Marking microelectrode penetrations with fluorescent dyes

James J. DiCarlo, John W. Lane, Steven S. Hsiao, Kenneth O. Johnson

Research output: Contribution to journalArticlepeer-review

101 Scopus citations


Fluorescent dyes were used to mark and identify the tracks left by extracellular microelectrodes in neurophysiological experiments. Forty-two penetrations were made into the postcentral gyrus of 3 Macaque monkeys with electrodes coated with 1 of 5 fluorescent dyes (DiI, DiO, DiI-C5, PyPO, and Fast Blue). The electrodes were driven at rates ranging from 10 to 1000 μm/min, to a depth of about 4000 μm, where a small electrolytic lesion was made. Histological sections were viewed under fluorescent optics and the electrode tracks were reconstructed from the dye traces. Fluorescent traces (width 50-400 μm) were observed in 41 of 42 penetrations with 24 traces extending to the lesion site. Of the electrodes driven in less than 3 h, those coated with DiI (8/8) and DiI-C5 (8/8) left a trace to the lesion site, while 57% (4/7) of the DiO, 40% (2/5) of the Fast Blue and only 11% (1/9) of the PyPO tracks were fully marked. This method of marking penetrations can be used with any extracellular recording configuration, does not require tissue sections to be processed or stained, does not require electrical lesions, and causes no detectable tissue damage. Because the dyes fluoresce at different wavelengths, closely spaced tracks can be uniquely identified.

Original languageEnglish (US)
Pages (from-to)75-81
Number of pages7
JournalJournal of Neuroscience Methods
Issue number1
StatePublished - Jan 1996
Externally publishedYes


  • Cortex
  • Fluorescence
  • Lamina
  • Mapping
  • Microelectrode
  • Monkey
  • Neural recording
  • Reconstruction

ASJC Scopus subject areas

  • Neuroscience(all)


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