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

Year: 2024

Type: preprint

Abstract: We present open-source tools for 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: (i) 3D reconstruct a volume from the photographs and, optionally, a surface scan; and (ii) 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 post mortem 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).

Source: eLife

DOI: 10.7554/elife.91398.3

Institutions: Harvard University, Massachusetts General Hospital, Athinoula A. Martinos Center for Biomedical Imaging, University College London, Universitat Politècnica de Catalunya, University of Washington, Aalto University

Language: English

Topic: Medical Image Segmentation Techniques

Subfield: Computer Vision and Pattern Recognition

Field: Computer Science

Domain: Physical Sciences

SDG: Good health and well-being

Open Access status: gold

Estimated APC paid: $2,500

Funders: European Commission, Alzheimer’s Research UK, National Institutes of Health, National Institute on Aging, National Institute of Mental Health, National Institute of Neurological Disorders and Stroke, National Institute of Biomedical Imaging and Bioengineering, National Center for Research Resources

Awards: Molecular Mechanisms of Synergistic TDP-43 and Tau Proteotoxicity in Alzheimer's Disease, Computational Imaging Biomarkers of Multiple Sclerosis, Segmenting Brain Structures for Neurological Disorders, Inferring in Vivo Cytoarchitectural Borders in the Medial Temporal Lobe, Algorithms for MR and OCT-based Architectonic and Laminar Segmentation, The Human Connectome Project (HCP), OCTology: histology using optical coherence tomography, Deep Learning Algorithms for FreeSurfer, Accelerated Software Tools for Neuroimaging Analysis, Nobrainer: A robust and validated neural network tool suite for imagers, G6073090889, Computeserver Structural &Functional Image Analysis, G6296793415, MRI, Genetics & Cognitive Precursors of AD and Dementia, Open-source software for multi-scale mapping of the human brain, Software Tools for Automated Modeling of White Matter Fascicles from Diffusion MR, Epidemiology of Dementia in the Framingham Study, A Storage Area Network for Structural and Functional Image Analysis, Imaging and Analysis Techniques to Construct a Cell Census Atlas of the Human Brain, G9000163195, G9000287168, G9000300321, A Longitudinal Analysis Stream for FreeSurfer, Functionally guided adult whole brain cell atlas in human and NHP, Adult Changes in Thought (ACT) Research Program, VCID Biomarkers Coordinating Center, FreeSurfer Development, Maintenance, and Hardening, Center for Mesoscale Mapping, Portable, Low Field Brain Magnetic Resonance Imaging (MRI) for Acute Stroke, Diagnosing the undiagnosable: studies of Alzheimer disease mimics and confounders via "neuropathometry" of dissection photos with 3D scanning, Massachusetts Alzheimer's Disease Research Center (MADRC), A multimodal brain cell atlas and community resource of Alzheimer's disease and comorbid dementias., Silicon Graphics Prism Extreme 128P/1TB

OpenAlex ID: W4393039843