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Nat Neurosci. 2013 Aug;16(8):1154-61. doi: 10.1038/nn.3447. Epub 2013 Jun 23.

SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction.

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Laboratory for Sensory Circuit Formation, RIKEN Center for Developmental Biology, Kobe, Japan.


We report a water-based optical clearing agent, SeeDB, which clears fixed brain samples in a few days without quenching many types of fluorescent dyes, including fluorescent proteins and lipophilic neuronal tracers. Our method maintained a constant sample volume during the clearing procedure, an important factor for keeping cellular morphology intact, and facilitated the quantitative reconstruction of neuronal circuits. Combined with two-photon microscopy and an optimized objective lens, we were able to image the mouse brain from the dorsal to the ventral side. We used SeeDB to describe the near-complete wiring diagram of sister mitral cells associated with a common glomerulus in the mouse olfactory bulb. We found the diversity of dendrite wiring patterns among sister mitral cells, and our results provide an anatomical basis for non-redundant odor coding by these neurons. Our simple and efficient method is useful for imaging intact morphological architecture at large scales in both the adult and developing brains.

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