示例#1
0
def test_kinesin():

    # create Confocal Microscopy for off-lattice model (Kinesin)
    confm = KinesinConfigs()

    confm.set_LightSource(
        source_type="LASER", wave_mode="TEM00", M2_factor=1.00, wave_length=473, power=500e-6, radius=0.32e-3
    )
    confm.set_BeamExpander(expander_type="Keplerian", focal_length1=30e-3, focal_length2=20e-3, pinhole_radius=13e-6)
    confm.set_Fluorophore(fluorophore_type="EGFP")
    # confm.set_Fluorophore(fluorophore_type='Gaussian', wave_length=508, width=(70.0, 140.0))
    # confm.set_Fluorophore(fluorophore_type='Point-like', wave_length=508)
    confm.set_Objective(NA=1.20, Nm=1.37, focal_length=1.9e-3, efficiency=0.90)
    confm.set_TubeLens1(focal_length=160e-3)
    confm.set_ScanLens(focal_length=50e-3)
    confm.set_PinholeLens(focal_length=200e-3, radius=13e-6)
    confm.set_Detector(
        detector="PMT",
        zoom=2,
        emgain=1e7,
        focal_point=(0.5, 0.5, 0.5),
        start_time=0,
        end_time=30,
        fps=1 / 30e-3,
        exposure_time=30e-3,
    )
    confm.set_Movie(image_file_dir="./images_kinesin", movie_filename="./movies/kinesin_m100_movie.mp4")
    # confm.set_DataFile(['./data/lattice/satyaKinesinVisualLog.csv'])
    confm.set_DataFile(["./data/lattice/CoordinateLog_act0.15_m100.csv"])

    # create image and movie
    create = KinesinVisualizer(configs=confm)
    # create.get_plots(plot_filename='./plots/kinesin_plots.pdf')
    # create.output_frames(num_div=16)
    create.output_movie(num_div=16)
示例#2
0
def test_b3c(t0, t1) :

	# create EPIF Microscopy
	epifm = KinesinConfigs()

	epifm.set_LightSource(source_type='LASER', wave_mode='TEM00', M2_factor=1.00, wave_length=473, power=10e-3, radius=0.32e-3)
	epifm.set_BeamExpander(expander_type='Keplerian', focal_length1=300e-3, focal_length2=20e-3, pinhole_radius=23e-6)
	#epifm.set_Fluorophore(fluorophore_type='Tetramethylrhodamine(TRITC)')
	epifm.set_Fluorophore(fluorophore_type='Gaussian', wave_length=578, width=(10.0, 20.0))
	#epifm.set_Fluorophore(fluorophore_type='Point-like', wave_length=578)
	epifm.set_Objective(NA=1.49, Nm=1.37, focal_length=1.9e-3, efficiency=0.90)
	#epifm.set_DichroicMirror('FF562-Di03-25x36')
	#epifm.set_EmissionFilter('FF01-593_40-25')
	epifm.set_TubeLens1(focal_length=160e-3)
	epifm.set_ScanLens(focal_length=50e-3)
	epifm.set_TubeLens2(focal_length=200e-3)
	epifm.set_Detector(detector='EMCCD', zoom=1, emgain=100, pixel_length=0.16e-6, focal_point=(0.0,0.5,0.5), \
			start_time=t0, end_time=t1, fps=1, exposure_time=1)
	epifm.set_Movie(image_file_dir='./images_b3c', movie_filename='./movies/band3_cluster.mp4')
	epifm.set_DataFile(['./data/lattice/band3_cluster.csv'])

	# create image and movie
	create = KinesinVisualizer(configs=epifm)
	#create.get_plots(plot_filename='./plots/epifm_plots.pdf')
	create.output_frames(num_div=16)