new macro

Author: volker-baecker

volker/macros/incucyte_tracking.ijm

@@ -0,0 +1,40 @@
+dir = getDir("Select the input folder!");
+files = getFileList(dir);
+outFolder = dir + File.separator + "results"
+
+if (!File.exists(outFolder)) {
+	File.makeDirectory(outFolder);
+}
+
+
+for (i=0; i<files.length; i++) {
+	print("Processing image nr: " + i);
+	run("Clear Results");
+	file = files[i];
+	file = toLowerCase(file); 
+	if (!endsWith(file, ".tif")) continue;
+	open(dir + File.separator + file);
+	analyzeImage();
+	baseName = replace(file, ".tif", ""); 
+	xlsFile = replace(file, ".tif", ".xls");
+	selectWindow("Results");
+	saveAs("results", dir + File.separator + xlsFile);
+	save(outFolder + File.separator + baseName + "-labels.tif");
+	close();
+	save(outFolder + File.separator + baseName + "-mask.tif");
+	close();
+	save(outFolder + File.separator + baseName + "-paths.tif");
+	close();
+}
+
+
+function analyzeImage() {
+	run("Image Stabilizer", "transformation=Translation maximum_pyramid_levels=1 template_update_coefficient=0.90 maximum_iterations=200 error_tolerance=0.0000001");
+	setThreshold(0, 124);
+	setOption("BlackBackground", false);
+	run("Convert to Mask", "background=Light");
+	run("Fill Holes", "stack");
+	run("Remove Outliers...", "radius=2 threshold=50 which=Dark stack");
+	run("Dilate", "stack");
+	run("MTrack2 ", "minimum=10 maximum=400 maximum_=50 minimum_=2 show show_0 show_1");
+}