BrainSec: Automated Brain Tissue Segmentation Pipeline for Scalable Neuropathological Analysis.

As neurodegenerative disease pathological hallmarks have been reported in both grey matter (GM) and white matter (WM) with different density distributions, automating the segmentation process of GM/WM would be extremely advantageous for aiding in neuropathologic deep phenotyping. Standard segmentation methods typically involve manual annotations, where a trained researcher traces the delineation of GM/WM in ultra-high-resolution Whole Slide Images (WSIs). This method can be time-consuming and subjective, preventing a scalable analysis on pathology images.