Connectomics is an emerging field that aims to generate and analyse neuronal connectivity data with high-throughput to gain knowledge about the brain. The realization of this goal largely depends on the development of innovative microscopy techniques that can produce large-scale three-dimensional images of brain tissue at nanoscale resolution and automated analysis tools that can extract relevant information from these images. This review surveys the challenges associated with generating the images needed for neuronal connectivity maps and how these challenges may be overcome by novel optical methods that allow sub-diffraction-limit imaging.
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