There are some suggestions about this; please take a look at it.
•Alexa Fluor Dyes: These are widely used and offer a range of excitation and emission wavelengths, allowing for compatibility with different lasers and filters on the confocal microscope.
•FITC (Fluorescein Isothiocyanate): This classic green fluorescent dye can effectively label proteins.
•Rhodamine Dyes: These provide red fluorescence and can be used with green dyes for dual labeling experiments.
•Cy Dyes are versatile and offer a range of excitation and emission spectra for multi-color labeling.