First, make sure you are exciting and detecting the dye in the appropriate wavelengths. Next, try optimizing the dye concentration with your controls, as well as the dye staining time. Our manuals have some guidelines. If you are using a live-cell system, we also recommend washing out any unreacted dye for many of our products to reduce background fluorescence, or adding a background suppressor such as BackDrop Suppressor ReadyProbes Reagent. Check your instrument settings; some plate readers, for instance, may have a means of adjusting the gain setting to get the best signal-to-background. Finally, some dyes are better than others for degree of change upon ion detection. Contact Tech Support by sending an email to techsupport@thermofisher.com if you would like to discuss dye options.
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Cell Analysis Support Center.