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2025-12-04 16:07:30 +08:00
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164
docs/source/05_reference/implementations/configurations/configuration_OPMv2.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:
OPMv2:
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: /Dev5/port0/line1
camera_trigger_out_line: /Dev5/ctr0
trigger_source: /Dev5/PFI0
zoom:
hardware:
type: SyntheticZoom
servo_id: 1
position:
1x: 0
pixel_size:
1x: 0.15
shutter:
hardware:
type: SyntheticShutter
channel: none/line0
camera:
hardware:
name: camera
type: HamamatsuOrca
serial_number: 304064
defect_correct_mode: 2.0
delay: 7.5 #ms
settle_down: 0.0 #ms
remote_focus_device:
hardware:
type: NI
channel: Dev5/ao3
min: 0
max: 5
# Optotune EL-16-40-TC-VIS-5D-1-C
galvo:
# -
# name: xgalvo
# hardware:
# name: daq
# type: NI
# channel: Dev5/ao0
# min: -5
# max: 5
# frequency: 99.9
# amplitude: 2.5
# offset: 0
# duty_cycle: 50
# phase: 1.57079 # pi/2
-
name: ygalvo
hardware:
type: NI
channel: Dev5/ao1
min: -5
max: 5
phase: 1.57079 # pi/2
-
name: sheargalvo
hardware:
name: daq
type: NI
channel: Dev5/ao2
min: -5
max: 5
phase: 1.57079 # pi/2
stage:
hardware:
-
name: fake_stage
type: SyntheticStage
serial_number: 123
axes: [x,y,theta,f]
-
name: galvo-stage
type: GalvoNIStage
serial_number: 123
axes: [z]
axes_mapping: [Dev5/ao0]
min: -5
max: 5
volts_per_micron: 0.01*x + 0
x_max: 500
x_min: -500
y_max: 500
y_min: -500
z_max: 500
z_min: -500
f_max: 100000
f_min: -100000
theta_max: 360
theta_min: 0
x_offset: 0
y_offset: 0
z_offset: 0
f_offset: 0
theta_offset: 0
filter_wheel:
hardware:
type: SyntheticFilterWheel
wheel_number: 1
port: COM6
baudrate: 9600
filter_wheel_delay: .030 # in seconds
available_filters:
FRFP - BLP01-664R-25: 0
RFP - FF01-598/25-25: 1
GFP - 527/20: 2
GFPRFP - ZET488/561m: 3
Empty-Alignment: 4
Blocked2: 5
Blocked3: 6
Blocked4: 7
Blocked5: 8
Blocked6: 9
lasers:
# Omicron LightHub Ultra
# 488 and 640 are LuxX+ Lasers
# 561 is a Coherent OBIS Laser
# Digital Laser Outputs
- wavelength: 488
power:
hardware:
type: NI
channel: Dev5/ao12
min: 0
max: 5
type: LuxX
- wavelength: 562
onoff:
hardware:
type: NI
channel: Dev5/port1/line5
min: 0
max: 5
power:
hardware:
type: NI
channel: Dev5/ao13
min: 0
max: 5
type: Obis
- wavelength: 642
power:
hardware:
type: NI
channel: Dev5/ao14
min: 0
max: 5
type: LuxX
gui:
channels:
count: 5

311
docs/source/05_reference/implementations/configurations/configuration_OPMv3.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:
ProjectionScope:
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: /PCIe-6738/port0/line1
camera_trigger_out_line: /PCIe-6738/ctr0 #PFI7 Camera trigger
trigger_source: /PCIe-6738/PFI0
mirror:
hardware:
name: mirror
type: ImagineOpticsMirror
flat_path: D:\WaveKitX64\MirrorFiles\BeadsCoverslip_20231212.wcs
n_modes: 32
zoom:
hardware:
type: SyntheticZoom
