added solution for exercise 05

05_example_code_and_data/analyse_rounding_assay.ijm

+
+// configuration
+folder = "C:/structure/teaching/lecture_applied_bioimage_analysis/05_example_data/rounding_assay/";
+image_file = "rounding_assay0035.tif";
+result_csv_file = "summary.csv";
+
+// configure measurement
+run("Set Measurements...", "fit shape redirect=None decimal=3");
+
+// process imagge
+open(folder + image_file);
+
+setAutoThreshold("MaxEntropy dark");
+setOption("BlackBackground", true);
+run("Convert to Mask");
+
+// get rid of single pixels
+run("Erode");
+run("Dilate");
+
+// measure properties
+run("Analyze Particles...", "summarize");
+
+// save the result table
+IJ.renameResults("Summary", "Results");
+saveAs("Results", folder + result_csv_file);

05_example_code_and_data/analyse_rounding_assay_folder.ijm

+
+// configuration
+folder = "C:/structure/teaching/lecture_applied_bioimage_analysis/05_example_data/rounding_assay/";
+result_csv_file = "summary.csv";
+
+// configure measurement
+run("Set Measurements...", "fit shape redirect=None decimal=3");
+
+// retrieve all files in the folder in an array
+filelist = getFileList(folder);
+
+for (i = 0; i < lengthOf(filelist); i++) {
+	image_file = filelist[i];
+	if ( endsWith(image_file, ".tif")) {
+		// process imagge
+		open(folder + image_file);
+		
+		setAutoThreshold("MaxEntropy dark");
+		setOption("BlackBackground", true);
+		run("Convert to Mask");
+		
+		// get rid of single pixels
+		run("Erode");
+		run("Dilate");
+		
+		// measure properties
+		run("Analyze Particles...", "summarize");
+		close();
+	}
+}
+
+// save the result table
+IJ.renameResults("Summary", "Results");
+saveAs("Results", folder + result_csv_file);