SIMVIEW_Multistack-ZProj_FijiMacro

gistfile1.txt

path = getDirectory("Choose a Directory");
filename = getFileList(path);
newDir = path + "Max Projections" + File.separator;
if (File.exists(newDir))
   exit("Destination directory already exists; remove it and then run this macro again");
File.makeDirectory(newDir);
for (i=0; i<filename.length; i++) {
        if(endsWith(filename[i], ".stack")) {
                run("Raw...", "open=["+path+filename[i]+"] image=[16-bit Unsigned] width=1024 height=624 number=20000 little-endian");      
                //run("Z Project...", "projection=[Max Intensity]");
                run("Z Project...", "projection=[Average Intensity]");
                saveAs("tiff", newDir + getTitle);
                close(); close();
        }
}