servo_id: 1
position:
1x: 0
pixel_size:
1x: 0.15
shutter:
hardware:
type: SyntheticShutter
channel: none/line0
camera:
hardware:
name: camera
type: HamamatsuOrca
serial_number: 001301
defect_correct_mode: 2.0
delay: 10 #ms
settle_down: 0.0 #ms
remote_focus_device:
hardware:
type: SyntheticRemoteFocus
channel: none
min: 0
max: 5
galvo:
-
# shear galvo measured: 351.04 um/V
name: sheargalvo
hardware:
type: NI # SyntheticGalvo
channel: PCIe-6738/ao12
min: -5
max: 5
# waveform: halfsaw
waveform: sawtooth
phase: 1.57079
-
name: xgalvo
hardware:
type: NI # SyntheticGalvo
channel: PCIe-6738/ao0
min: -5
max: 5
waveform: sawtooth
phase: 1.57079
stage:
hardware:
-
name: fake_stage
type: SyntheticStage
serial_number: 123
axes: [x,y,theta,z]
-
name: snouty_piezo
type: GalvoNIStage
serial_number: 124
axes: [f]
axes_mapping: [PCIe-6738/ao14]
min: 0
max: 10
volts_per_micron: (10/15.4)*x + 5.0
x_max: 50
x_min: -50
y_max: 50
y_min: -50
z_max: 500
z_min: -500
f_max: 100000
f_min: -100000
theta_max: 360
theta_min: 0
x_offset: 0
y_offset: 0
z_offset: 0
f_offset: 0
theta_offset: 0
filter_wheel:
hardware:
type: SyntheticFilterWheel
wheel_number: 1
port: COM6
baudrate: 9600
filter_wheel_delay: .030 # in seconds
available_filters:
FRFP - BLP01-664R-25: 0
RFP - FF01-598/25-25: 1
GFP - 527/20: 2
GFPRFP - ZET488/561m: 3
Empty-Alignment: 4
Blocked2: 5
Blocked3: 6
Blocked4: 7
Blocked5: 8
Blocked6: 9
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: PCIe-6738/port1/line2
min: 0
max: 5
power:
hardware:
type: NI
channel: PCIe-6738/ao5
min: 0
max: 5
type: Obis
- wavelength: 561
onoff:
hardware:
type: NI
channel: PCIe-6738/port1/line3
min: 0
max: 5
power:
hardware:
type: NI
channel: PCIe-6738/ao11
min: 0
max: 5
type: Obis
StackingScope:
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: /PCIe-6738/port0/line1
camera_trigger_out_line: /PCIe-6738/ctr0 #PFI7 Camera trigger
trigger_source: /PCIe-6738/PFI0
mirror:
hardware:
name: mirror
type: ImagineOpticsMirror
flat_path: D:\WaveKitX64\MirrorFiles\BeadsCoverslip_20231212.wcs
n_modes: 32
zoom:
hardware:
type: SyntheticZoom
servo_id: 1
position:
1x: 0
pixel_size:
1x: 0.15
shutter:
hardware:
name: shutter
type: SyntheticShutter
channel: none/line0
camera:
hardware:
name: camera
type: HamamatsuOrca
serial_number: 001301
defect_correct_mode: 2.0
delay: 10 #ms
remote_focus_device:
hardware:
type: SyntheticRemoteFocus
channel: none
min: 0
max: 10
# Optotune EL-16-40-TC-VIS-5D-1-C
galvo:
-
name: sheargalvo
hardware:
type: NI # SyntheticGalvo
channel: PCIe-6738/ao12
min: -5
max: 5
phase: 1.57079
stage:
hardware:
-
name: fake_stage
type: SyntheticStage
serial_number: 123
axes: [x,y,theta]
-
name: snouty_piezo
type: GalvoNIStage
serial_number: 124
axes: [f]
axes_mapping: [PCIe-6738/ao14]
min: 0
max: 10
volts_per_micron: (10/15.4)*x + 5.0
-
name: z_galvo
type: GalvoNIStage
serial_number: 125
axes: [z]
