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Dear all,

I was wondering if somebody has worked with a 'smart' average 
z-projection, that is a average projection of a z-stack that does not 
average of the entire stack size but only over the slides where a signal 
is actually present. So, for example, one has an oblique structure in a 
large stack, lets say the structure has a z-extension of 4 slides but 
the whole stack is 30 stacks large. As I understand the regular average 
z-projection algorithm in ImageJ, every pixel is summed and devided by 
the total number of slides in the stack. Then the signal of only 4 
slides would be averaged over 30 slides, therefore reducing signal 
intensity dramatically without further reducing background noise.
Of course, one would have to define 'signal' somehow, but I guess that 
could be done manually by binarization of the image slides individually.

Any suggestions welcome,

Thanks alot,

-- 
Philipp Bethge