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Dr_analysis_Automated.ijm

+function action(input, output, filename) {
+        open(input + filename);
+        run("Duplicate...", "duplicate");
+		setMinAndMax(1, 2);
+		run("Apply LUT", "stack");
+		setThreshold(2, 255);
+		setOption("BlackBackground", true);
+		run("Convert to Mask", "method=Default background=Dark black");
+        saveAs("AVI", output + filename);
+        close();
+        for (i = 0; i < nSlices; i++) {
+					run("Create Selection");
+					run("Fit Ellipse");
+					//setTool("dropper");
+					setForegroundColor(0, 0, 0);
+					setForegroundColor(0, 0, 0);
+					run("Fill", "slice");
+					run("Measure");
+					run("Next Slice [>]");}
+		selectWindow("Results");			
+		saveAs("Results", path + name + "result.csv");
+		run("Clear Results");
+		close("*");
+}
+input = getDirectory("input Directory");
+output = getDirectory("output directory");
+list = getFileList(input);
+for (i = 0; i < list.length; i++)
+        action(input, output, list[i]);
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