# axes_channels: [PCIe-6738/ao0]
axes_mapping: [PCIe-6738/ao0]
min: -3.5
max: 3.5
volts_per_micron: 0.007*x
x_max: 50
x_min: -50
y_max: 50
y_min: -50
z_max: 500
z_min: -500
f_max: 100000
f_min: -100000
theta_max: 360
theta_min: 0
x_offset: 0
y_offset: 0
z_offset: 0
f_offset: 0
theta_offset: 0
filter_wheel:
hardware:
type: SyntheticFilterWheel
wheel_number: 1
port: COM6
baudrate: 9600
filter_wheel_delay: .030 # in seconds
available_filters:
FRFP - BLP01-664R-25: 0
RFP - FF01-598/25-25: 1
GFP - 527/20: 2
GFPRFP - ZET488/561m: 3
Empty-Alignment: 4
Blocked2: 5
Blocked3: 6
Blocked4: 7
Blocked5: 8
Blocked6: 9
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: PCIe-6738/port1/line2
min: 0
max: 5
power:
hardware:
type: NI
channel: PCIe-6738/ao5
min: 0
max: 5
type: Obis
- wavelength: 561
onoff:
hardware:
type: NI
channel: PCIe-6738/port1/line3
min: 0
max: 5
power:
hardware:
type: NI
channel: PCIe-6738/ao11
min: 0
max: 5
type: Obis
gui:
channels:
count: 5

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docs/source/05_reference/implementations/configurations/configuration_biofrontiers.yaml Normal file
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microscopes:
OPM:
daq:
hardware:
type: NI
sample_rate: 100000
master_trigger_out_line: PXI6723/port0/line1
camera_trigger_out_line: /PXI6723/ctr0
trigger_source: /PXI6723/PFI0
laser_port_switcher: PXI6723/port0/line0
laser_switch_state: False
camera:
hardware:
type: HamamatsuOrca
serial_number: 000646
defect_correct_mode: 2.0
delay: 10.0 #ms
settle_down: 0.0 #ms
flip_x: False
flip_y: False
remote_focus_device:
hardware:
type: SyntheticRemoteFocus
channel: PXI6723/ao2
min: 0
max: 5
galvo:
-
hardware:
type: NI
channel: PXI6723/ao0
min: -10
max: 10
waveform: sine
phase: 1.57079
filter_wheel:
hardware:
type: ASI
wheel_number: 1
port: COM13
baudrate: 115200
filter_wheel_delay: .030
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: ASI
serial_number: 123456789
axes: [x, y, f]
axes_mapping: [X, Y, Z]
volts_per_micron: None
max: None
min: None
port: COM13
baudrate: 115200
timeout: 0.25
-
type: GalvoNIStage
serial_number: 987654321
axes: [z]
axes_mapping: [ PXI6723/ao1 ]
volts_per_micron: 0.05*x
distance_threshold: None
settle_duration_ms: 20 #ms
max: 10
min: -10
-
type: SyntheticStage
serial_number: 123
axes: [theta]
axes_mapping: [theta]
max: 360
min: 0
joystick_axes: [x, y, z]
x_max: 100000
x_min: -100000
y_max: 100000
y_min: -100000
z_max: 100000
z_min: -100000
f_max: 100000
f_min: -100000
theta_max: 360
theta_min: 0
x_offset: 0
y_offset: 0
z_offset: 0
theta_offset: 0
f_offset: 0
flip_x: False
flip_y: False
flip_z: False
zoom:
hardware:
type: SyntheticZoom
servo_id: 1
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: 0
1x: 1
2x: 2
3x: 3
4x: 4
5x: 5
6x: 6
shutter:
hardware:
type: SyntheticShutter #NI
channel: PXI6723/port0/line0
min: 0
max: 5
lasers:
- wavelength: 405
onoff:
hardware:
type: NI
