def test_image(): # create TIRF Microscopy tirfm = TIRFMSettings() # Spectral Arrangement #tirfm.set_Fluorophore(fluorophore='Tetramethylrhodamine(TRITC)') tirfm.set_GaussPSF(intensity=1.0, gauss_sigma=200e-9) tirfm.set_IncidentBeam(wlength=561, power=10, radius=3.0, position=0.7, excitation=None) tirfm.set_Objective(mag=60, NA=1.49, Nm=1.37, efficiency=0.90) tirfm.set_DichroicMirror('FF562-Di03-25x36') tirfm.set_EmissionFilter('FF01-593_40-25') tirfm.set_TubeLens(mag=4, wl_range=(350, 750), efficiency=0.9987) tirfm.set_camera(image_size=(512, 512), pixel_length=16e-6, zoom=0.1, focal_point=(0.0, 0.5, 0.5)) tirfm.set_movie(frame_interval=0.033, exposure_time=0.0033, frame_end_time=1.00) #tirfm.get_SpectrumPlot(plot_filename='./plots/spectrum_plots.pdf') # create image and movie image = TIRFMVisualizer(['./data/lattice/test_model_volume.h5'], movie_filename='./test_model.mp4', settings=tirfm) image.output_movie(num_div=16)
def test_tirfm(t0, t1, index=None) : # create TIRF Microscopy tirfm = TIRFMConfigs() tirfm.set_LightSource(source_type='LASER', wave_length=532, flux_density=10, angle=65.7) tirfm.set_Fluorophore(fluorophore_type='Tetramethylrhodamine(TRITC)') #tirfm.set_Fluorophore(fluorophore_type='EGFP') #tirfm.set_Fluorophore(fluorophore_type='Gaussian', wave_length=532, intensity=0.55, width=(200,400)) tirfm.set_DichroicMirror('FF562-Di03-25x36') tirfm.set_EmissionFilter('FF01-593_40-25') tirfm.set_Magnification(Mag=198) # Detector : CMOS Camera # tirfm.set_Detector(detector='CMOS', image_size=(600,600), pixel_length=6.5e-6, \ # focal_point=(0.0,0.5,0.5), exposure_time=30e-3, QE=0.73) # tirfm.set_ADConverter(bit=16, offset=100, fullwell=30000) # Detector : EMCCD Camera tirfm.set_Detector(detector='EMCCD', image_size=(512,512), pixel_length=16e-6, \ focal_point=(0.0,0.5,0.5), exposure_time=30e-3, QE=0.92, readout_noise=50, emgain=300) tirfm.set_ADConverter(bit=14, offset=200, fullwell=800000) ### Output data tirfm.set_OutputData(image_file_dir='./images') ### Input data tirfm.set_InputData('./data/tmr_tirfm', start=t0, end=t1, observable="A") # create physical effects physics = PhysicalEffects() physics.set_Conversion(ratio=1e-6) physics.set_Background(mean=10) # create image and movie create = TIRFMVisualizer(configs=tirfm, effects=physics) create.output_frames(num_div=16)