Determining x at ymax in the z-plot of an image stack

[Bertram Becher]

Hi group,

I've got a problem with extracting the slice number from that picture within a stack (256 images) at which the maximum intensity (in the Z-profile) is reached; or in other words:

a macro that gets the slice# n of that image where Y is at its maximum (max intensity of the Z-profile) and assign the slice# to a new gray tone (8-bit) of a resulting image.

Any suggestions?

Thank you in advance!

Bertram Becher



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Dr. rer. nat. Bertram Becher
Institut für Physiologie
Medizinische Fakultät der Ernst-Moritz-Arndt Universität Greifswald
Greifswalder Str. 11c
D-17495 Karlsburg (Germany)
Tel: [phone]
E-mail: [hidden email],  [hidden email]
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[Wayne Rasband]

> I've got a problem with extracting the slice number from that  
> picture within a stack (256 images) at which the maximum intensity  
> (in the Z-profile) is reached; or in other words:
>
> a macro that gets the slice# n of that image where Y is at its  
> maximum (max intensity of the Z-profile) and assign the slice# to a  
> new gray tone (8-bit) of a resulting image.
>
> Any suggestions?

Here is macro that finds the slice in a stack that has the maximum  
mean intensity, and then it creates a new image filled with that  
intensity value. If there is a selection, the means are calculated  
only from the selection.

-wayne

   max = 0;
   slice = 0;
   if (nSlices==1)
       exit("Stack required");
   for (i=1; i<=nSlices; i++) {
       setSlice(i);
       getRawStatistics(nPixels, mean);
       if (mean>max) {
           max = mean;
           slice = i;
       }
   }
   print("slice=", slice, ", mean=", max);
   run("Select None");
   run("Duplicate...", "title=MaxMean");
   setColor(max);
   fill();