Theoretical insight on the saturated stimulated emission intensity of a squaraine dye for STED nanoscopy

•We explore the key factors determining the stimulated emission cross section by theoretical calculations based on two dyes.•The increase of transition dipole moment and smaller molecular weight are beneficial for the increase of stimulated emission cross section.•Molecular flexibility results in the efficient depletion with TICT process of MitoEsq-635 than molecule vibration process of Atto647N.