A public generalizable AI tool for automated segmentation of coronal brain tissue slabs for 3D neuropathology.

Overview

1. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
2. Massachusetts Alzheimer’s Disease Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
3. Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
4. Department of Neurological Surgery, University of Washington School of Medicine, Seattle, Washington, United States of America
5. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Boston, Massachusetts, United States of America
6. Hawkes Institute, University College London, London, United Kingdom

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.

Reproduced under the paper's license (CC BY), from the paper cited above.

Code

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Data

Datasets cited

• zenodo:20647553, at Zenodo; found in “Data Availability”

Data Availability

All training images and labels for the segmentation model are publicly available at https://zenodo.org/records/20647553 with DOI: https://doi.org/10.48550/arXiv.2508.09805.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

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Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 19 authors, 6 MeSH terms, 11 funders, 31 references.

Cite

This paper

Williams Ramirez, J., Zemlyanker, D., Deden-Binder, L., Herisse, R., Garcia Pallares, E., Gopinath, K., Gazula, H., Mount, C., Kozanno, L. N., Marshall, M. S., Connors, T. R., Frosch, M. P., Montine, M., Oakley, D. H., Mac Donald, C. L., Keene, C. D., Hyman, B. T., Fischl, B., & Iglesias, J. E. (2026). A public generalizable AI tool for automated segmentation of coronal brain tissue slabs for 3D neuropathology. PloS one, 21(8), e0355740. https://doi.org/10.1371/journal.pone.0355740

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