channel: PCI6321/port0/line3
min: 0
max: 5
power: #analog
hardware:
type: SyntheticLaser
channel: PCI6321/ao1
min: 0
max: 5
type: LuxX
- wavelength: 488
onoff: #digital
hardware:
type: NI
channel: PCI6321/port0/line5
min: 0
max: 5
power: #analog
hardware:
type: SyntheticLaser
channel: PCI6321/ao0
min: 0
max: 5
type: LuxX
- wavelength: 561
onoff:
hardware:
type: NI
channel: PCI6321/port0/line7
min: 0
max: 5
power: #analog
hardware:
type: SyntheticLaser
channel: PCI6321/ao1
min: 0
max: 5
type: Obis
- wavelength: 640
onoff: #digital
hardware:
type: NI
channel: PCI6321/port0/line1
min: 0
max: 5
power: #analog
hardware:
type: SyntheticLaser
channel: PCI6321/ao2
min: 0
max: 5
type: LuxX
gui:
channels:
count: 5

194
docs/source/05_reference/implementations/configurations/configuration_ctaslmv1.yaml Normal file
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microscopes:
CTASLMv1:
daq:
hardware:
type: NI
sample_rate: 100000
# triggers
master_trigger_out_line: PCI6738/port0/line1
camera_trigger_out_line: /PCI6738/ctr0
trigger_source: /PCI6738/PFI0
# Digital Laser Outputs
laser_port_switcher: PCI6738/port0/line0
laser_switch_state: False
camera:
hardware:
type: HamamatsuOrca
serial_number: 000420
defect_correct_mode: 2.0
delay: 2.0 #ms
settle_down: 0.0 #ms
flip_x: False
flip_y: False
remote_focus_device:
hardware:
type: EquipmentSolutions # NI
channel: PCI6738/ao2 #45/46
port: COM1
baudrate: 9600
min: -5
max: 5
galvo:
-
hardware:
type: NI
channel: PCI6738/ao0 #10/11
min: -5
max: 5
waveform: sawtooth
phase: 1.57079 # pi/2
filter_wheel:
hardware:
type: SutterFilterWheel
wheel_number: 1
port: COM34
baudrate: 9600
filter_wheel_delay: .030 # in seconds
available_filters:
445-20: 6
525-30: 0
550-49: 9 # switched
600-53: 7
665LP: 8
EMPTY: 1
BLOCKED1: 2
BLOCKED2: 3
BLOCKED3: 4
BLOCKED4: 5
# 665LP: 0
# 550-49: 1
# 525-30: 2
# 445-20: 3
# Blocked1: 4
# Blocked2: 5
# Blocked3: 6
# Blocked4: 7
# Blocked5: 8
# Blocked6: 9
stage:
hardware:
-
type: MP285
serial_number: 0000
axes: [y, x, f]
axes_mapping: [z, y, x]
volts_per_micron: None
max: 25000
min: 0
port: COM2
timeout: 0.25
baudrate: 9600
-
type: syntheticstage
serial_number: 0000
axes: [theta]
axes_mapping: [theta]
max: 360
min: 0
-
type: GalvoNIStage
serial_number: 0000
axes: [z]
axes_mapping: [PCI6738/ao6]
volts_per_micron: 0.02*x
max: 10
min: 0
# joystick_axes: [x, y, f]
x_max: 12500
x_min: -12500
y_max: 12500
y_min: -12500
z_max: 500
z_min: 0
f_max: 100000
f_min: -100000
theta_max: 360
theta_min: 0
x_offset: 0
y_offset: 0
z_offset: 0
theta_offset: 0
f_offset: 0
zoom:
hardware:
type: synthetic
servo_id: 1
position:
16X: 0
pixel_size:
16X: 0.425
stage_positions:
BABB:
f:
16X: 0
shutter:
hardware:
type: synthetic
channel: PCI6738/port0/line10
min: 0
max: 5
lasers:
- wavelength: 642
onoff:
hardware:
type: NI
channel: PCI6738/port1/line5 # 38/35
min: 0
max: 5
power:
hardware:
type: NI
