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_DKR_AutoMaxProject.ijm
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_DKR_AutoMaxProject.ijm
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//20090703 ciclistadan
//quick way to max project 2um of an image
// updated, 20130716
macro "go [q]"{
dir1 = getDirectory("home")+"/Desktop";
// Create an output directory within dir1
dir2 = dir1+File.separator+"crop";
if (File.exists(dir2)){}
else{
File.makeDirectory(dir2);
if (!File.exists(dir2))
exit("Unable to create directory");
}
//set the total um you want projected
depth=1.5;
//assume each slice is 500nm apart
slicedepth=depth/0.5;
Stack.getPosition(channel,slice,frame);
getDimensions(width, height, channels, slices, frames);
if(slice-1<=0) bottom=0;
else bottom = slice-1;
if(slice+1>=slices) top=slices;
else top = slice+1;
name = getTitle();
//duplicate, this will crop an ROI if present, otherwise do the whole image
run("Duplicate...", "title=dup duplicate");
run("Z Project...", "start="+bottom+" stop="+top+" projection=[Max Intensity]");
//append the new file with prj
newname = name;
newname = replace(newname,".tif","-prj.tif");
selectWindow("MAX_dup");
rename(newname);
saveAs("Tiff", dir2+File.separator+newname);
close();
selectWindow("dup");
close();
}