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001048666 0247_ $$2datacite_doi$$a10.34734/FZJ-2025-04794
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001048666 1001_ $$0P:(DE-Juel1)131650$$aKedo, Olga$$b0$$eCorresponding author$$ufzj
001048666 1112_ $$aINM Retreat 2025$$cJülich$$d2025-11-28 - 2025-11-28$$wGermany
001048666 245__ $$aThe hippocampal formation mapped in the BigBrain: The deep-learning supported high-resolution mapping and 3D reconstruction
001048666 260__ $$c2025
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001048666 520__ $$aThe 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.
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001048666 7001_ $$0P:(DE-Juel1)196766$$aLothmann, Kimberley$$b1$$ufzj
001048666 7001_ $$0P:(DE-Juel1)170068$$aSchiffer, Christian$$b2$$ufzj
001048666 7001_ $$0P:(DE-Juel1)131660$$aMohlberg, Hartmut$$b3$$ufzj
001048666 7001_ $$0P:(DE-Juel1)165746$$aDickscheid, Timo$$b4$$ufzj
001048666 7001_ $$0P:(DE-Juel1)131631$$aAmunts, Katrin$$b5$$ufzj
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