feature: more robust bead segmentation

src/main/resources/scripts/Plugins/NoiSee/NoiSee_Bead_Analysis.ijm

@@ -542,8 +542,8 @@ function mapTo8bitPreservingSaturation(effectiveBits) {
     run("Divide...", "value=" + divisor + " stack");
     setMinAndMax(0, 255);
     run("8-bit");
-
-    return divisor;
+
+    return divisor;
 }
 
 function clear_workspace() {
@@ -694,7 +694,7 @@ function process_beads() {
 
     ////////// find beads and create a mask (binary image) ////////// ////////// //////////
     imgs_beadmask = duplicateImage(imgs_orig, "beadmask", false);
-    // run("Convert to Mask", "method=IsoData background=Dark calculate black"); // does not work anymore somehow
+    run("Mean...", "radius=2");
     run("Auto Threshold", "method=MaxEntropy white stack use_stack_histogram");
     roi_beads = binaryToSelection(imgs_beadmask, "beads", respath);
     // now the background is 0 and beads are 255
@@ -807,9 +807,9 @@ function process_beads() {
     ////////// measure (evaulate) using the above determined points ////////// ////////// //////////
     // DISCUSS: should this be normalized (bit depth) to allow comparing different sensors?
     measureSelection(img_std, "StdDev", respath, false, save_measurements);
-    getStatistics(_, mean_std, _, _, std_std);  // mean and std from the Noise
-    print("StdDev stats:   mean=" + mean_std + "   std=" + std_std);
-
+    getStatistics(_, mean_std, _, _, std_std);  // mean and std from the Noise
+    print("StdDev stats:   mean=" + mean_std + "   std=" + std_std);
+
     measureSelection(img_snr, "SNR", respath, false, save_measurements);
     getStatistics(_, mean_snr, _, _, std_snr);  // mean and std from the SNR
     print("SNR stats:   mean=" + mean_snr + "   std=" + std_snr);
@@ -944,8 +944,8 @@ function process_beads() {
     pairs = Array.concat(pairs, "", "");
     pairs = Array.concat(pairs, "-- Input --", "");
     pairs = Array.concat(pairs, "Filename", fname);
-    pairs = Array.concat(pairs, "Rescaling divisor used", divisor);
-
+    pairs = Array.concat(pairs, "Rescaling divisor used", divisor);
+
 
     createTable(title, pairs, respath + "/" + "NoiSee-summary.txt");
     img_summary = createTableImage(title, pairs);