Charting and understanding the full wiring diagram of complex neuronal structures such as the central nervous system or the brain (Connectomics) is one of the big remaining challenges in life sciences. Although at first it appears nearly impossible to map out a full diagram of, e.g., a mouse brain with sufficient resolution to identify each and every connection between neurons, recent technological advances move such an ambitious undertaking into the realms of possibility without spending decades at a microscope. However there are still many challenges to address in order to pave the way for fast and systematic neurobiological understanding of whole networks. These challenges range from a more robust and reproducible sample preparation to automated image data acquisition, more efficient data storage strategies and powerful data analysis tools. Here we will review novel imaging techniques developed for the challenge of mapping out the full connectome of a nervous system, brain or eye to name just a few examples. The imaging techniques reviewed cover light sheet illumination methods, single and multi-beam scanning electron microscopy, and we will briefly mention the possible combination of both light and electron microscopy. In particular we will review ‘clearing’ and in vivo methods that can be performed with light sheet fluroescence microscopes such as the ZEISS Lightsheet Z.1. We will then focus on scanning electron microscopy with single and multi-beam instruments including methods such as serial blockface imaging and array tomography methods.

Conventional scanning electron microscopes are limited in their ultimate data acquisition rate at a given resolution by statistical electron-electron interaction (so-called Coulomb interaction) as well as band width of detectors and deflection systems. We increased imaging speed dramatically by using multiple electron beams in a single column and parallel detection of the secondary electrons. The multi-beam SEM generates multiple overlapping images during a single scan pass, thereby covering a larger area in shorter time as compared to a single-beam SEM at the same pixel size. This addresses the upcoming need for high speed imaging at electron microscopic resolution to investigate larger and larger areas and volumes.