solution of exercise 06

06_example_code/visualise_area_and_shape_in_colors.ijm

+//@File(style="directory") folder
+//@int maximum_aspect_ratio
+//@int minimum_cell_size
+//@int maximum_cell_size
+//
+// This script analyses a time lapse of images showing yeast cells.
+// It counts the number of round cells over time and visualises
+// cells in different colors depending on their features:
+// * red: too small or too large
+// * yellow: round (dying)
+// * green: elongated (alive)
+//
+// Robert Haase, rhaase@mpi-cbg.de
+// May 2019
+//
+
+// configuration
+//folder = "C:/structure/teaching/lecture_applied_bioimage_analysis/05_example_code_and_data/rounding_assay/";
+
+result_file = "result_shape_count.csv";
+
+// how are round cells identified?
+//maximum_aspect_ratio = 2;
+
+// size constraints for yeast-cells
+//minimum_cell_size = 10; // in pixels
+//maximum_cell_size = 200; // in pixels
+
+// prepare resulting CSV file
+if ( File.exists(folder + result_file) ) {
+	File.delete(folder + result_file);	
+}
+File.append("File, Number of round cells, Number of elongated cells", folder + result_file);
+
+// access the folder
+filelist = getFileList(folder);
+
+for (i = 0; i < lengthOf(filelist); i++) {
+//for (i = 30; i < 31; i++) {
+	
+	filename = folder + filelist[i];
+
+	if (endsWith(filename, ".tif")) {
+		
+		// open an image from the rounding assay
+		open(filename);
+		
+		// save the window title for later - we want to switch to this image
+		original_image_title = getTitle();
+		
+		// duplicate the image and segment it
+		run("Duplicate...", " ");
+		setAutoThreshold("Triangle dark");
+		run("Convert to Mask");
+		// binary closing
+		run("Dilate");
+		run("Dilate");
+		run("Erode");
+		run("Erode");
+		
+		// connected components analysis -> send results to ROI Manager
+		run("Analyze Particles...", "  show=Nothing add");
+		
+		// switch back to original image
+		selectWindow(original_image_title);
+		roiManager("Show None");
+	
+		number_of_round_regions = 0;
+		number_of_elongated_regions = 0;
+		
+		number_of_regions = roiManager("count");
+		for (j = 0; j < number_of_regions; j++ ) {
+		
+			// measure area ( = pixel count) and shape
+			run("Set Measurements...", "area shape redirect=None decimal=3");
+			roiManager("Select", j);
+			roiManager("Measure");
+			pixel_count = getResult("Area", nResults - 1);
+			aspect_ratio = getResult("AR", nResults - 1);
+		
+			// visualise if ROIs are too small or not
+			if (pixel_count > minimum_cell_size && pixel_count < maximum_cell_size) {
+				if (aspect_ratio > maximum_aspect_ratio) {
+					number_of_elongated_regions ++;
+					Overlay.addSelection("green");
+				} else {
+					number_of_round_regions ++;
+					Overlay.addSelection("yellow");
+				}
+			} else {
+				Overlay.addSelection("red");
+			}
+		}
+		File.append(filename + "," + number_of_round_regions + ", " + number_of_elongated_regions , folder + result_file);
+	
+		// clean up after the job is done
+		if (number_of_regions > 0) {
+			roiManager("deselect");
+			roiManager("delete");
+		}
+		run("Clear Results");
+	
+		run("Flatten");
+		save(filename + "_result_visualisation.jpg");
+		run("Close All");
+	}
+}
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06_example_code/visualise_area_and_shape_in_colors_ui.ijm

+// @File(style="directory") folder
+// @int(value=2, persistent=False) maximum_aspect_ratio
+// @int(value=10, persistent=False) minimum_cell_size
+// @int(value=200, persistent=False) maximum_cell_size
+//
+// This script analyses a time lapse of images showing yeast cells.
+// It counts the number of round cells over time and visualises
+// cells in different colors depending on their features:
+// * red: too small or too large
+// * yellow: round (dying)
+// * green: elongated (alive)
+//
+// Robert Haase, rhaase@mpi-cbg.de
+// May 2019
+//
+
+// configuration
+//folder = "C:/structure/teaching/lecture_applied_bioimage_analysis/05_example_code_and_data/rounding_assay/";
+
+result_file = "result_shape_count.csv";
+
+// how are round cells identified?
+//maximum_aspect_ratio = 2;
+
+// size constraints for yeast-cells
+//minimum_cell_size = 10; // in pixels
+//maximum_cell_size = 200; // in pixels
+
+// prepare resulting CSV file
+if ( File.exists(folder + result_file) ) {
+	File.delete(folder + result_file);	
+}
+File.append("File, Number of round cells, Number of elongated cells", folder + result_file);
+
+// access the folder
+filelist = getFileList(folder);
+
+for (i = 0; i < lengthOf(filelist); i++) {
+//for (i = 30; i < 31; i++) {
+	
+	filename = folder + filelist[i];
+
+	if (endsWith(filename, ".tif")) {
+		
+		// open an image from the rounding assay
+		open(filename);
+		
+		// save the window title for later - we want to switch to this image
+		original_image_title = getTitle();
+		
+		// duplicate the image and segment it
+		run("Duplicate...", " ");
+		setAutoThreshold("Triangle dark");
+		run("Convert to Mask");
+		// binary closing
+		run("Dilate");
+		run("Dilate");
+		run("Erode");
+		run("Erode");
+		
+		// connected components analysis -> send results to ROI Manager
+		run("Analyze Particles...", "  show=Nothing add");
+		
+		// switch back to original image
+		selectWindow(original_image_title);
+		roiManager("Show None");
+	
+		number_of_round_regions = 0;
+		number_of_elongated_regions = 0;
+		
+		number_of_regions = roiManager("count");
+		for (j = 0; j < number_of_regions; j++ ) {
+		
+			// measure area ( = pixel count) and shape
+			run("Set Measurements...", "area shape redirect=None decimal=3");
+			roiManager("Select", j);
+			roiManager("Measure");
+			pixel_count = getResult("Area", nResults - 1);
+			aspect_ratio = getResult("AR", nResults - 1);
+		
+			// visualise if ROIs are too small or not
+			if (pixel_count > minimum_cell_size && pixel_count < maximum_cell_size) {
+				if (aspect_ratio > maximum_aspect_ratio) {
+					number_of_elongated_regions ++;
+					Overlay.addSelection("green");
+				} else {
+					number_of_round_regions ++;
+					Overlay.addSelection("yellow");
+				}
+			} else {
+				Overlay.addSelection("red");
+			}
+		}
+		File.append(filename + "," + number_of_round_regions + ", " + number_of_elongated_regions , folder + result_file);
+	
+		// clean up after the job is done
+		if (number_of_regions > 0) {
+			roiManager("deselect");
+			roiManager("delete");
+		}
+		run("Clear Results");
+	
+		run("Flatten");
+		save(filename + "_result_visualisation.jpg");
+		run("Close All");
+	}
+}
\ No newline at end of file