def confm_pulses(t0, t1) : # create Point-scanning Confocal Microscopy confm = PointScanConfocalConfigs() confm.set_LightSource(source_type='LASER', wave_length=488, flux=100e-6, radius=200e-9) confm.set_Fluorophore(fluorophore_type='EGFP') confm.set_Pinhole(radius=28.8e-6) confm.set_Magnification(Mag=60) # PMT : Analog mode confm.set_Detector(detector='PMT', mode="Analog", image_size=(1024,1024), focal_point=(0.3,0.5,0.5), \ pixel_length=207.16e-9, scan_time=1.15, QE=0.3, gain=1e+6, dyn_stages=11, pair_pulses=18e-9) confm.set_ADConverter(bit=12, offset=0, fullwell=4096) confm.set_OutputData(image_file_dir='./images_erk102') # Input data : EGF model file confm.set_InputData('./data/erk102', start=t0, end=t1, observable="ERK") # create physical effects physics = PhysicalEffects() physics.set_Conversion(ratio=1e-6) #physics.set_Background(mean=5) #physics.set_DetectorCrosstalk(width=1.00) # create image and movie create = PointScanConfocalVisualizer(configs=confm, effects=physics) create.output_frames(num_div=16)
def test_confm(t0, t1, index=None) : # create Point-scanning Confocal Microscopy confm = PointScanConfocalConfigs() confm.set_LightSource(source_type='LASER', wave_length=532, flux=10e-6, radius=400e-9) #confm.set_Fluorophore(fluorophore_type='Tetramethylrhodamine(TRITC)') confm.set_Fluorophore(fluorophore_type='EGFP') confm.set_Pinhole(radius=90e-6) confm.set_Magnification(Mag=60) # # PMT : Photon-counting mode # confm.set_Detector(detector='PMT', mode="Photon-counting", image_size=(1024,1024), focal_point=(0.4,0.5,0.5), \ # pixel_length=207.16e-9, scan_time=1.15, gain=1e+6, dyn_stages=11, pair_pulses=18e-9) # confm.set_ADConverter(bit=12, offset=0, fullwell=4096) # confm.set_OutputData(image_file_dir='./images_erk102_pulses') # PMT : Anlalog mode confm.set_Detector(detector='PMT', mode="Analog", image_size=(1024,1024), focal_point=(0.4,0.5,0.5), \ pixel_length=207.16e-9, scan_time=1.15, gain=1e+6, dyn_stages=11, pair_pulses=18e-9) confm.set_ADConverter(bit=12, offset=0, fullwell=4096) confm.set_OutputData(image_file_dir='./images') # Input data : EGF model file confm.set_InputData('./data/tmr_lscm', start=t0, end=t1, observable="A") # create physical effects physics = PhysicalEffects() physics.set_Conversion(ratio=1e-6) #physics.set_Background(mean=10) #physics.set_DetectorCrosstalk(width=1.00) # create image and movie create = PointScanConfocalVisualizer(configs=confm, effects=physics) create.output_frames(num_div=16)
def test_fcs(t0, t1): # create FCS fcs = FCSConfigs() fcs.set_LightSource(source_type='LASER', wave_length=473, power=100e-6, radius=200e-9) fcs.set_Fluorophore(fluorophore_type='Qdot 605') #fcs.set_Fluorophore(fluorophore_type='Gaussian', wave_length=605, width=(100.0, 200.0)) fcs.set_Magnification(Mag=336) fcs.set_Pinhole(radius=16e-6) fcs.set_Detector(detector='PMT', zoom=1, emgain=1e+6, focal_point=(0.5, 0.5, 0.5), bandwidth=50e+3, mode='Pulse') fcs.set_ADConverter(bit=16, offset=2000, fullwell=20000) # for Pulse fcs.set_OutputData(image_file_dir='./output_fcs_0001') fcs.set_InputData('/home/masaki/ecell3/latest/data/csv/test_fcs_0001', start=t0, end=t1) # create physical effects physics = PhysicalEffects() physics.set_Conversion(ratio=1e-6) #physics.set_Background(mean=30) # create image and movie create = FCSVisualizer(configs=fcs, effects=physics) create.output_frames(num_div=1)
def pten_confm(t0, t1) : # create Point-scanning Confocal Microscopy confm = PointScanConfocalConfigs() confm.set_LightSource(source_type='LASER', wave_length=561, flux=100e-6, radius=200e-9) confm.set_Fluorophore(fluorophore_type='Tetramethylrhodamine(TRITC)') confm.set_Pinhole(radius=20.0e-6) confm.set_Magnification(Mag=60) # PMT : Anlalog mode confm.set_Detector(detector='PMT', mode="Analog", image_size=(512,512), focal_point=(0.4,0.5,0.5), pixel_length=414.3e-9, scan_time=5.00, gain=1e+6, dyn_stages=11, pair_pulses=18e-9) confm.set_ADConverter(bit=12, offset=0, fullwell=4096) confm.set_OutputData(image_file_dir='./images_pten') # Input data : EGF model file confm.set_InputData('./data/csv/pten', start=t0, end=t1, observable="PTEN") # create physical effects physics = PhysicalEffects() physics.set_Conversion(ratio=1e-6) #physics.set_Background(mean=20) #physics.set_DetectorCrosstalk(width=1.00) # create image and movie create = PointScanConfocalVisualizer(configs=confm, effects=physics) 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=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_epifm(t0, t1): # create EPIF Microscopy epifm = EPIFMConfigs() epifm.set_LightSource(source_type='LASER', wave_length=532, power=20e-3, radius=20e-6) epifm.set_Fluorophore(fluorophore_type='Tetramethylrhodamine(TRITC)') #epifm.set_Fluorophore(fluorophore_type='Gaussian', wave_length=578, width=(70.0, 140.0)) epifm.set_DichroicMirror('FF562-Di03-25x36') epifm.set_EmissionFilter('FF01-593_40-25') epifm.set_Magnification(Mag=336) epifm.set_Detector(detector='EMCCD', zoom=1, emgain=1, focal_point=(0.3, 0.5, 0.5), exposure_time=30e-3) epifm.set_ADConverter(bit=16, offset=2000, fullwell=370000) # for EMCCD #epifm.set_OutputData(image_file_dir='./images_dicty_02_epifm_zaxis09') epifm.set_OutputData(image_file_dir='./images_test') epifm.set_InputData('/home/masaki/ecell3/latest/data/csv/simple_dicty_02', start=t0, end=t1) # create physical effects physics = PhysicalEffects() physics.set_Conversion(ratio=1e-6) #physics.set_Background(mean=30) physics.set_DetectorCrosstalk(width=1.00) # for EMCCD # create image and movie create = EPIFMVisualizer(configs=epifm, effects=physics) create.output_frames(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_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)
def __init__(self, configs=TIRFMConfigs(), effects=PhysicalEffects()): assert isinstance(configs, TIRFMConfigs) self.configs = configs assert isinstance(effects, PhysicalEffects) self.effects = effects """ Check and create the folder for image file. """ if not os.path.exists(self.configs.image_file_dir): os.makedirs(self.configs.image_file_dir) #else: # for file in os.listdir(self.configs.movie_image_file_dir): # os.remove(os.path.join(self.configs.movie_image_file_dir, file)) """ set optical path from source to detector """ self.configs.set_Optical_path()