Optimizing conditions and avoiding pitfalls for prolonged axonal tracing with carbocyanine dyes in fixed rat spinal cords

Bingkun K. Chen, Steven M. Miller, Carlos B. Mantilla, Lou Ann Gross, Michael J. Yaszemski, Anthony J. Windebank

Research output: Contribution to journalArticlepeer-review

14 Scopus citations


We have characterized a method of labeling of axons in the post-mortem spinal cord using a silastic disc holding pins coated with DiI and DiO at the rostral and caudal ends of the cord. We optimized the DiI and DiO tracing techniques under different conditions of fixative concentration (1% versus 4% paraformaldehyde, PF), at room temperature (RT) versus 37 °C for up to 24 weeks. Crystal coated pins embedded in a silastic disc provided a novel method of dye application. Confocal microscopy of longitudinal sections showed DiI and DiO labeled both the axonal membrane and myelin sheath. DiI diffused significantly longer distances than DiO. Both dyes migrated greater distances at 37 °C compared with RT. No significant difference of dye labeling was found between 1% and 4% PF fixation. After prolonged incubation there was evidence that dye diffused through the aqueous medium and produced circumferential labeling of the cord. Placing a wax seal around the labeling site prevented this non-contiguous labeling. Labeling of myelin sheaths at extended distances into the cord suggested that dye could migrate between cells with prolonged incubation periods. Our data suggested that higher temperature facilitated dye diffusion along the axons, and demonstrated that with caution DiI and DiO could be used as specific tracers in the same spinal cords.

Original languageEnglish (US)
Pages (from-to)256-263
Number of pages8
JournalJournal of Neuroscience Methods
Issue number1-2
StatePublished - Jun 30 2006


  • Axon tracing
  • DiI
  • DiO
  • Spinal cord injury
  • Trans-cellular migration

ASJC Scopus subject areas

  • General Neuroscience


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