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Dear John,
You may be interested in another solution to measuring pixel intensities in
Zeiss files. I have written a program that reads lsm files (uncompressed)
and allows pixel based analysis (including F/Fo). The program is available
from my website here in Cambridge.
http://rct-cjs3.physiol.cam.ac.uk
It allows background subtraction and F/Fo images to be produced easily and
quickly, leaving the time domain intact (i.e. it does not assume that all
images are taken at the same rate).
Greetings,
Christof