To determine the brain-wide distribution of DNs when Aβ plaques cause selective loss of synapses, we first acquired three-dimensional whole-brain imaging of 5xFAD (a widely used AD mouse model with mutations in APP and PSEN1 genes leading to Aβ accumulation) mice with Thy1-YFP reporter at 6 months of age (5xFAD; Thy1-YFP). Here, APP is linked to Alzheimer disease.