Dear Puneeta Bathla,

Have you considered using Fluorescence Lifetime? You can use FLIM for detecting FRET. It is possible to upgrade your fluorescence microscope with a HTS FLIM system that can automatically image your 96 well plates and show you the Lifetime results per well.

To be clear following link can be considered as a commercial response:

For an impression of how such a system works, please have a look at following link: https://goo.gl/JAVbNV

I hope this can help you further in your research.

Greetings,

Johan