Juan C. Vizcarra
BME PhD Defense Presentation

Date: 2024-01-05
Time: 3:00 PM-5:00 PM
Location / Meeting Link: HSRB-II N600 Conference Room / https://emory.zoom.us/j/99439330760?pwd=cnlYYXNNSHhzay90ZTVEVGFmYWpxUT09

Committee Members:
David A. Gutman, MD/PhD (Advisor); May D. Wang, PhD; Jia Shu, PhD; Eva L. Dyer, PhD; Thomas M. Pearce, MD/PhD


Title: Machine Learning in Digital Neuropathology: Towards a Large-Scale Analysis Platform for Federated Cohorts

Abstract:
Millions of people suffer from neurodegenerative diseases, including Alzheimer’s disease, Parkinson’s disease, and related disorders. Post-mortem analysis of brain tissue is essential in improving our understanding of the underlying biological mechanisms of neurodegeneration. Modern techniques allow digitization of brain tissue glass slides into large images that are rich in data for computational analysis. Developing effective image analysis tools for these datasets is challenging because datasets vary widely, are rarely reported completely, and need to be developed with the expert user, neuropathologist, in mind. To address these concerns, this dissertation focused on the intersection between neuropathology, modern computational analysis and data management. In Aim 1, I implemented an inter-rater and inter-annotator study to measure the variability amongst experts and novices in two important tasks related to Alzheimer’s disease pathology: detection of neurofibrillary tangles (NFTs) in tissue images and Braak NFT staging. In Aim 2 I explored the ability to utilize modern computational approaches in machine learning to perform the tasks in Aim 1 and show that even with imperfect ground truth, computational approaches can mimic and perform similar to experts in the field. Finally in Aim 3, I developed a suite of tools, including the NeuroTK platform, to provide all the necessary tools for neuropathologists to run novel large scale image analysis studies. The results of this work highlight the impact of machine learning in neuropathology and provide a suite of powerful open-source tools that will open up large scale computational analysis of neuropathological datasets.