NeuriteNet: A convolutional neural network for assessing morphological parameters of neurite growth.

Journal: Journal of neuroscience methods
PMID: 34480956

Abstract

BACKGROUND: During development or regeneration, neurons extend processes (i.e., neurites) via mechanisms that can be readily analyzed in culture. However, defining the impact of a drug or genetic manipulation on such mechanisms can be challenging due to the complex arborization and heterogeneous patterns of neurite growth in vitro. New Method: NeuriteNet is a Convolutional Neural Network (CNN) sorting model that uses a novel adaptation of the XRAI saliency map overlay, which is a region-based attribution method. NeuriteNet compares neuronal populations based on differences in neurite growth patterns, sorts them into respective groups, and overlays a saliency map indicating which areas differentiated the image for the sorting procedure.

Authors

  • Joseph T Vecchi
    Departments of Molecular Physiology and Biophysics, Otolaryngology Head-Neck Surgery, and Neurology, Iowa Neuroscience Institute, Pappajohn Biomedical Institute, University of Iowa, 51 Newton Rd., Iowa City, IA 52242, USA.
  • Sean Mullan
    Iowa Institute for Biomedical Imaging, Electrical and Computer Engineering, University of Iowa, 169 Newton Rd., Iowa City, IA 52242, USA.
  • Josue A Lopez
    Departments of Molecular Physiology and Biophysics, Otolaryngology Head-Neck Surgery, and Neurology, Iowa Neuroscience Institute, Pappajohn Biomedical Institute, University of Iowa, 51 Newton Rd., Iowa City, IA 52242, USA.
  • Marlan R Hansen
    Departments of Molecular Physiology and Biophysics, Otolaryngology Head-Neck Surgery, and Neurology, Iowa Neuroscience Institute, Pappajohn Biomedical Institute, University of Iowa, 51 Newton Rd., Iowa City, IA 52242, USA.
  • Milan Sonka
    Department of Electrical and Computer Engineering, The University of Iowa, Iowa City, IA, 52242, United States; Department of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, IA, 52242, United States.
  • Amy Lee
    Dept of Neuroscience, University of Texas-Austin, 100 E. 24th St., Austin, TX 78712, USA. Electronic address: amy.lee1@austin.utexas.edu.

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