Photo- and bio-physical characterization of novel violet and near-infrared lipophilic fluorophores for neuronal tracing

J Microsc. 2010 Aug 1;239(2):117-34. doi: 10.1111/j.1365-2818.2009.03363.x.


Lipophilic fluorescent dyes have been used to trace neuronal connections because of their ability to diffuse laterally within nerve cell membranes. Given the hundreds to thousands of connections that a typical neuron makes with its neighbours, a diffusion-matched set of spectrally distinct dyes is desirable. To extend a set of these dyes to obtain six independent labels, we have characterized the properties of novel violet and near-infrared candidates. By combining two-photon and confocal microscopy all of these candidates can be imaged using a single Titanium Sapphire laser. Here we present measurements of the two-photon action cross-sections and diffusion properties of the dyes, using either the relative diffusion distance or fluorescence recovery after photobleaching techniques, and demonstrate six-colour neuronal tracing within the spinal cord and brain tissue.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Brain / cytology
  • Fluorescent Dyes / pharmacology*
  • Mice
  • Microscopy, Confocal / methods*
  • Neurons / cytology*
  • Spinal Cord / cytology
  • Staining and Labeling / methods*


  • Fluorescent Dyes