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2025-12-04 16:07:30 +08:00
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docs/source/05_reference/implementations/configurations/configuration_upright.yaml Normal file
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# Only one microscope can be active in the GUI at a time, but all microscopes will be accessible
microscopes:
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/line1
laser_switch_state: False
camera:
hardware:
type: HamamatsuOrcaLightning #SyntheticCamera
serial_number: 000035
defect_correct_mode: 2.0
delay: 10 #ms
settle_down: 0.0 #ms
remote_focus_device:
hardware:
type: NI
channel: PXI6259/ao3
min: -0.5
max: 0.5
# Optotune EL-16-40-TC-VIS-5D-1-C
galvo:
-
hardware:
type: NI
channel: PXI6259/ao1
min: 0
max: 5
phase: 1.57079 # pi/2
filter_wheel:
hardware:
type: ASI #SyntheticFilterWheel
wheel_number: 2
port: COM8
baudrate: 115200
filter_wheel_delay: .030 # in seconds
available_filters:
BLU - FF01-442/42-32: 0
GFP - FF01-515/30-32: 1
RFP - FF01-595/31-32: 2
Far-Red - FF01-670/30-32: 3
Blocked1: 4
Empty: 5
Blocked3: 6
Blocked4: 7
Blocked5: 8
Blocked6: 9
stage:
hardware:
-
type: ASI
serial_number: 123456789
port: COM8
baudrate: 115200
axes: [x, y, z, f] # Software
axes_mapping: [M, Y, X, Z] # M Shear axis mapping
#axes_mapping: [M, X, Y, Z] #testing y
#axes_mapping: [M, X, Z, Y] #testing Z
# axes_mapping: [Z, Y, X, M]
feedback_alignment: [90, 90, 90, 90]
-
name: stage
type: SyntheticStage
serial_number: 987654321
axes: [theta]
x_max: 0 # Swapped from Z
x_min: -22708.3 # Swapped from Z
y_max: 1361.3
y_min: -3496.3
z_max: 3521.9 # Swapped from X
z_min: -4551.1 # Swapped from X
f_max: 3233.0 #=m
f_min: -9382.0 #=m
theta_max: 360
theta_min: 0
external_trigger: /PXI6259/PFI1
# joystick_axes: [x, y, z, f]
x_offset: 0
y_offset: 0
z_offset: 0
f_offset: 0
theta_offset: 0
zoom:
hardware:
type: SyntheticZoom
servo_id: 1
position:
N/A: 0
pixel_size:
N/A: 0.168
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: 405
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: 488
onoff:
hardware:
type: NI
channel: PXI6733/port0/line3
min: 0
max: 5
power:
hardware:
type: NI
channel: PXI6733/ao1
min: 0
max: 5
type: LuxX
- wavelength: 561
onoff:
hardware:
type: NI
channel: PXI6733/port0/line4
min: 0
max: 5
power:
hardware:
type: NI
channel: PXI6733/ao2
min: 0
max: 5
type: Obis
- wavelength: 642
onoff:
hardware:
type: NI
channel: PXI6733/port0/line5
min: 0
max: 5
power:
hardware:
type: NI
channel: PXI6733/ao3
min: 0
max: 5
type: LuxX
- wavelength: LED
power:
hardware:
type: NI
channel: PXI6733/ao4
min: 0
max: 5
Macroscale:
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/line1
laser_switch_state: True
camera:
hardware:
type: Photometrics #SyntheticCamera
serial_number: 1
camera_connection: PMPCIECam00
x_pixels: 5056.0
y_pixels: 2960.0
pixel_size_in_microns: 4.25
defect_correct_mode: 2.0
delay: 25 #8 #5.0
settle_down: 0.0 #ms
remote_focus_device:
hardware:
type: NI
channel: PXI6259/ao3
min: -0.5
max: 0.5
# Optotune EL-16-40-TC-VIS-5D-1-C
galvo:
-
hardware:
type: NI
channel: PXI6259/ao1
min: 0
max: 5
phase: 1.57079 # pi/2
filter_wheel:
hardware:
type: ASI #SyntheticFilterWheel
wheel_number: 2
port: COM8
baudrate: 115200
filter_wheel_delay: .030 # in seconds
available_filters:
BLU - FF01-442/42-32: 0
GFP - FF01-515/30-32: 1
RFP - FF01-595/31-32: 2
Far-Red - FF01-670/30-32: 3
Blocked1: 4
Empty: 5
Blocked3: 6
Blocked4: 7
Blocked5: 8
Blocked6: 9
stage:
hardware:
-
name: stage
type: ASI
port: COM8
baudrate: 115200
serial_number: 123456789
axes: [x, y, z, f] #Software
# axes_mapping: [M, Y, X, Z]
axes_mapping: [M, Y, X, Z] #M shear
feedback_alignment: [90, 90, 90, 90]
-
name: stage
type: SyntheticStage
serial_number: 987654321
axes: [theta]
x_max: 0 # Swapped from Z
x_min: -22708.3 # Swapped from Z
y_max: 1361.3
y_min: -3496.3
z_max: 3521.9 # Swapped from X
z_min: -4651.1 # Swapped from X
f_max: 3233.0 #=m
f_min: -9382.0 #=m
theta_max: 360
theta_min: 0
external_trigger: /PXI6259/PFI1
# joystick_axes: [x, y, z, f]
x_offset: 0
y_offset: 0
z_offset: 0
f_offset: 0
theta_offset: 0
zoom:
hardware:
type: SyntheticZoom
servo_id: 1
position:
N/A: 0
pixel_size:
N/A: 1.06
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: 405
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: 488
onoff:
hardware:
type: NI
channel: PXI6733/port0/line3
min: 0
max: 5
power:
hardware:
type: NI
channel: PXI6733/ao1
min: 0
max: 5
type: LuxX
- wavelength: 561
onoff:
hardware:
type: NI
channel: PXI6733/port0/line4
min: 0
max: 5
power:
hardware:
type: NI
channel: PXI6733/ao2
min: 0
max: 5
type: Obis
- wavelength: 642
onoff:
hardware:
type: NI
channel: PXI6733/port0/line5
min: 0
max: 5
power:
hardware:
type: NI
channel: PXI6733/ao3
min: 0
max: 5
type: LuxX
- wavelength: LED
power:
hardware:
type: NI
channel: PXI6733/ao4
min: 0
max: 5
gui:
channels:
count: 5