Dataset Open Access
Tang, Ziqi;
Chuang, Kangway;
DeCarli, Charles;
Jin, Lee-Way;
Beckett, Laurel;
Keiser, Michael;
Dugger, Brittany
Datasets containing 63 whole slide images (WSIs) and their segmented 256x256 pixel tiles with approximately 80,000 tile-level amyloid-β pathology expert annotations.
Paper: "Interpretable classification of Alzheimer's disease pathologies with a convolutional neural network pipeline", bioRxiv 454793; DOI: https://doi.org/10.1101/454793.
Details: A total of 63 WSIs for 63 unique decedent cases spanning Alzheimer’s disease (AD) to non-AD and possessing a variety of CERAD scores. WSIs comprise three datasets as follows:
Datasets 1 and 2 were color-normalized and segmented to 256x256 pixel image tiles for model training set (61,370 images), validation set (8,630 images), and hold-out test set (10,873 images). Dataset 3 was color-normalized but not segmented.
Expert labels of plaques for Dataset 1 and 2 tiles are included in corresponding CSV files.
Slide source and preparation: All samples were retrieved from archives of the University of California, Davis Alzheimer’s Disease Center Brain Bank (https://www.ucdmc.ucdavis.edu/alzheimers/). Archival samples analyzed in this study were 5 μm formalin fixed, paraffin embedded sections of the superior and middle temporal gyrus from human brain. The tissue had been previously stained with an amyloid-β antibody (4G8, recognizing residues 17-24, BioLegend, formerly Covance) that were first pretreated with formic acid to rid samples of endogenous protein. All slides were digitized using an Aperio AT2 up to 40x magnification.
Code: Please visit https://github.com/keiserlab/plaquebox-paper
Name | Size | |
---|---|---|
Dataset 1a Development_train.zip
md5:f1b8413b61799a3350f7b431ecf2026f |
35.3 GB | Download |
Dataset 1b Development_validation.zip
md5:ffd0c30e55154901621972c16c259efa |
3.9 GB | Download |
Dataset 2 Hold-out.zip
md5:f0f69ccc39fe9e3072909ec48a1c057a |
41.2 GB | Download |
Dataset 3 CERAD-like hold-out.zip
md5:2200d5d0209fb35e77dfa0692eece03f |
26.3 GB | Download |
Tiles.zip
md5:1420e454def8f09eb945643ba5cfac53 |
3.3 GB | Download |
All versions | This version | |
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