Modern microscopes are becoming increasingly complex instruments enabling registration of image sets far beyond a single field of view. This is being achieved by integration of sophisticated scanning stages, capable of moving the field of view in precise synchrony with acquisition, providing reliable meta data encoding time, space and multiple imaging modalities. As a result, increasingly complex multi-dimensional microscopic data sets are being generated and analyzed. For all these reasons, multifaceted workflows are required from sample preparation, through imaging to structuring and analyses of the image data. Studies of neuronal networks are a prime example of where complex image data facilitates our understanding of structural organization of neuronal circuits. The needs of large image data sets is amplified by the fact that in the CNS, elements of a single neuron span very large volumes, which ideally should be included in the image sets at appropriate resolution. It is also important to identify the neuropathological process at its emergence, where only rare events, representing foci of the nascent pathological process are present in otherwise normal brain tissue. In this webinar, we provide several examples of how modern light, electron and correlative microscopy facilitated our efforts to identify the underlying pathology associated with feeding and swallowing deficits present in a mouse model of 22q11D.2DS (LgDel). The webinar will highlight high-resolution confocal imaging approaches of a whole cleared embryos and reconstructions and analysis of single neurons. The values of large area light-to-SEM correlative workflows will be presented, followed by elastic backscatter imaging to produce TEM-like image sets both for generation of large area/high-resolution or 3D data sets for structural cellular analyses. Finally, the talk will underscore the value of postembedding immunogold detection of GABA-neurotransmitter using SEM backscatter imaging.