390 lines
8.7 KiB
YAML
390 lines
8.7 KiB
YAML
# Only one microscope can be active in the GUI at a time, but all microscopes will be accessible
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microscopes:
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Mesoscale:
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daq:
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hardware:
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name: daq
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type: NI
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# NI PCIe-1073 Chassis with PXI-6259 and PXI-6733 DAQ Boards.
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# Sampling rate in Hz
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sample_rate: 100000
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sweep_time: 0.2
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# triggers
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master_trigger_out_line: PXI6259/port0/line1
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camera_trigger_out_line: /PXI6259/ctr0
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trigger_source: /PXI6259/PFI0
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# Digital Laser Outputs
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laser_port_switcher: PXI6733/port0/line0
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laser_switch_state: False
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camera:
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hardware:
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name: camera
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type: HamamatsuOrca
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serial_number: 302352
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x_pixels: 2048.0
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y_pixels: 2048.0
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pixel_size_in_microns: 6.5
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subsampling: [1, 2, 4]
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sensor_mode: Normal # 12 for progressive, 1 for normal.
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readout_direction: Top-to-Bottom # Top-to-Bottom', 'Bottom-to-Top'
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lightsheet_rolling_shutter_width: 608
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defect_correct_mode: 2.0
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binning: 1x1
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readout_speed: 0x7FFFFFFF
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trigger_active: 1.0
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trigger_mode: 1.0 # external light-sheet mode
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trigger_polarity: 2.0 # positive pulse
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trigger_source: 2.0 # 2 = external, 3 = software.
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exposure_time: 20 # Use milliseconds throughout.
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delay_percent: 10
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pulse_percent: 1
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line_interval: 0.000075
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display_acquisition_subsampling: 4
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average_frame_rate: 4.969
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frames_to_average: 1
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exposure_time_range:
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min: 1
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max: 1000
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step: 1
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flip_x: False
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flip_y: False
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x_pixels_step: 4
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y_pixels_step: 4
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x_pixels_min: 4
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y_pixels_min: 4
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remote_focus_device:
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hardware:
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name: daq
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type: NI
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channel: PXI6259/ao2
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min: -5
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max: 5
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# Optotune EL-16-40-TC-VIS-5D-1-C
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delay_percent: 7.5
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ramp_rising_percent: 85
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ramp_falling_percent: 2.5
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amplitude: 0.7
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offset: 2.3
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smoothing: 0.0
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galvo:
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-
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hardware:
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name: daq
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type: NI
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channel: PXI6259/ao0
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min: -5
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max: 5
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frequency: 99.9
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amplitude: 2.5
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offset: 0
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duty_cycle: 50
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phase: 1.57079 # pi/2
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filter_wheel:
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hardware:
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name: filter_wheel
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type: SutterFilterWheel
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wheel_number: 1
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port: COM2
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baudrate: 9600
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filter_wheel_delay: .030 # in seconds
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available_filters:
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Empty-Alignment: 5
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GFP - FF01-515/30-32: 6
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RFP - FF01-595/31-32: 7
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Far-Red - BLP01-647R/31-32: 8
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Blocked1: 4
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Blocked2: 0
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Blocked3: 1
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Blocked4: 2
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Blocked5: 3
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Blocked6: 9
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stage:
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hardware:
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name: stage
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type: PI
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serial_number: 119060508
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axes: [x, y, z, theta, f]
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controllername: C-884
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stages: L-509.20DG10 L-509.40DG10 L-509.20DG10 M-060.DG M-406.4PD NOSTAGE
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refmode: FRF FRF FRF FRF FRF FRF
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x_max: 100000
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x_min: -100000
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y_max: 100000
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y_min: -100000
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z_max: 100000
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z_min: -100000
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f_max: 100000
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f_min: 0
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theta_max: 360
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theta_min: 0
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x_offset: 0
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y_offset: 0
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z_offset: 0
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f_offset: 0
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theta_offset: 0
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flip_x: False
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flip_y: False
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flip_z: False
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zoom:
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hardware:
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type: DynamixelZoom
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servo_id: 1
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port: COM9
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baudrate: 1000000
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position:
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0.63x: 0
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1x: 627
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2x: 1711
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3x: 2301
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4x: 2710
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5x: 3079
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6x: 3383
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pixel_size:
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0.63x: 9.7
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1x: 6.38
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2x: 3.14
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3x: 2.12
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4x: 1.609
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5x: 1.255
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6x: 1.044
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stage_positions:
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BABB:
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f:
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0.63x: 67410
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1x: 70775
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2x: 72455
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3x: 72710
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4x: 72795
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5x: 72850
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6x: 72880
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CUBIC:
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f:
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0.63x: 67410
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1x: 70775
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2x: 72455
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3x: 72710
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4x: 72795
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5x: 72850
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6x: 72880
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shutter:
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hardware:
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type: NI
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channel: PXI6259/port0/line0
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min: 0
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max: 5
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lasers:
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# Omicron LightHub Ultra
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# 488 and 640 are LuxX+ Lasers
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# 561 is a Coherent OBIS Laser
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# Digital Laser Outputs
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- wavelength: 488
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onoff:
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hardware:
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type: NI
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channel: PXI6733/port0/line2
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min: 0
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max: 5
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power:
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hardware:
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type: NI
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channel: PXI6733/ao0
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min: 0
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max: 5
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type: LuxX
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- wavelength: 562
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onoff:
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hardware:
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type: NI
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channel: PXI6733/port0/line3
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min: 0
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max: 5
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power:
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hardware:
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type: NI
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channel: PXI6733/ao1
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min: 0
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max: 5
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type: Obis
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- wavelength: 642
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onoff:
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hardware:
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type: NI
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channel: PXI6733/port0/line4
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min: 0
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max: 5
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power:
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hardware:
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type: NI
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channel: PXI6733/ao2
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min: 0
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max: 5
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type: LuxX
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Nanoscale:
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daq:
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hardware:
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type: NI
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# NI PCIe-1073 Chassis with PXI-6259 and PXI-6733 DAQ Boards.
