/*
 * Go through your stack, marking ROIs
 * Rename the ROI in the following convention:
 * 		NAMEofTHING_LowerSlice-UpperSlice
 * 		Name of thing can NOT contain either '_' or '-'
 * Once all is complete, run below script
 * 
 * Save output as ROI file for CTan input
 */

roiManager("deselect");
run("Select None");
run("Duplicate...", "duplicate");
run("Select All");
setBackgroundColor(0, 0, 0);
run("Clear", "stack");

n = roiManager('count');
for (i = 0; i < n; i++) {
    roiManager('select', i);
    // process roi here
    getSelectionBounds(x, y, width, height);
    roiSlices = split(Roi.getName,"_");
    roiRange = split(roiSlices[1], "-");
    
    roiLower = roiRange[0];
    roiUpper = roiRange[1];
    
    for(s=roiLower; s<=roiUpper; s++) {
    	setSlice(s);
    	fill();
    }
    
}