processor = frame.getProcessor() filters = RankFilters() filters.setup("median", frame) filters.rank(processor, filter_window, filters.MEDIAN) # Perform gamma correction processor.gamma(gamma) frame = ImagePlus("Frame " + str(frame_i), processor) # Rolling ball background subtraction processor = frame.getProcessor() bg_subtractor = BackgroundSubtracter() bg_subtractor.setup("", frame) bg_subtractor.rollingBallBackground(processor, rolling_ball_size/pixel_size, False, False, False, False, True) frame = ImagePlus("Frame " + str(frame_i), processor) # Calibrate pixels calibration = Calibration() calibration.setUnit("pixel") calibration.pixelWidth = pixel_size calibration.pixelHeight = pixel_size calibration.pixelDepth = 1.0 frame.setCalibration(calibration) # Save to output dir file_name = output_dir + "/" + str(frame_i).zfill(4) + ".tif"