diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..56fd0e8
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+/debug
\ No newline at end of file
diff --git a/particle-beads.ijm b/particle-beads.ijm
index 28414ce..faa27af 100644
--- a/particle-beads.ijm
+++ b/particle-beads.ijm
@@ -1,13 +1,15 @@
-// 1. Ask the user for the input folder
 inputDir = getDirectory("Choose Input Directory");
-
-// 2. Create the output folder automatically inside the input folder
 outputDir = inputDir + "particle_analyze" + File.separator;
 if (!File.exists(outputDir)) {
     File.makeDirectory(outputDir);
 }
 
-// 3. Prepare the environment (Clear old results/summaries)
+// config - roi styling
+roiColor = "yellow";
+roiThickness = 3;
+fillColor = "none";
+
+// prepare the environment (Clear old results/summaries)
 run("Clear Results");
 if (isOpen("Summary")) {
     selectWindow("Summary");
@@ -15,10 +17,9 @@ if (isOpen("Summary")) {
 }
 
 list = getFileList(inputDir);
-setBatchMode(true); // Run in the background (much faster)
+setBatchMode(true);
 
 for (i = 0; i < list.length; i++) {
-    // Process only PNG files
     if (endsWith(toLowerCase(list[i]), ".png")) {
         processFile(inputDir, outputDir, list[i]);
     }
@@ -31,7 +32,6 @@ if (isOpen("Summary")) {
     saveAs("Results", outputDir + "Summary_Report.csv");
 }
 
-
 if (isOpen("Results")) {
     selectWindow("Results");
     run("Close");
@@ -46,43 +46,37 @@ function processFile(input, output, filename) {
         roiManager("delete");
     }
 
-    // Open the PNG
     open(input + filename);
     
-    // Create a TIFF filename for the output
+    // create a filename for the output
     basename = File.nameWithoutExtension;
-    newName = basename + ".tif";
+    newName = basename + ".png";
 
-    // --- Your recorded steps ---
     run("Set Scale...", "distance=2691 known=1000 unit=micron global");
     run("Specify...", "width=2691 height=2691 x=476 y=476 constrain");
     run("Crop");
     
-    // Save the cropped version as TIFF in the particle_analyze folder
-    saveAs("Tiff", output + newName);
     currentImage = getTitle();
 
-    // Image Processing for Masking
+    // prepare binary image for analyzer
     run("Duplicate...", " ");
     setThreshold(0, 85, "raw");
     setOption("BlackBackground", true);
     run("Convert to Mask");
     run("Fill Holes");
-    run("Watershed");
-    
-    // Analyze Particles (the 'summarize' flag builds the report window)
-    run("Analyze Particles...", "size=78.5-120 circularity=0.75-1.00 display exclude clear summarize add");
-    
-    // Close the mask (duplicate)
+    run("Watershed");    
+    run("Analyze Particles...", "size=78.5-120 circularity=0.75-1.00 display exclude clear summarize add");    
     close(); 
     
-    // Select the cropped TIFF and save it with the ROIs
+    // select the cropped image and save it with the ROIs
     selectImage(currentImage); 
     if (roiManager("count") > 0) {
+        roiManager("deselect");
+        roiManager("Set Color", roiColor);
+        roiManager("Set Line Width", roiThickness);
         roiManager("Show All without labels");
-        run("Save"); 
-    }
-    
-    // Close everything to free memory
+        run("Flatten");
+        saveAs("PNG", output + newName);
+    }    
     run("Close All");
 }
\ No newline at end of file