imp.setT(frame_idx) timepoint_data = edges_dct[idx] t = timepoint_data['time_point_s'] membranes = timepoint_data['membranes'] membrane_indices_available = [ membrane['position number'] for membrane in membranes ] for membrane_index in membrane_indices_available: print("Analysing frame " + str(frame_idx) + ", membrane_index = " + str(membrane_index)) membrane_xy_list = membranes[membrane_indices_available.index( membrane_index)]['roi'] roi = PolygonRoi([x for x, y in membrane_xy_list], [y for x, y in membrane_xy_list], Roi.FREELINE) imp.setRoi(roi) roi.setStrokeWidth(line_width) if line_width > 1: IJ.run(imp, "Line to Area", "") roi = imp.getRoi() stats = roi.getStatistics() output.append((t, membrane_index, stats.mean, stats.max, stats.min, stats.median, stats.stdDev)) imp.killRoi() print(output) # save output to csv csv_path = os.path.join(os.path.dirname(edges_file_path), "intensity_stats.csv") f = open(csv_path, 'wb') try: writer = csv.writer(f)