DiD triflate is widely used as a fluorescent labeling agent in biological research, particularly for cell membrane staining and tracking. Its lipophilic nature allows it to integrate into cell membranes, making it ideal for long-term cell tracing and imaging studies.

It is commonly employed in fluorescence microscopy and flow cytometry to monitor cell migration, proliferation, and interactions in live-cell assays. Additionally, DiD triflate is utilized in multicolor imaging experiments due to its far-red emission, which minimizes interference from autofluorescence and enables deep tissue imaging.

Its stability and low cytotoxicity make it a valuable tool for in vitro and in vivo studies, including tumor cell tracking and neuronal mapping.