background subtraction (again, but more questions)

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background subtraction (again, but more questions)

I am doing intensity measurements in two channels (ratio of blue/green )

And I have been struggling with the background subtraction.  

Consider you can open LSM using the plug in. Now you have to Backgroundsubract
from a ROI, but two channels have different background(?)

What happenes consequently is that sometimes, one channels is subracted more or
less giving erroneous representation of intensities in two channels.

One way to get around this, I think, is to do single background roi on both
channel images... Is this valid? (if not, why? )

Can I take a RGB merged image of the imported LSM file and background subract
from a given ROI in that?  Then, RGB-split them to get different images in two

Also what are the differences between Tiff file format (from LSM broswer) vs
LSm file opened using the Plugin?

Is there a difference?

I'm a little confused, so thanks all for any comments in advance.