PathFlowAI: A High-Throughput Workflow for Preprocessing, Deep Learning and Interpretation in Digital Pathology.

ABSTRACT: The diagnosis of disease often requires analysis of a biopsy. Many diagnoses depend not only on the presence of certain features but on their location within the tissue. Recently, a number of deep learning diagnostic aids have been developed to classify digitized biopsy slides. Clinical workflows often involve processing of more than 500 slides per day. But, clinical use of deep learning diagnostic aids would require a preprocessing workflow that is cost-effective, flexible, scalable, rapid, interpretable, and transparent. Here, we present such a workflow, optimized using Dask and mixed precision training via APEX, capable of handling any patch-level or slide level classification and prediction problem. The workflow uses a flexible and fast preprocessing and deep learning analytics pipelin

SUBMITTER: Levy JJ 

PROVIDER: S-EPMC6919317 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature