November 1, 2018 Dataset Open Access

Data for: Tang et al., Interpretable classification of Alzheimer's disease pathologies with a convolutional neural network pipeline. bioRxiv 2018.

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:

1. Development (Phases I-II). 33 WSIs used for convolutional neural network (CNN) model development (29 training, 4 validation).
2. Hold-out (Phase III). 10 WSIs selected by an expert neuropathologist as a held-out test set to assess the generalizability of the CNN model.
3. CERAD-like hold-out. 20 blinded WSIs collected solely for use in a CERAD-like scoring comparison study.

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