Preprint

FZJ-2025-04528

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png CytoNet: A Foundation Model for the Human Cerebral Cortex

Schiffer, C. (Corresponding author)FZJ* ; Boztoprak, Z.FZJ* ; Kropp, J.-O.FZJ* ; Thönnißen, J.FZJ* ; Berr, K. ; Spitzer, H. ; Amunts, K.FZJ* ; Dickscheid, T.FZJ*

2025
arXiv

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Please use a persistent id in citations: doi:10.48550/ARXIV.2511.01870  doi:10.34734/FZJ-2025-04528

Abstract: To study how the human brain works, we need to explore the organization of the cerebral cortex and its detailed cellular architecture. We introduce CytoNet, a foundation model that encodes high-resolution microscopic image patches of the cerebral cortex into highly expressive feature representations, enabling comprehensive brain analyses. CytoNet employs self-supervised learning using spatial proximity as a powerful training signal, without requiring manual labelling. The resulting features are anatomically sound and biologically relevant. They encode general aspects of cortical architecture and unique brain-specific traits. We demonstrate top-tier performance in tasks such as cortical area classification, cortical layer segmentation, cell morphology estimation, and unsupervised brain region mapping. As a foundation model, CytoNet offers a consistent framework for studying cortical microarchitecture, supporting analyses of its relationship with other structural and functional brain features, and paving the way for diverse neuroscientific investigations.

Keyword(s): Neurons and Cognition (q-bio.NC) ; Artificial Intelligence (cs.AI) ; Machine Learning (cs.LG) ; FOS: Biological sciences ; FOS: Computer and information sciences ; I.2.6; I.2.10; I.4.7; I.5.1; I.5.4

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Contributing Institute(s):

1. Strukturelle und funktionelle Organisation des Gehirns (INM-1)

Research Program(s):

1. 5251 - Multilevel Brain Organization and Variability (POF4-525) (POF4-525)
2. EBRAINS 2.0 - EBRAINS 2.0: A Research Infrastructure to Advance Neuroscience and Brain Health (101147319) (101147319)
3. JL SMHB - Joint Lab Supercomputing and Modeling for the Human Brain (JL SMHB-2021-2027) (JL SMHB-2021-2027)
4. HIBALL - Helmholtz International BigBrain Analytics and Learning Laboratory (HIBALL) (InterLabs-0015) (InterLabs-0015)
5. X-BRAIN (ZT-I-PF-4-061) (ZT-I-PF-4-061)
6. DFG project G:(GEPRIS)501864659 - NFDI4BIOIMAGE - Nationale Forschungsdateninfrastruktur für Mikroskopie und Bildanalyse (501864659) (501864659)

Appears in the scientific report 2025

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Database coverage:

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