Substract uneven background value from ROIs in image

[Spongiforma squarepantsii]

I have fluorescent images, with ROIs I detect (clusters, a few hundred in each image). However, the background fluorescence is very variable in the image. Some ROIs are surrounded by very little background, and some by a very intense background fluoresence. I would like to subtract a value for each ROI that best fits the background surrounding that particular ROI. How might I be able to do this?