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"
