JC-1 is not very photostable so you have to minimise the amount of light you use for imaging. Use your detector with the max sensitivity that does not produce problomatic noise. Reduce your resolution, (open the pinhole, fewer pixcels, less averaging) so you can use less light overall. Take fewer images of the same region.

thanks for your reply, yes i have already done all the points you mentioned plus I am doing bidirectional resonance scanning. I was hoping maybe there is another thing I can improve!

You can also try to use an objective lens with less magnification.