From 7a95c415e0255174628bb782c7649fa7dc341082 Mon Sep 17 00:00:00 2001
From: Adien Akhmad <adien.mufaqih@formulatrix.com>
Date: Sat, 21 Feb 2026 10:00:02 +0700
Subject: [PATCH] initial working version

---
 particle-beads.ijm | 88 ++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 88 insertions(+)
 create mode 100644 particle-beads.ijm

diff --git a/particle-beads.ijm b/particle-beads.ijm
new file mode 100644
index 0000000..28414ce
--- /dev/null
+++ b/particle-beads.ijm
@@ -0,0 +1,88 @@
+// 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)
+run("Clear Results");
+if (isOpen("Summary")) {
+    selectWindow("Summary");
+    run("Close");
+}
+
+list = getFileList(inputDir);
+setBatchMode(true); // Run in the background (much faster)
+
+for (i = 0; i < list.length; i++) {
+    // Process only PNG files
+    if (endsWith(toLowerCase(list[i]), ".png")) {
+        processFile(inputDir, outputDir, list[i]);
+    }
+}
+
+setBatchMode(false);
+
+if (isOpen("Summary")) {
+    selectWindow("Summary");
+    saveAs("Results", outputDir + "Summary_Report.csv");
+}
+
+
+if (isOpen("Results")) {
+    selectWindow("Results");
+    run("Close");
+}
+print("Done! Files and summary saved to: " + outputDir);
+
+function processFile(input, output, filename) {
+    
+    // Clear ROI Manager for each new image
+    if (roiManager("count") > 0) {
+        roiManager("deselect");
+        roiManager("delete");
+    }
+
+    // Open the PNG
+    open(input + filename);
+    
+    // Create a TIFF filename for the output
+    basename = File.nameWithoutExtension;
+    newName = basename + ".tif";
+
+    // --- 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
+    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)
+    close(); 
+    
+    // Select the cropped TIFF and save it with the ROIs
+    selectImage(currentImage); 
+    if (roiManager("count") > 0) {
+        roiManager("Show All without labels");
+        run("Save"); 
+    }
+    
+    // Close everything to free memory
+    run("Close All");
+}
\ No newline at end of file