lsm plugin and background ROI subtration

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lsm plugin and background ROI subtration

how does LSM import plug in work?

Coudl the plugin underrrepresent an intesity in one channel in two channel LSM

I'm doing background subtraction in two channels LSM file separately using same
coorinate and same size ROI,  and sometimes one channels seems to get subracted
more(gets much less intense) using the same exact ROIs in both channels.

I don't knwo if this subttraction issue of having an LSM plugin open..

Not sure if anyone else have a similar exprience/problem.