Exemple #1
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def test_tirfm(t0, t1) :

	# create TIRF Microscopy
	tirfm = TIRFMConfigs()
        tirfm.set_LightSource(source_type='LASER', wave_mode='TEM00', M2_factor=1.0, wave_length=473, power=10e-3, radius=0.32e-3)
        tirfm.set_BeamExpander(expander_type='Keplerian', focal_length1=300e-3, focal_length2=20e-3, pinhole_radius=23e-6)
	tirfm.set_Fluorophore(fluorophore_type='Tetramethylrhodamine(TRITC)')
	#tirfm.set_Fluorophore(fluorophore_type='Gaussian', wave_length=578, width=(20.0, 140.0))
	#tirfm.set_Fluorophore(fluorophore_type='Point-like', wave_length=578)
	tirfm.set_EvanescentField(depth=200)
	tirfm.set_Objective(NA=1.49, Nm=1.37, focal_length=1.90e-3, efficiency=0.90)
	tirfm.set_DichroicMirror('FF562-Di03-25x36')
	tirfm.set_EmissionFilter('FF01-593_40-25')
        tirfm.set_TubeLens1(focal_length=160e-3)
        tirfm.set_ScanLens(focal_length=50e-3)
        tirfm.set_TubeLens2(focal_length=200e-3)
	tirfm.set_Detector(detector='EMCCD', zoom=1, emgain=150, focal_point=(0.0,0.5,0.5), \
			start_time=t0, end_time=t1, fps=1.0/3.3e-3, exposure_time=33e-3)
	tirfm.set_Movie(image_file_dir='./images_nishida', movie_filename='./movies/tirfm_movie.mp4')
	tirfm.set_DataFile(['./data/lattice/test_model_07.h5'])

	# create physical effects
	physics = PhysicalEffects()
	physics.set_Conversion(ratio=1e-7)
	physics.set_Background(mean=0, width=100)
	#physics.set_DepthOfFocus(a=0.5, b=0.0)
	physics.set_DetectorCrosstalk(width=3.0)
	#physics.set_Photobleaching(rate=1/2.00)
	#physics.set_Photoblinking(P0=0.5, alpha_on=0.0048, alpha_off=0.0055)

	# create image and movie
	create = TIRFMVisualizer(configs=tirfm, effects=physics)
	#create.get_plots(plot_filename='./plots/tirfm_plots.pdf')
	create.output_frames(num_div=16)
Exemple #2
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def test_tirfm(t0, t1, Molecule) :

        # create TIRF Microscopy
        tirfm = TIRFMConfigs()

        tirfm.set_LightSource(source_type='LASER', wave_mode='TEM00', M2_factor=1.00, wave_length=473, power=1e-3, radius=0.32e-3)
        #tirfm.set_BeamExpander(expander_type='Keplerian', focal_length1=300e-3, focal_length2=20e-3, pinhole_radius=23e-6)
        #tirfm.set_Fluorophore(fluorophore_type='mCherry')
        tirfm.set_Fluorophore(fluorophore_type='EGFP')
        #tirfm.set_Fluorophore(fluorophore_type='Gaussian', wave_length=578, width=(70.0, 140.0))
        #tirfm.set_Fluorophore(fluorophore_type='Point-like', wave_length=578)
        tirfm.set_Objective(NA=1.49, Nm=1.37, focal_length=1.9e-3, efficiency=0.90)
        tirfm.set_EvanescentField(depth=200)
        tirfm.set_DichroicMirror('FF562-Di03-25x36')
        tirfm.set_EmissionFilter('FF01-593_40-25')
        tirfm.set_TubeLens1(focal_length=160e-3)
        tirfm.set_ScanLens(focal_length=50e-3)
        tirfm.set_TubeLens2(focal_length=200e-3)
        tirfm.set_Detector(detector='EMCCD', zoom=1, emgain=300, focal_point=(0.0,0.5,0.5), \
                        start_time=t0, end_time=t1, fps=1/33e-3, exposure_time=33e-3)
        tirfm.set_Movie(image_file_dir='./images_egfm_%s' % (Molecule), movie_filename='./movies/egfm_movie.mp4')
        tirfm.set_DataFile(['/home/kiwamoto/share/EGF_model_20130603/LogHDF5_Raf_1.h5'], observable=Molecule)
        tirfm.set_BCFile(['/home/kiwamoto/share/EGF_model_20130603/LogCoordinate_Shape.csv'])

        # create physical effects
        physics = PhysicalEffects()
        physics.set_Conversion(ratio=1e-6)
        #physics.set_Background(mean=30)
        #physics.set_DepthOfFocus(a=0.5, b=0.0)
        #physics.set_DetectorCrosstalk(width=2.0)
        #physics.set_Photobleaching(rate=1/5.0)
        #physics.set_Photoblinking(P0=0.5, alpha_on=0.0048, alpha_off=0.0055)

        # create image and movie
        create = TIRFMVisualizer(configs=tirfm, effects=physics)
        #create.get_plots(plot_filename='./plots/tirfm.plots.pdf')
        create.output_frames(num_div=16)
Exemple #3
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def test_tirfm(t0, t1):

    # create TIRF Microscopy
    tirfm = TIRFMConfigs()
    tirfm.set_LightSource(
        source_type="LASER", wave_mode="TEM00", M2_factor=1.0, wave_length=473, power=1.0e-3, radius=10e-6
    )
    tirfm.set_Fluorophore(fluorophore_type="Tetramethylrhodamine(TRITC)")
    # tirfm.set_Fluorophore(fluorophore_type='Gaussian', wave_length=578, width=(20.0, 20.0))
    # tirfm.set_Fluorophore(fluorophore_type='Point-like', wave_length=578)
    tirfm.set_EvanescentField(depth=200)
    tirfm.set_Objective(NA=1.49, Nm=1.37, focal_length=1.90e-3, efficiency=0.90)
    tirfm.set_TubeLens1(focal_length=160e-3)
    tirfm.set_ScanLens(focal_length=50e-3)
    tirfm.set_TubeLens2(focal_length=200e-3)
    tirfm.set_Detector(
        detector="EMCCD",
        zoom=1,
        emgain=300,
        focal_point=(0.0, 0.5, 0.5),
        start_time=t0,
        end_time=t1,
        fps=1.0 / 3.3e-3,
        exposure_time=33e-3,
    )
    tirfm.set_Movie(image_file_dir="./images", movie_filename="./movies/tirfm_movie.mp4")
    tirfm.set_DataFile(["./data/lattice/test_model_11.h5"])

    # create physical effects
    physics = PhysicalEffects()
    physics.set_Conversion(ratio=1e-6)
    physics.set_DetectorCrosstalk(width=2.00)

    # create image and movie
    create = TIRFMVisualizer(configs=tirfm, effects=physics)
    create.output_frames(num_div=16)