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# Sampling rate in Hz
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sample_rate: 100000
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# triggers
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master_trigger_out_line: PXI6259/port0/line1
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camera_trigger_out_line: /PXI6259/ctr0
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trigger_source: /PXI6259/PFI0
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# Digital Laser Outputs
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laser_port_switcher: PXI6733/port0/line0
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laser_switch_state: True
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camera:
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hardware:
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type: HamamatsuOrca
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serial_number: 500502
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defect_correct_mode: 2.0
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delay: 10 #ms
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settle_down: 0.0 #ms
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remote_focus_device:
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hardware:
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type: EquipmentSolutions #NI
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channel: PXI6259/ao3
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port: COM6
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min: -5
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max: 5
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# waveform: trig_remote_focus_ramp
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galvo:
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-
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hardware:
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type: NI
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channel: PXI6259/ao1
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min: -5
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max: 5
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filter_wheel:
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hardware:
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type: SutterFilterWheel
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wheel_number: 2
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port: COM2
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baudrate: 9600
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filter_wheel_delay: .030 # in seconds
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available_filters:
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Empty-Alignment: 0
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GFP - FF01-515/30-32: 1
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RFP - FF01-595/31-32: 2
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Far-Red - BLP01-647R/31-32: 3
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Blocked1: 4
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Blocked2: 5
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Blocked3: 6
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Blocked4: 7
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Blocked5: 8
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Blocked6: 9
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stage:
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hardware:
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-
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type: PI
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serial_number: 119060508
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axes: [x, y, z, theta]
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controllername: C-884
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stages: L-509.20DG10 L-509.40DG10 L-509.20DG10 M-060.DG M-406.4PD NOSTAGE
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refmode: FRF FRF FRF FRF FRF FRF
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-
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type: PI
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serial_number: 0116049747
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axes: [f]
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controllername: E-709
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stages: P-726.1CD
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refmode: ATZ
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# -
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# name: stage2
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# type: MCL
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# serial_number: 4011
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# axes: [f]
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x_max: 100000
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x_min: -100000
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y_max: 100000
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y_min: -100000
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z_max: 100000
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z_min: -100000
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f_max: 100000
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f_min: 0
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theta_max: 360
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theta_min: 0
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x_offset: 500 # -1000
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y_offset: 300 # -70
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z_offset: -18396 # -17842
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# x_offset: 0
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# y_offset: 0
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# z_offset: 0
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f_offset: 0
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theta_offset: 0
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zoom:
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position:
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N/A: 0
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pixel_size:
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N/A: 0.167
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shutter:
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hardware:
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type: NI
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channel: PXI6259/port2/line0
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lasers:
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# Omicron LightHub Ultra
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# 488 and 640 are LuxX+ Lasers
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# 561 is a Coherent OBIS Laser
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# Digital Laser Outputs
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- wavelength: 488
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onoff:
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hardware:
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type: NI
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channel: PXI6733/port0/line2
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min: 0
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max: 5
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power:
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hardware:
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type: NI
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channel: PXI6733/ao0
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min: 0
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max: 5
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type: LuxX
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- wavelength: 562
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onoff:
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hardware:
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type: NI
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channel: PXI6733/port0/line3
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min: 0
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max: 5
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power:
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hardware:
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type: NI
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channel: PXI6733/ao1
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min: 0
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max: 5
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type: Obis
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- wavelength: 642
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onoff:
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hardware:
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type: NI
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channel: PXI6733/port0/line4
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min: 0
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max: 5
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power:
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hardware:
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type: NI
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channel: PXI6733/ao2
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min: 0
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max: 5
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type: LuxX
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gui:
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channels:
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count: 5
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