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Structure-photophysical relationship chart of visible and NIR dyes. From ‘top to down’ or ‘left to right’ within the core, increase in absorption and emission (red-xanthene substituent /orange-phenyl ring substituent), Increase in quantum yield (green), increase in cell permeability (purple), and increase in solubility in water (blue). Compound naming consist of first letter (F, R, X, or C) of core scaffold and its maximum absorption. R group is HaloTag ligand.
