Cy5.5 NHS ester is widely used in bioimaging and molecular labeling due to its near-infrared fluorescence properties. It is particularly valuable in in vivo imaging studies because its emission wavelength penetrates tissues deeply, minimizing background autofluorescence. This makes it ideal for tracking biological processes, such as tumor targeting, cell migration, and drug delivery, in live animals. Additionally, it is commonly conjugated to antibodies, peptides, or proteins for specific labeling in fluorescence microscopy and flow cytometry. Its stability and high sensitivity also make it suitable for diagnostic applications, including the detection of biomarkers in complex biological samples.