diff --git a/06_example_code/visualise_area_and_shape_in_colors.ijm b/06_example_code/visualise_area_and_shape_in_colors.ijm
new file mode 100644
index 0000000000000000000000000000000000000000..eb2429130a2f720e32353c1e09de3dbf662ecc9e
--- /dev/null
+++ b/06_example_code/visualise_area_and_shape_in_colors.ijm
@@ -0,0 +1,107 @@
+//@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");
+ }
+}
\ No newline at end of file
diff --git a/06_example_code/visualise_area_and_shape_in_colors_ui.ijm b/06_example_code/visualise_area_and_shape_in_colors_ui.ijm
new file mode 100644
index 0000000000000000000000000000000000000000..a9771001204fcf0b643e95d2f4d8c35bf6ae2fae
--- /dev/null
+++ b/06_example_code/visualise_area_and_shape_in_colors_ui.ijm
@@ -0,0 +1,107 @@
+// @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