Cy®3 dye

Invitrogen Cy3 dye is a bright, orange-fluorescent dye that can be excited using the 532 nm laser line and visualized with TRITC (tetramethylrhodamine) filter sets. In addition to immunocytochemistry applications, Cy3 dye is commonly used to label nucleic acids.

The Cy3 fluorophore is also the basis for the lipophilic neuronal and long-term DiI cell tracing reagents, which append alkyl tails (≥12 carbons) onto the core fluorophore.

Invitrogen Alexa Fluor 555 dye is a Cy3 dye alternative that is generally more fluorescent and more photostable than Cy3 dye, making it well suited for applications such as imaging and flow cytometry.

Cy3 dye dashboard

Initial brightness

The Cy3 dye is a traditional orange-fluorescent label for protein and nucleic acid conjugates used for imaging, flow cytometry, and genomic applications. It is also the basis for the classic lipophilic tracer DiI and its variants.  

Photostability in buffer


Photostability in antifade


  488/532 TRITC 554 568  
Laser line

Common filter set

Excitation max

Emission max

Cy3 products

We offer a range of Cy3 dye and DiI products including secondary antibodies, streptavidin conjugates, kits, and more. Learn more here:

Learn more about fluorescent dyes in the Cy3 dye wavelength range

See all Cyanine3 Primary Antibodies
See all Cyanine3 Secondary Antibodies


Double labeling of tubulin and HA-tagged tubulin in T. thermophila using Cy3-goat anti-rabbit and FITC-goat anti-mouse.

High-performance alternatives to Cy3 dye

Fluorescent conjugates

The Alexa Fluor 555 dye—with nearly identical spectral properties to Cy3 dye—produces brighter, more photostable conjugates. These conjugates are ideal for imaging and other applications requiring increased sensitivity and environmentally insensitive fluorescence detection.

We offer Alexa Fluor 555 dye conjugated to a variety of antibodies, peptides, proteins, tracers, and amplification substrates optimized for cellular labeling and detection. In addition, reactive dye forms and protein labeling kits are available to allow you to generate your own antibody conjugates or probes.

Learn more about Alexa Fluor 555 dye

Comparison of the relative fluorescence of goat anti–rabbit IgG antibody conjugates of Alexa Fluor 555 and Cy3 dyes (prepared in our laboratories) at different dye:protein ratios in the conjugate.


Molecular Probes Handbook

Cell stain tool

The significantly revised 11th Edition is the most complete fluorescence labeling and detection reference available. The Molecular Probes Handbook can help you achieve the best experimental results for your fluorescence labeling and detection experiments. View the handbook online or order your own copy.

Go to the Handbook online
Order your copy of the Handbook

Antifade reagents

Cell stain tool

Antifade reagents suppress photobleaching and preserve the signals of your fluorescently labeled target molecules. They offer excellent compatibility with a multitude of dyes across the spectrum, making them especially valuable tools for multicolor applications. For added convenience, some formulations include the nuclear counterstain DAPI, eliminating the need for a separate counterstaining step.

See the performance of this dye in SlowFade Antifade reagents
See the performance of this dye in ProLong Antifade reagents

Cell stain tool

Cell stain tool

Stain your own cell by using our simulation tool to develop reproducible results with many of our signature fluorescent dyes. Develop your multiplexing strategy for antibody probes, reactive dyes, and counterstains to create your perfectly labeled fluorescent cell.

Go to the cell stain tool

Fluorescence SpectraViewer


Plot and compare spectra and check the spectral compatibility for common fluorophores including all of the fluorescent probes from Thermo Fisher Scientific. The Fluorescence SpectraViewer tool is formatted for both microscope imaging and flow cytometry applications.

Go to the Fluorescence SpectraViewer

Not for resale. Super Bright Polymer Dyes are sold under license from Becton, Dickinson and Company.