Useful for tissue sections, in vivo neurons, fixed tissue sections and cultured cells, these lipophilic neuronal tracers are used in both anterograde and retrograde transport studies.
Carbocyanine dyes, such as DiI and its derivatives, label cell membranes without appreciably affecting cell viability and can be used for long-term studies. The dyes uniformly label neurons via lateral diffusion in the plasma membrane, which is supplemented by active dye transport processes in living tissues. Crystal and paste preparations provide convenient options for loading tissues. Lipophilic tracers can be used to trace neuronal projections in fixed tissue sections. |
 Axons in the dorsonasal retina of a zebrafish embryo labeled with DiI, and nuclei counterstained with SYTOX® Green nucleic acid stain. |
Properties
| Readout | Labels cell membranes and does not appreciably affect cell viability. The dyes uniformly label neurons via lateral diffusion in the plasma membrane, supplemented by active dye transport processes in living tissues. Crystal and paste preparations provide convenient loading optons for tissue sections. | ||
| Tissue sections | Yes | ||
| In vivo neurons | Yes | ||
| Fixed tissue sections | Yes | ||
| Cultured cells | Yes | ||
| Cell loading | Iontophoresis, microinjection, or crystal/paste placement | ||
| Staining mode | Exogenous | ||
| Best for | Cell populations | ||
| Transport | Bidirectional | ||
| Photobleaching resistance |  |
||
| Synaptic transfer | No | ||
| Gap junction transfer | No | ||
| Bibliography | Citations—DiI | Citations—DiD | Citations—DiR |
Selection Guide
| Standard filter set(s) |
Fluorophore/ conjugate |
Ex/Em (nm) | Fixable | Format | Cat. No. | |
|---|---|---|---|---|---|---|
| "DiI" — DiIC18(3) | Rhodamine | DiI | 449/565 | No | Solid | D282 |
| "DiI" — DiIC18(3), crystalline | Crystal | D3911 | ||||
| NeuroTrace® DiI Tissue-Labeling Paste | Paste | N22880 | ||||
| Vybrant® DiI Cell-Labeling Solution | Solution | V22885 | ||||
| CellTracker™ CM-DiI | CM DiI | 449/565 | Yes | Solid | C7001 | |
| NeuroTrace® CM-DiI Tissue-Labeling Paste | Paste | N22883 | ||||
| Vybrant® CM-DiI Cell-Labeling Solution | Solution | V22888 | ||||
| "DiD" — DiIC18(5) | Cy®5 | DiD | 644/665 | No | Solid | D7757 |
| "DiR" — DiIC18(7) | Cy®5.5 | DiR | 750/780 | Solid | D12731 |