createVNSorthogViews.ijm

name = getArgument;
if (name=="") exit ("No argument!");
setBatchMode(true);
sep=lastIndexOf(name, File.separator);
path = "";
file = name;
if (sep>-1) {
  path = substring(name, 0, sep);
  file = substring(name, sep);
}
run("Nrrd ...", "load=[" + name + "]");
run("Nrrd ...", "load=[/Volumes/Macintosh HD/Users/robertcourt/GIT/DrosAdultTAGdomains/template/Neuropil_padded_LPS.nrrd]");
run("Merge Channels...", "c1=Neuropil_padded_LPS.nrrd c2=" + file + " c3=Neuropil_padded_LPS.nrrd create keep ignore");
run("Z Project...", "projection=[Max Intensity]");
saveAs("PNG", path+File.separator+replace(file,".nrrd","_zMAX.png"));
close();
run("Reslice [/]...", "output=0.460 start=Left rotate avoid");
run("Z Project...", "projection=[Max Intensity]");
saveAs("PNG", path+File.separator+replace(file,".nrrd","_xMAX.png"));
close();
close();
run("Reslice [/]...", "output=0.460 start=Top avoid");
run("Z Project...", "projection=[Max Intensity]");
saveAs("PNG", path+File.separator+replace(file,".nrrd","_yMAX.png"));
close();
close();
close();
close();
close();
run("Quit");