ABSTRACT A comprehensive census of neural cell types in the brain, together with molecular-genetic resources for cell-type specific labeling, is revolutionizing our ability to detect and monitor age, disease, and experience-dependent changes in neural connectivity. Fluorescence-based methods for quantitative synapse analysis would be easily adopted by the scientific community and have been widely used in neuronal cultures, but have not been well-developed for analysis of connectivity in brain networks, due to concerns about resolution and accuracy of detected contacts and difficulty of reagent use. Here we will use recently-developed tools for fluorescent synaptic labeling to develop a workflow to evaluate and mitigate concerns about fluorescence- based measurements in brain tissue using state-of-the-art Expansion Microscopy methods. We will then test the ability of these reagents to drive new insights about input-specific plasticity during learning, using a well-characterized training paradigm where electrophysiological changes in thalamocortical synaptic strength have been demonstrated.