multilevel Brain Organization and Variability
                      (POF4-525) / HIBALL - Helmholtz International BigBrain
                      Analytics and Learning Laboratory (HIBALL) (InterLabs-0015)},
      pid          = {G:(DE-HGF)POF4-5251 / G:(DE-HGF)InterLabs-0015},
      typ          = {PUB:(DE-HGF)24},
      url          = {https://juser.fz-juelich.de/record/1048413},
}