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)
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)
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, 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)
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)
