Macro to make Z-projections from .lif stacks

Posted by Luis Boero on Jul 06, 2016; 7:42pm
URL: http://imagej.273.s1.nabble.com/Macro-to-make-Z-projections-from-lif-stacks-tp5016822.html

Hi! I´ve been trying to develop a macro to get z projections from the stacks I take in the microscope.

run("Bio-Formats Macro Extensions");
inputFolder=getDirectory("");
images=getFileList(inputFolder);
NewDir=inputFolder+"Procesadas";
//File.makeDirectory(NewDir); // creo la carpeta

for (i=0; i<images.length; i++) {
        path=inputFolder+images[i];
        filename=images[i];
        Ext.setId(path);
        Ext.getSeriesCount(seriesCount);
       
        for (j=1; j<=seriesCount; j++) {
                       
                run("Bio-Formats", "open=path autoscale color_mode=Default view=Hyperstack split_channels stack_order=XYCZT,j);
               
                list = getList("image.titles");
  if (list.length==0)
             print("No image windows are open");
  else {
             //print("Image windows:");
             for (k=0; k<=list.length; k++) {
            print("   "+list[k]);
            selectWindow();
            run("Z Project...", "projection=[Max Intensity]");
            close(title);
  }
  }
}

When I run the macro, I only get the Max Projection from the channel that corresponds to k=1, but the other one remains as a substack. What can I do?

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