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