Automated multiscale high-content imaging connects plaque population heterogeneity to localized synapse loss

Synapse loss is a major correlate of cognitive decline in neurodegenerative disease, yet its relationship to localized pathology remains difficult to study at scale. Conventional confocal imaging approaches are limited by low throughput, selection bias, and restricted sampling of pathological features. Here, we describe an automated high-content imaging and analysis workflow that enables large-scale quantification of amyloid beta plaque-associated synapse loss within mouse brain tissue. Using Preciscan-based multiscale acquisition on the Opera Phenix platform, this workflow combines tissue-wide pathology mapping with targeted high-magnification imaging and subcellular analysis. We apply this framework to acquire and analyze hundreds of plaque images in the CRND8 mouse model of Aβ proteinopathy, demonstrating plaque-associated synapse loss within developing plaque populations over disease progression. We find that small diffuse plaques accumulate rapidly at late stages in CRND8, but that the primary synapse loss comes from large cored plaques. More broadly, this scalable framework enables systematic investigation of subcellular phenomena across pathological microenvironments in disease models.