I am working with plant extract, and I measure its antibacterial activity by measuring the fluorescent signal from the live cells by using Tecan System (work with multitier plate). I faced an issue in which the treated well with the water extract showed lower signal compared to the control (non-treated wells). I think this is due to the chlorophyl or pigment within the extract.

I already treat the extract with non-polar solvent like hexan or chloroform but still the pigment was not removed and signal was blocked.

In the extraction method, I extracted with water.

Is there any practical method to get ride from this effect?