arXiv AI By Christian Schiffer, Zeynep Boztoprak, Jan-Oliver Kropp, Julia Th\"onni{\ss}en, Katia Berr, Hannah Spitzer, Mathis Bode, Thomas Lippert, Katrin Amunts, Timo Dickscheid

CytoNet: A Foundation Model for the Human Cerebral Cortex at Cellular Resolution

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CytoNet is a foundation model trained on 1 million unlabeled microscopic image patches from over 4,000 histological sections of nine postmortem brains, and evaluated on 2,000 sections from five additional brains. By using co‑localization in the cortical sheet for self‑supervision, it learns expressive, anatomically meaningful feature representations that enable downstream tasks such as area classification, laminar segmentation, microarchitectural quantification, and exploratory mapping of cortical subdivisions. Functional parcellation analyses demonstrate links between cytoarchitecture and macroscale functional organization, establishing CytoNet as a unified framework for scalable analysis of cortical microarchitecture and its relationship to structure‑function organization in the human cerebral cortex.

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