macro "Background Corrected Density [F12]" {

//  Written by Paul Werten and Wayne Rasband (10.03.2005)
//
//  This macro uses the points along the selection boundary to calculate the
//  background of the selection, and then uses this value to calculate the
//  background-corrected integrated density. Size and shape of the selection
//  may be changed at any time during the measurements. To obtain meaningful
//  results, background values should be smaller than the actual data values
//  (i.e., the background should appear dark, while data should be light). It
//  may therefore be necessary to invert the image before analyzing it. Also,
//  for the macro to work, "Area" and "Mean" must first be selected in the 
//  "Analyze / Set Measurements" menu option. To actually measure, make an 
//  appropriate selection and use F12 to get the results.

    requires('1.34h');
     if (selectionType==-1)
        exit("Selection required");

    run("Measure");
    mean=getResult('Mean',nResults-1);
    stddev=getResult('StdDev',nResults-1);
    background=stddev*3.5 + mean;
    if (isNaN(mean))
        exit("StdDev and Mean must be be selected in Analyze>Set Measurements");
    setResult('Background',nResults-1,background);
    updateResults();
   print('The value of background: ', background);
run("Select None");
    setThreshold(0,background,'red');
run("Threshold...");
}



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