Fluorescent dyes can have similar maximal excitation and emission wavelengths but may have differing brightness. Bright fluorescent dyes are preferred for low abundance markers and rare events, while dimmer dyes are preferred for high abundance markers. In panel design, knowing the relative brightness of all your dyes will help improve your panel design, make analysis easier, and enable you to build bigger, better panels.

This page provides a handy reference guide when choosing a fluorescent dye for your experiment. We have calculated the stain index of our new StarBright Dyes and other commonly used dyes in flow cytometry on the ZE5 Cell Analyzer to help you choose the right dyes for your experiments.

355 nm Ultraviolet Excitable Dyes

Fig. 1. Stain index comparison.


Fig. 1. Stain index comparison. Stain index of human peripheral blood stained with various 355 nm excitable StarBright UltraViolet, Brilliant Ultraviolet, and conventional dyes conjugated to CD4 (MCA1267). Data generated are the average of 3–4 donors, antibodies were titrated before use and analyzed on the ZE5 Cell Analyzer. Purple, StarBright Dyes, red, Brilliant Violet, yellow, other non-polymer dyes.


405 nm Violet Excitable Dyes

Fig 2. Stain index comparison.


Fig. 2. Stain index comparison. Stain index of human peripheral blood stained with various 405 nm excitable StarBright Violet, Brilliant Violet, Super Bright, and conventional dyes conjugated to CD4 (MCA1267). Data generated are the average of 3–4 donors, antibodies were titrated prior to use and analyzed on the ZE5 Cell Analyzer. Purple, StarBright Dyes; red, Brilliant Violet; green, Super Bright; yellow, non-polymer dyes.


Many factors can influence the appearance of data. This can be the flow cytometer, filters and laser used to excite the fluorophore, the laser power, and instrument settings as well as the type of plot chosen. For this reason, we recommend using this data as a guide only and calculating the stain index on your own instrument.

For more information about fluorophores and immunophenotyping, refer to our flow cytometry resources. Click on the links below to find more in-depth information on each topic and view our popular flow cytometry basics guide.