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Dear Philipp,
Duplicate the stack, threshold for the structure then make the tholded stack binary
dividing by 255 converts the binarized stack from 0+255 to 0+1
multiply the 2 stacks and project the result.  
this function does all this, choosing middle slice for setting the threshold

Maybe this is helpful,

function thresholdprojection(){
	stackid=getImageID;
	no=nSlices;
	stackname=getTitle;
	run("Duplicate...", "title=[dup] duplicate range=1-no");
	setSlice((floor(no/2)));
	run("Threshold...");
	waitForUser("Set Threshold then click 'OK'.");
	setBatchMode(true);
	getThreshold(lower,upper);
	run("Make Binary", "black");
	run("Divide...", "value=255 stack");
	rename("divided");
	bindupid=getImageID;
	imageCalculator("Multiply create stack", stackid ,bindupid);
	run("Z Project...", "start=1 stop=no projection=[Sum Slices]");
	rename(stackname+"sum");
	sumid=getImageID;
	setBatchMode(false);
	selectImage(bindupid);//closing and renaming actions must occur outside of the batch mode
	close();
}

Regards,
Glen
Glen MacDonald
Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
Box 357923
University of Washington
Seattle, WA 98195-7923  USA
(206) 616-4156
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On Mar 21, 2012, at 8:20 AM, Philipp Bethge wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
> 
> 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