Three-dimensional U-Net with transfer learning improves automated whole brain delineation from MRI brain scans of rats, mice, and monkeys.

Journal: Computers in biology and medicine
Published Date: Jun 20, 2025

Abstract

BACKGROUND: Automated whole-brain delineation (WBD) techniques often struggle to generalize across pre-clinical studies due to variations in animal models, magnetic resonance imaging (MRI) scanners, and tissue contrasts. We developed a 3D U-Net neural network for WBD pre-trained on organophosphate intoxication (OPI) rat brain MRI scans. We used transfer learning (TL) to adapt this OPI-pretrained network to other animal models: rat model of Alzheimer's disease (AD), mouse model of tetramethylenedisulfotetramine (TETS) intoxication, and titi monkey model of social bonding.

Authors

  • Valerie A Porter
    Department of Biomedical Engineering, University of California, Davis, One Shields Ave, Davis, CA, USA; Department of Radiology, University of California, Davis, One Shields Ave, Davis, CA, USA.
  • Brad A Hobson
    Department of Biomedical Engineering, University of California, Davis, One Shields Ave, Davis, CA, USA; Center for Molecular and Genomic Imaging, University of California, Davis, One Shields Ave, Davis, CA, USA.
  • Alita J D'Almeida
    Department of Biomedical Engineering, University of California, Davis, One Shields Ave, Davis, CA, USA; Department of Radiology, University of California, Davis, One Shields Ave, Davis, CA, USA.
  • Karen L Bales
    Department of Psychology, University of California, Davis, One Shields Ave, Davis, CA, USA; California National Primate Research Center, One Shields Ave, Davis, CA, USA.
  • Pamela J Lein
    Department of Molecular Biosciences, University of California, Davis, One Shields Ave, Davis, CA, USA.
  • Abhijit J Chaudhari
    Department of Radiology, University of California, Davis, Davis, California, USA.

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