Data for: Tang et al., Interpretable classification of Alzheimer's disease pathologies with a convolutional neural network pipeline. bioRxiv 2018.
Creators
- 1. Institute for Neurodegenerative Diseases, University of California, San Francisco
- 2. Department of Neurology, University of California, Davis School of Medicine
- 3. Department of Pathology and Laboratory Medicine, University of California, Davis School of Medicine
- 4. Department of Public Health Sciences, University of California, Davis
Description
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:
- Development (Phases I-II). 33 WSIs used for convolutional neural network (CNN) model development (29 training, 4 validation).
- 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.
- 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
Notes
Files
Dataset 1a Development_train.zip
Files
(110.0 GB)
Name | Size | Download all |
---|---|---|
md5:f1b8413b61799a3350f7b431ecf2026f
|
35.3 GB | Preview Download |
md5:ffd0c30e55154901621972c16c259efa
|
3.9 GB | Preview Download |
md5:f0f69ccc39fe9e3072909ec48a1c057a
|
41.2 GB | Preview Download |
md5:2200d5d0209fb35e77dfa0692eece03f
|
26.3 GB | Preview Download |
md5:1420e454def8f09eb945643ba5cfac53
|
3.3 GB | Preview Download |
Additional details
Related works
- Is supplement to
- 10.1101/454793 (DOI)
- https://github.com/keiserlab/plaquebox-paper (URL)