A public generalizable AI tool for automated segmentation of coronal brain tissue slabs for 3D neuropathology
Year: 2026
Type: article
Abstract: Advances in image registration and machine learning have recently enabled volumetric analysis of postmortem brain tissue from conventional photographs of coronal slabs, which are routinely collected in brain banks and neuropathology laboratories around the world. One caveat of this methodology is the requirement of segmentation of the tissue from the background and out-of-slice tissue in photographs, which currently requires laborious manual intervention. Manual delineation is a bottleneck in this process and poses challenges in scalability, and resources, restricting adoption of these methods. In this article, we present a deep learning model to automate this process. The automatic segmentation tool relies on a U-Net architecture that was trained with a combination of 1,414 manually segmented images of both fixed and fresh tissue, from specimens with varying diagnoses, photographed at two different sites. Automated model predictions on a subset of photographs not seen in training were analyzed to estimate performance compared to manual labels, including both inter- and intra-rater variability. Our model achieved a median Dice score over 0.98, mean surface distance under 0.4 mm, and 95% Hausdorff distance under 1.60 mm, which approaches inter-/intra-rater levels. Our tool is publicly available at surfer.nmr.mgh.harvard.edu/fswiki/PhotoTools and training data is available at https://zenodo.org/records/20647553.
Source: PLoS ONE
Authors: Jonathan Williams Ramirez, Dina Zemlyanker, Lucas Deden-Binder, Rogeny Herisse, Erendira Garcia Pallares, Karthik Gopinath, Harshvardhan Gazula, Christopher Mount, Liana N. Kozanno, Michael S. Marshall, Theresa R. Connors, Matthew P. Frosch, Mark Montine, Derek H. Oakley, Christine L. Mac Donald, C. Dirk Keene, Bradley T. Hyman, Bruce Fischl, Juan E. Iglesias
Language: English
Subfield: Computer Vision and Pattern Recognition
Field: Computer Science
Domain: Physical Sciences
Open Access status: gold
Estimated APC paid: $2,382
Funders: U.S. Department of Defense, Kaiser Permanente, Nancy and Buster Alvord Endowment, National Institutes of Health, Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in St. Louis, 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: G1013228188, G1182324995, G1614942108, Acquisition-independent machine learning for morphometric analysis of underrepresented aging populations with clinical and low-field brain MRI, G2327712927, G2940391972, G2998073318, Segmenting Brain Structures for Neurological Disorders, G3865632432, Deep Learning for Detecting the Early Anatomical Effects of Alzheimer's Disease, G4119534169, Algorithms for MR and OCT-based Architectonic and Laminar Segmentation, The Human Connectome Project (HCP), G4295136713, OCTology: histology using optical coherence tomography, G5850682332, Nobrainer: A robust and validated neural network tool suite for imagers, Computeserver Structural &Functional Image Analysis, MRI, Genetics & Cognitive Precursors of AD and Dementia, Open-source software for multi-scale mapping of the human brain, Measuring Brain Health Using Low-Field Portable MRI, Deep Learning Algorithms for FreeSurfer, G7439732511, Software Tools for Automated Modeling of White Matter Fascicles from Diffusion MR, G824017836, A Storage Area Network for Structural and Functional Image Analysis, Imaging and Analysis Techniques to Construct a Cell Census Atlas of the Human Brain, Federated digital pathology platform for AD/ADRD research and diagnostics, A Longitudinal Analysis Stream for FreeSurfer, Center for Multi-Scale Multi-Omic Human and non-human primate Brain Atlas, An Acquisition and Analysis Pipeline for Integrating MRI and Neuropathology in TBI-related Dementia and VCID, Functionally guided adult whole brain cell atlas in human and NHP, Adult Changes in Thought (ACT) Research Program, FreeSurfer Development, Maintenance, and Hardening, Center for Mesoscale Mapping, Portable, Low Field Brain Magnetic Resonance Imaging (MRI) for Acute Stroke, Brain Digital Slide Archive: An Open Source Platform for data sharing and analysis of digital neuropathology, Interdisciplinary Research Network on Biologically Active Tau Aggregate Polymorphs from Alzheimer's Disease and Related Dementias, University of Washington Alzheimer's Disease Research Center, MGH/HMS Internship in NeuroImaging Analysis, Diagnosing the undiagnosable: studies of Alzheimer disease mimics and confounders via "neuropathometry" of dissection photos with 3D scanning, Neuroimaging and clinical Endpoints With High-dimensional analysis Of Pathological Endophenotypes in TBI (NEW-HOPE-TBI), Transdisciplinary Research Accelerating Neuropathology Studies and Facilitating Open Research Methods in TBI (TRANSFORM-TBI), BRAIN CONNECTS: Mapping Connectivity of the Human Brainstem in a Nuclear Coordinate System, BRAIN CONNECTS: The center for Large-scale Imaging of Neural Circuits (LINC), A multimodal brain cell atlas and community resource of Alzheimer's disease and comorbid dementias., Silicon Graphics Prism Extreme 128P/1TB
OpenAlex ID: W7203628080