Example #1
0
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)
Example #3
0
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)
Example #4
0
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)
Example #5
0
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)
Example #6
0
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)
Example #7
0
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)
Example #8
0
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)
Example #9
0
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)
Example #10
0
    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()