channel: PCI6738/ao8 #16/50 #ao1 # 44/11
min: 0
max: 5
type: Obis
- wavelength: 561
onoff:
hardware:
type: NI
channel: PCI6738/port1/line2 # 5/39
min: 0
max: 5
power:
hardware:
type: NI
channel: PCI6738/ao9 #17/50 #ao3 # 12/46
min: 0
max: 5
type: Obis
- wavelength: 488
onoff:
hardware:
type: NI
channel: PCI6738/port1/line3 # 6/39
min: 0
max: 5
power:
hardware:
type: NI
channel: PCI6738/ao10 #51/50 #ao4 13/14
min: 0
max: 5
type: Obis
- wavelength: 405
onoff:
hardware:
type: NI
channel: PCI6738/port1/line4 # 40/41
min: 0
max: 5
power:
hardware:
type: NI
channel: PCI6738/ao11 #52/18 #ao5 #47/14
min: 0
max: 5
type: Obis
gui:
channels:
count: 5

173
docs/source/05_reference/implementations/configurations/configuration_ctaslmv2.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:
CTASLMv2:
daq:
hardware:
type: NI
sample_rate: 100000
# triggers
master_trigger_out_line: PCI6738/port0/line1 #3
camera_trigger_out_line: /PCI6738/ctr0 #9/42
trigger_source: /PCI6738/PFI0 #4
# Digital Laser Outputs
laser_port_switcher: PCI6738/port0/line0
laser_switch_state: False
camera:
hardware:
type: HamamatsuOrca
serial_number: 302153
flip_x: True
flip_y: False
defect_correct_mode: 2.0
delay: 20
remote_focus_device:
hardware:
type: EquipmentSolutions # NI
channel: PCI6738/ao2 #45/46
port: COM7
min: -5
max: 5
galvo:
-
hardware:
type: NI
channel: PCI6738/ao0 #10/11
min: -5
max: 5
waveform: sawtooth
phase: 1.57079 # pi/2
filter_wheel:
hardware:
type: SutterFilterWheel
wheel_number: 1
port: COM10
baudrate: 9600
filter_wheel_delay: .030 # in seconds
available_filters:
Empty-1: 0
525-30: 1
600-52: 2
670-30: 3
647-LP: 4
Empty-2: 5
Empty-3: 6
Empty-4: 7
stage:
hardware:
-
name: stage1
type: MP285
serial_number: 0000
axes: [y, x, f]
axes_mapping: [z, y, x]
volts_per_micron: None
max: 25000
min: 0
port: COM2
timeout: 0.25
baudrate: 9600
-
name: stage2
type: syntheticstage
serial_number: 0000
axes: [theta]
axes_mapping: [theta]
max: 360
min: 0
-
name: stage3
type: GalvoNIStage
serial_number: 0000
axes: [z]
axes_mapping: [PCI6738/ao6] #48/49
volts_per_micron: 0.05*x
max: 10
min: 0
distance_threshold: 20
settle_duration_ms: 100
x_max: 12500
x_min: -12500
y_max: 12500
y_min: -12500
z_max: 200
z_min: 0
f_max: 12500
f_min: -12500
theta_max: 360
theta_min: 0
x_offset: 0
y_offset: 0
z_offset: 0
theta_offset: 0
f_offset: 0
coupled_axes:
z: f
zoom:
hardware:
type: synthetic
servo_id: 1
position:
36X: 0
pixel_size:
36X: 0.180
stage_positions:
BABB:
f:
36X: 0
shutter:
hardware:
type: SyntheticShutter
channel: PCI6738/port0/line10
min: 0
max: 5
lasers:
- wavelength: 488
onoff:
hardware:
type: NI
channel: PCI6738/port1/line5 # 7/41
min: 0
max: 5
power:
hardware:
type: NI
channel: PCI6738/ao8 #1 # 44/11
min: 0
max: 5
type: Obis
- wavelength: 561
onoff:
hardware:
type: NI
channel: PCI6738/port1/line2 # 5/39
min: 0
max: 5
power:
hardware:
type: NI
channel: PCI6738/ao9 # 3 # 12/46
min: 0
max: 5
