Create count_rosettes.ijm

Author: volker-baecker

volker/macros/count_rosettes.ijm

@@ -0,0 +1,38 @@
+CHANNEL = 1;
+SIGMA = 10;
+PROEMINENCE = 0;
+TABLE = "Number of Rosettes";
+
+folder = getDir("Select the input folder!");
+outFolder = getDir("Select_the output folder!");
+files = getFileList(folder);
+
+for (i = 0; i < files.length; i++) {
+    file = files[i];
+    run("Bio-Formats", "open=["+folder + file+"] autoscale color_mode=Default rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");
+    makeRectangle(408, 393, 1374, 1353);
+    inputImageID = getImageID();
+    title = getTitle();
+    if (!isOpen(TABLE)) {
+        Table.create(TABLE);
+    }
+    run("Clear Results");
+    run("Duplicate...", "duplicate channels="+CHANNEL);
+    run("Invert");
+    run("FeatureJ Laplacian", "compute smoothing="+SIGMA);
+    run("Find Maxima...", "prominence="+PROEMINENCE+" exclude light output=[Point Selection]");
+    run("Measure");
+    numberOfRosettes = nResults;
+    row = Table.size(TABLE);
+    Table.set("image", row, title, TABLE);
+    Table.set("number", row, numberOfRosettes, TABLE);
+    close();
+    run("Restore Selection");
+    selectImage(inputImageID);
+    close();
+    run("Invert");
+    parts = split(file, ".");
+    filename = parts[0];
+    saveAs("tiff", outFolder + filename + ".tif");
+    close();
+}