Quick visualization of neurons in brain tissues using an optical clearing technique

Anat Sci Int. 2019 Mar;94(2):199-208. doi: 10.1007/s12565-018-00473-z. Epub 2019 Jan 1.


Neurons are classified into several morphological types according to the locations of their somata and the branching patterns of their axons and dendrites. Recent studies suggest that these morphological features are related to their physiological properties, including firing characteristics, responses to neuromodulators, and wiring patterns. Therefore, rapid morphological identification of electrophysiologically recorded neurons promises to advance our understanding of neuronal circuits. One of the most common anatomical cell identification methods is neuronal reconstruction with biocytin delivered through whole-cell patch-clamp pipettes. However, conventional reconstruction methods usually take longer than 24 h and limit the throughput of electrophysiological experiments. Here, we developed a quick, simple cell reconstruction method by optimizing the tissue clearing protocol ScaleSQ. We found that adding 200 mM NaCl almost entirely prevented tissue swelling without compromising optical clearing ability. This solution, termed IsoScaleSQ, allowed us to increase the transparency of the gray matter of 500-µm-thick slices within 30 min, meaning that the total time required to reconstruct whole-cell recorded neurons was reduced to 1 h. This novel method will improve the efficacy and effectiveness of electrophysiological experiments linked to cell morphology.

Keywords: Isotropic; Optical clearing; Patch-clamp recording; ScaleSQ; Visualization.

MeSH terms

  • Animals
  • Brain / cytology*
  • Electrophysiology / methods*
  • Lysine / analogs & derivatives
  • Membrane Potentials
  • Mice, Inbred ICR
  • Mice, Transgenic
  • Neurons / cytology*
  • Neurons / physiology*
  • Patch-Clamp Techniques / methods*


  • biocytin
  • Lysine