Learning fast and fine-grained detection of amyloid neuropathologies from coarse-grained expert labels

• Published in: Communications biology Vol. 6; no. 1; p. 668
• Main Authors: Wong, Daniel R., Magaki, Shino D., Vinters, Harry V., Yong, William H., Monuki, Edwin S., Williams, Christopher K., Martini, Alessandra C., DeCarli, Charles, Khacherian, Chris, Graff, John P., Dugger, Brittany N., Keiser, Michael J.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 24.06.2023; Nature Publishing Group; Nature Portfolio
• Subjects: 13/51; 14/1; 14/63; 59; 631/114/1305; 631/114/1564; 692/617/375/1937; 692/699/375/364; 692/699/375/365/1283; Amyloid; Amyloidogenic Proteins; Biology; Biomedical and Life Sciences; Cerebral amyloid angiopathy; Deep learning; Humans; Life Sciences; Neuropathology; Plaque, Amyloid; Plaques; Records; Sensors; Staining and Labeling; Virion; Work stations
• ISSN: 2399-3642; 2399-3642
• DOI: 10.1038/s42003-023-05031-6

Precise, scalable, and quantitative evaluation of whole slide images is crucial in neuropathology. We release a deep learning model for rapid object detection and precise information on the identification, locality, and counts of cored plaques and cerebral amyloid angiopathy (CAA). We trained this object detector using a repurposed image-tile dataset without any human-drawn bounding boxes. We evaluated the detector on a new manually-annotated dataset of whole slide images (WSIs) from three institutions, four staining procedures, and four human experts. The detector matched the cohort of neuropathology experts, achieving 0.64 (model) vs. 0.64 (cohort) average precision (AP) for cored plaques and 0.75 vs. 0.51 AP for CAAs at a 0.5 IOU threshold. It provided count and locality predictions that approximately correlated with gold-standard human CERAD-like WSI scoring ( p  = 0.07 ± 0.10). The openly-available model can quickly score WSIs in minutes without a GPU on a standard workstation. A deep learning model rapidly identifies locality and counts of cored plaques and cerebral amyloid angiopathy in whole slide images comparably to human experts and without a GPU on a standard workstation.