Our labeling reagents enable researchers to create their own labeled biomolecule for use in immunochemistry, fluorescence in situ hybridization (FISH), cell tracing, receptor labeling, and cytochemistry applications as well as for probing biological structure, function, and interactions.

We also offer our fluorophores conjugated to a variety of antibodies, streptavidin, peptides, proteins, tracers, and amplification substrates optimized for cellular labeling and detection.

Use these quick guides to select the right tools for your application or explore the resource links for more options.

Broad range of available fluorophores

We have developed an extensive catalog of fluorescent products using a range of technologies, and some of the most widely used are listed below. Which fluorophore you choose depends on the experiment you are doing and the instrument that you will use to measure the signal. find more detailed information on the fluorophore and its use by clicking on a hyperlinked dye name below.

Invitrogen fluorescent dyes
  Alexa Fluor 350   Alexa Fluor 647   Oregon Green
  Alexa Fluor 405   Alexa Fluor 680   Fluorescein (FITC)
  Alexa Fluor 488   Alexa Fluor 750   Cy3
  Alexa Fluor 532   Pacific Blue   Pacific Orange
  Alexa Fluor 546   Coumarin   Tetramethylrhodamine (TRITC)
  Alexa Fluor 555   BODIPY FL   Texas Red
  Alexa Fluor 568   Pacific Green   Cy5
  Alexa Fluor 594        
Super Bright dyes
  Super Bright 436   Super Bright 600   Super Bright 645
  Super Bright 702
Invitrogen DNA Stains
  DAPI
  SYTOX Green
  SYTO 9
  TO-PRO-3
  Propidium Iodide
   
   
Invitrogen Qdot probes
  Qdot 525
  Qdot 565
  Qdot 605
  Qdot 655
  Qdot 705
  Qdot 800
   
Fluorescent protein labels
  R-Phycoerythrin (R-PE)
  Allophycocyanin (APC)
Expressed fluorescent proteins
  CFP
  GFP (emGFP)
  RFP (tagRFP)

Fluorophore dashboards

The fluorophore dashboard (sample below) allows you to visualize the performance of a selected fluorophore and determine whether it is suitable for your application and where it can be used to best effect. The dashboard provides a summary of key properties—more details are available on the product page.

  • Initial brightness indicates the relative brightness of the fluorophore, which is a product of the molar extinction coefficient and quantum yield, both of which are specific to each fluor. Fluorophores with high initial brightness can be used to detect lower-abundance targets
  • Photostability in buffer is a relative measure of the percentage of initial fluorescence intensity remaining following 30 seconds of continuous illumination using a 40x/1.4NA objective and a 100-watt Hg-arc lamp as the light source with samples mounted in phosphate buffer; high photostability in buffer is ideal for live-cell imaging and detection
  • Photostability in antifade buffer is a relative measure of the percentage of initial fluorescence intensity remaining following 30 seconds of continuous illumination using a 40x/1.4NA objective and a 100-watt Hg-arc lamp as the light source with samples mounted in Invitrogen ProLong Gold or SlowFade Gold antifade reagent; high photostability in antifade reagent is ideal for fixed-cell imaging and detection
  • Stain index is a normalized value that allows users to compare the brightness of various dyes in flow cytometry applications; it is derived by subtracting the mean fluorescence intensity (MFI) of the negative population from the MFI of the positive population and dividing the resulting value by twice the standard deviation of the negative population
  • Laser line indicates the commonly used laser line(s) for detection using flow cytometry
  • Common filter set indicates the standard microscope filter set that generates the best imaging results
  • Excitation max indicates the peak excitation wavelength (see the Fluorescence SpectraViewer for a complete profile)
  • Emission max indicates the peak emission wavelength (see the Fluorescence SpectraViewer for a complete profile)
  • Performance in SRM is a normalized value that allows users to compare the brightness of various dyes in SRM applications; SRM determinations were made in the optimum buffer type for each dye (MEA, BME, or TCEP) as described in the SRM buffer table.

Sample fluorophore dashboard


Initial brightness
 
 
 

 

  
   

 

Summary section highlighting the features of the fluorophore and its typical applications and multiplex compatibility.

 

  

Photostability in buffer
 
 
 
 
 
 
     

Photostability in antifade
 
 
 
 
 
 
   

Performance in SRM
 
 
 
 
 
  92 488 FITC 490 525  
 
Stain index
Laser line
Common filter set
Excitation max


Emission max

  

Resources

Molecular Probes Handbook

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

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.

Learn more about SlowFade Antifade reagents
Learn more about ProLong Antifade reagents

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

For Research Use Only. Not for use in diagnostic procedures.