Machine learning of dissection photographs and surface scanning for quantitative 3D neuropathology.

Journal: eLife
PMID: 38896568

Abstract

We present open-source tools for three-dimensional (3D) analysis of photographs of dissected slices of human brains, which are routinely acquired in brain banks but seldom used for quantitative analysis. Our tools can: (1) 3D reconstruct a volume from the photographs and, optionally, a surface scan; and (2) produce a high-resolution 3D segmentation into 11 brain regions per hemisphere (22 in total), independently of the slice thickness. Our tools can be used as a substitute for ex vivo magnetic resonance imaging (MRI), which requires access to an MRI scanner, ex vivo scanning expertise, and considerable financial resources. We tested our tools on synthetic and real data from two NIH Alzheimer's Disease Research Centers. The results show that our methodology yields accurate 3D reconstructions, segmentations, and volumetric measurements that are highly correlated to those from MRI. Our method also detects expected differences between confirmed Alzheimer's disease cases and controls. The tools are available in our widespread neuroimaging suite 'FreeSurfer' (https://surfer.nmr.mgh.harvard.edu/fswiki/PhotoTools).

Authors

  • Harshvardhan Gazula
    Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, United States.
  • Henry F J Tregidgo
    Centre for Medical Image Computing, University College London, London, United Kingdom.
  • Benjamin Billot
    Centre for Medical Image Computing, Department of Medical Physics and Biomedical Engineering, University College London, UK.
  • Yaël Balbastre
  • Jonathan Williams-Ramirez
    Martinos Center for Biomedical Imaging, MGH and Harvard Medical School, Charlestown, United States.
  • Rogeny Herisse
    Martinos Center for Biomedical Imaging, MGH and Harvard Medical School, Charlestown, United States.
  • Lucas J Deden-Binder
    Martinos Center for Biomedical Imaging, MGH and Harvard Medical School, Charlestown, United States.
  • Adria Casamitjana
    Centre for Medical Image Computing, University College London, London, United Kingdom.
  • Erica J Melief
    BioRepository and Integrated Neuropathology (BRaIN) Laboratory and Precision Neuropathology Core, UW School of Medicine, Seattle, United States.
  • Caitlin S Latimer
    Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
  • Mitchell D Kilgore
    BioRepository and Integrated Neuropathology (BRaIN) Laboratory and Precision Neuropathology Core, UW School of Medicine, Seattle, United States.
  • Mark Montine
    BioRepository and Integrated Neuropathology (BRaIN) Laboratory and Precision Neuropathology Core, UW School of Medicine, Seattle, United States.
  • Eleanor Robinson
    Centre for Medical Image Computing, Department of Medical Physics and Biomedical Engineering, University College, London, UK.
  • Emily Blackburn
    Centre for Medical Image Computing, Department of Medical Physics and Biomedical Engineering, University College, London, UK.
  • Michael S Marshall
    Massachusetts Alzheimer Disease Research Center, MGH and Harvard Medical School, Charlestown, United States.
  • Theresa R Connors
    Massachusetts Alzheimer Disease Research Center, MGH and Harvard Medical School, Charlestown, United States.
  • Derek H Oakley
  • Matthew P Frosch
    Department of Neuropathology, Massachusetts General Hospital, Boston, MA, USA.
  • Sean I Young
    MGH/HST Martinos Center for Biomedical Imaging, Harvard Medical School, Boston, MA, USA; CSAIL, Massachusetts Institute of Technology, Cambridge, MA, USA.
  • Koen Van Leemput
  • Adrian V Dalca
    Computer Science and Artificial Intelligence Lab, MIT, Cambridge, MA, USA; Martinos Center for Biomedical Imaging, Massachusetts General Hospital, HMS, Charlestown, MA, USA; School of Electrical and Computer Engineering, Cornell University, Ithaca, NY, USA. Electronic address: adalca@csail.mit.edu.
  • Bruce Fischl
    Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, 02129, United States; Department of Radiology, Harvard Medical School, United States; Division of Health Sciences and Technology and Engineering and Computer Science MIT, Cambridge, MA, United States.
  • Christine L MacDonald
    Department of Neurological Surgery, UW School of Medicine, Seattle, United States.
  • C Dirk Keene
    Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
  • Bradley T Hyman
  • Juan E Iglesias
    Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.

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