Brain slab dissection photograph segmentation dataset
Authors/Creators
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Williams Ramirez, Jonathan
(Contact person)1, 2
- Zemlyanker, Dina1, 2
- Deden-Binder, Lucas1, 2
- Garcia Pallares, Erendira1, 2
- Gopinath, Karthik1, 2
- Gazula, Harshvardhan1, 2
- Mount, Christopher3, 1, 2
- Kozanno, Liana N.3, 1, 2
- Marshall, Michael S.3, 1, 2
- Connors, Theresa R.3, 1, 2
- et al. Show all 18 authors
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Williams Ramirez, Jonathan
(Contact person)1, 2
- Zemlyanker, Dina1, 2
- Deden-Binder, Lucas1, 2
- Garcia Pallares, Erendira1, 2
- Gopinath, Karthik1, 2
- Gazula, Harshvardhan1, 2
- Mount, Christopher3, 1, 2
- Kozanno, Liana N.3, 1, 2
- Marshall, Michael S.3, 1, 2
- Connors, Theresa R.3, 1, 2
- Frosch, Matthew P.3, 1, 2
- Montine, Mark4, 5
- Oakley, Derek H.3, 1, 2
- Mac Donald, Christine L.6, 5
- Keene, C. Dirk4, 5
- Hyman, Bradley T.3, 1, 2
- Fischl, Bruce1, 2
- Iglesias, Juan E.1, 2, 7, 8
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1.
Massachusetts General Hospital
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2.
Harvard Medical School
- 3. Massachusetts Alzheimer's Disease Research Center
- 4. Department of Laboratory Medicine and Pathology
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5.
University of Washington School of Medicine
- 6. Department of Neurological Surgery
-
7.
MIT Computer Science and Artificial Intelligence Laboratory
- 8. Hawkes Institute, University College London
Description
This dataset consists of 1,573 paired dissection photographs and manual segmentation masks of brain tissue slabs, acquired at Massachusetts General Hospital's Alzheimers Disease Research Center, and University of Washington's Department of Laboratory Medicine and Pathology. Segmentations masks were manually annotated to delineate the slab face, excluding background and out-of-slice tissue. This dataset is released alongside the paper "A public generalizable AI tool for automated segmentation of coronal brain tissue slabs for 3D neuropathology."
This dataset is intended to support the workflow for volumetric analysis of postmortem brain tissue. The segmentation mask serve as training data for an automatic segmentation model, facilitating image preprocessing for volumetric analysis tools such as FreeSurfer's photo tools https://surfer.nmr.mgh.harvard.edu/fswiki/PhotoTools which require segmentation of the slab face.
Files
images.zip
Additional details
References
- Ramirez, J.W., Zemlyanker, D., Deden-Binder, L., Herisse, R., Pallares, E.G., Gopinath, K., Gazula, H., Mount, C., Kozanno, L.N., Marshall, M.S. and Connors, T.R., 2025. Automated Segmentation of Coronal Brain Tissue Slabs for 3D Neuropathology. arXiv preprint arXiv:2508.09805.