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2025-12-04 16:07:30 +08:00
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docs/source/05_reference/implementations/configurations/configuration_spectral_tirf.yaml Normal file
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microscopes:
SpectralTIRF_lt538:
daq:
hardware:
name: daq
type: NI
sample_rate: 100000
sweep_time: 0.2
master_trigger_out_line: PCIE6738/port0/line1
camera_trigger_out_line: /PCIE6738/ctr0
trigger_source: /PCIE6738/PFI0
laser_port_switcher: PCIE6738/port0/line0
laser_switch_state: False
# dichroic:
# hardware:
# name: ASI
# type: ASI #synthetic #ASI
# port: COM17
# axes: [S]
# baudrate: 115200
# available_dichroics:
# 510LP: 0
# 570LP: 1
# 640LP: 2
camera:
hardware:
name: camera
type: HamamatsuOrca
serial_number: 003055
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. Normal/Light-Sheet
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: 1.0
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
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: PCIE6738/ao2
min: 0
max: 5
delay_percent: 7.5
ramp_rising_percent: 85
ramp_falling_percent: 2.5
amplitude: 0.7
offset: 2.3
galvo:
-
hardware:
name: daq
type: NI
channel: PCIE6738/ao2 #galvo-x
min: -5
max: 5
waveform: sine
frequency: 99.9
period: 10
amplitude: 2.5
offset: 0
duty_cycle: 50
phase: 0
-
hardware:
name: daq
type: NI
channel: PCIE6738/ao3 #galvo-y
min: -5
max: 5
waveform: sine
frequency: 99.9
period: 10
amplitude: 2.5
offset: 0
duty_cycle: 50
phase: 90
filter_wheel:
-
hardware:
name: emission
type: ASI
wheel_number: 0
port: COM17
baudrate: 115200
filter_wheel_delay: .030 # in seconds
available_filters:
Empty 1: 0
482/35: 1
520/15: 2
NF03-488E: 3
Blocked2: 4
Blocked3: 5
Empty 2: 6
Blocked 4: 7
Blocked 5: 8
Blocked 6: 9
-
hardware:
name: emission
type: ASI
wheel_number: 1
port: COM17
baudrate: 115200
filter_wheel_delay: .030 # in seconds
available_filters:
Empty 1: 0
575/15: 1
647/57: 2
Blocked: 3
593/lp: 4
578/21: 5
Empty 2: 6
Blocked 4: 7
Blocked 5: 8
Blocked 6: 9
stage:
hardware:
-
name: ASI
type: ASI
port: COM17
baudrate: 115200
serial_number: 119060508
axes: [x, y, z]
axes_mapping: [X, Y, Z]
volts_per_micron: None
axes_channels: None
max: None
min: None
-
name: Synthetic
type: SyntheticStage
serial_number: 119060508
axes: [theta, f]
axes_mapping: [theta, f]
volts_per_micron: None
axes_channels: None
max: None
min: None
x_max: 50000
x_min: -50000
y_max: 50000
y_min: -50000
z_max: 50000
z_min: -50000
f_max: 50000
f_min: 0
theta_max: 360
theta_min: 0
x_step: 500
y_step: 500
z_step: 500
theta_step: 30
f_step: 500
velocity: 1000
zoom:
hardware:
name: zoom
type: synthetic
servo_id: 1
position:
110x: 0
pixel_size:
110x: 0.059
shutter:
hardware:
name: daq
type: synthetic
channel: PCIE6738/port0/line0
min: 0
max: 5
lasers:
- wavelength: 405
onoff:
hardware:
name: daq
type: NI
channel: PCIE6738/port1/line1 #38/35
min: 0
max: 5
power:
hardware:
name: daq
type: NI
channel: PCIE6738/ao21
min: 0
max: 5
type: Obis
index: 0
delay_percent: 10
pulse_percent: 87
- wavelength: 445
onoff:
hardware:
name: daq
type: NI
channel: PCIE6738/ao4
min: 0
max: 5
power:
hardware:
name: daq
type: NI
channel: PCIE6738/ao5
min: 0
max: 5
type: LuxX
index: 0
delay_percent: 10
pulse_percent: 87
- wavelength: 488
onoff:
hardware:
name: daq
type: NI
channel: PCIE6738/ao6
min: 0
max: 5
power:
hardware:
name: daq
type: NI
channel: PCIE6738/ao7
min: 0
max: 5
type: LuxX
index: 0
delay_percent: 10
pulse_percent: 87
- wavelength: 514
onoff:
hardware:
name: daq
type: NI
channel: PCIE6738/ao8
min: 0
max: 5
power:
hardware:
name: daq
type: NI
channel: PCIE6738/ao9
min: 0
max: 5
type: LuxX
index: 0
delay_percent: 10
pulse_percent: 87
- wavelength: 532
onoff:
hardware:
name: daq
type: NI
channel: PCIE6738/ao10
min: 0
max: 5
power:
hardware:
name: daq
type: NI
channel: PCIE6738/ao11
min: 0
max: 5
type: LuxX
index: 0
delay_percent: 10
pulse_percent: 87
- wavelength: 562
onoff:
hardware:
name: daq
type: NI
channel: PCIE6738/ao12
min: 0
max: 5
power:
hardware:
name: daq
type: NI
channel: PCIE6738/ao13
min: 0
max: 5
type: Obis
index: 1
delay_percent: 10
pulse_percent: 87
- wavelength: 592
onoff:
hardware:
name: daq
type: NI
channel: PCIE6738/ao14
min: 0
max: 5
power:
hardware:
name: daq
type: NI
channel: PCIE6738/ao15
min: 0
max: 5
type: LuxX
index: 0
delay_percent: 10
pulse_percent: 87
- wavelength: 642
onoff:
hardware:
name: daq
type: NI
channel: PCIE6738/ao16
min: 0
max: 5
power:
hardware:
name: daq
type: NI
channel: PCIE6738/ao17
min: 0
max: 5
type: LuxX
index: 2
delay_percent: 10
pulse_percent: 87
gui:
channels:
count: 5
laser_power:
min: 0
max: 100
step: 10
exposure_time:
min: 1
max: 1000
step: 5
interval_time:
min: 0
max: 1000
step: 5
stack_acquisition:
step_size:
min: 0.200
max: 1000
step: 0.1
start_pos:
min: -5000
max: 5000
step: 1
end_pos:
min: -5000
max: 10000
step: 1
timepoint:
timepoints:
min: 1
max: 1000
step: 1
stack_pause:
min: 0
max: 1000
step: 1