Alzheimer’s disease (AD) pathogenesis is complex and remains poorly understood, particularly with respect to its initiating mechanisms. Neuronal hyperactivity, hypersynchrony and disruption of circuit homeostasis are reported to be early manifestations of cortical dysfunction in AD, often preceding beta-Amyloid plaque deposition. We propose to use chronic in vivo imaging and circuit connectivity analysis to develop functional biomarkers (for example abnormal neuronal response functions) that can be used to identify individual cells destined to malfunction early in the disease progression. We then propose to combine for the first time, in vivo functional biomarker identification with a recent cell- specific high-throughput in situ RNA hybridization technique (MERFISH), to identify which pathways lead to the earliest neuronal/glial dysfunction. Gene expression of targeted pathways will be profiled cell by cell and clustered to reveal cell-type, while taking into account both relative proximity to amyloid deposits and whether or not the cell has abnormal electrophysiological profile. Here, we focus on synaptic plasticity and neurotransmitter pathways because they are strongly involved in the pathophysiology of early AD and contribute to the associated cognitive decline. The methods that will be developed here are general and can be used in the future to dissect systematically other pathways implicated in AD or other neurological disorders.