New contrasting methods, imaging tools, and data analysis strategies allow the observation of otherwise complex or hidden relationships between cellular, subcellular, and molecular constituents of cells and tissues. I will describe how advances in multi-tilt electron tomography, the development of new probes for correlated light microscopy, X-ray micro-CT, correlated multi-ion mass spectroscopy imaging and electron microscopy, and state-of-the-art 3D EM technologies add to our knowledge of structure and function in complex biological systems. Recent accomplishments include the determination of the higher-order structure and functional organization of chromatin in intact cell nuclei; the analysis of actin-associated structures within dendritic spines; and analyses of the extracellular matrix (ECM) around multiple synapse types in mammalian brains. The ECM work explores Roger Tsien’s theory that the brain stores life-long memories by regulating the activity of extracellular proteases and thereby influences the locations and relative strengths of synapses over a lifespan.