type: Obis
- wavelength: 647
onoff:
hardware:
type: NI
channel: PCI6738/port1/line3 # 6/39
min: 0
max: 5
power:
hardware:
type: NI
channel: PCI6738/ao10 # 4 # 13/14
min: 0
max: 5
type: Obis
gui:
channels:
count: 5

182
docs/source/05_reference/implementations/configurations/configuration_mesospimbt.yaml Normal file
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microscopes:
BTMesoSPIM:
daq:
hardware:
type: NI
sample_rate: 100000
# triggers
master_trigger_out_line: PCI6738/port0/line1 #3
camera_trigger_out_line: /PCI6738/ctr0 #9/42
trigger_source: /PCI6738/PFI0 #4
# Digital Laser Outputs
laser_port_switcher: PCI6738/port0/line0
laser_switch_state: False
camera:
hardware:
type: HamamatsuOrca
serial_number: 003209
defect_correct_mode: 2.0 #2.0
delay: 10 #ms
settle_down: 0.0 #ms
flip_x: True
flip_y: False
remote_focus_device:
hardware:
name: remote_focus
type: NI # SyntheticRemoteFocus #EquipmentSolutions # NI
channel: PCI6738/ao2 #45/46
port: COM7
min: 0
max: 5
galvo:
-
hardware:
type: NI
channel: PCI6738/ao0 #10/11
min: -5
max: 5
waveform: sawtooth
phase: 1.57079 # pi/2
filter_wheel:
hardware:
type: ASI #SyntheticFilterWheel #SutterFilterWheel
wheel_number: 0
port: COM8
baudrate: 115200
filter_wheel_delay: .030 # in seconds
available_filters:
525-30: 0
600-37: 1
647LP: 2
Empty1: 3
Empty2: 4
670-30: 5
Blocked2: 6
Empty3: 7
Blocked3: 8
Blocked4: 9
stage:
hardware:
-
type: ASI
serial_number: 0000
port: COM8
timeout: 0.25
baudrate: 115200
axes: [x, y, z, f, theta]
feedback_alignment: [88, 91, 91, 91, 85]
axes_mapping: [X, V, Z, Y, T]
volts_per_micron: None
axes_channels: None
max: 5
min: 0
joystick_axes: [x, y, z, theta, f]
x_max: 125000
x_min: -125000
y_max: 125000
y_min: -125000
z_max: 50000
z_min: -50000
f_max: 1000000
f_min: -1000000
theta_max: 360000
theta_min: -360000
flip_x: False
flip_y: False
flip_z: False
x_offset: 0
y_offset: 0
z_offset: 0
theta_offset: 0
f_offset: 0
zoom:
hardware:
type: SyntheticZoom
servo_id: 1
port: COM18
baudrate: 9600
position:
5X: 0
4X: 0
pixel_size:
5X: 1.2 # 1.2 in BABB
4X: 1.3 # 1.3 in BABB
stage_positions:
BABB:
f:
5X: 0
4X: 0
shutter:
hardware:
type: SyntheticShutter
channel: PCI6738/port0/line10
min: 0
max: 5
lasers:
- wavelength: 488
onoff:
hardware:
type: NI
channel: PCI6738/port1/line5 # 7/41
min: 0
max: 5
power:
hardware:
type: NI
channel: PCI6738/ao8 # 1 # 44/11
min: 0
max: 5
type: Obis
- wavelength: 561
onoff:
hardware:
type: NI
channel: PCI6738/port1/line2 # 5/39
min: 0
max: 5
power:
hardware:
type: NI
channel: PCI6738/ao9 # 3 # 12/46
min: 0
max: 5
type: Obis
- wavelength: 638
onoff:
hardware:
type: NI
channel: PCI6738/port1/line3 # 6/39
min: 0
max: 5
power:
hardware:
type: NI
channel: PCI6738/ao10 # 4 # 13/14
min: 0
max: 5
type: Obis
gui:
channels:
count: 5
# BDVParameters:
# # The following parameters are used to configure the BigDataViewer
# # visualization. See the BigDataViewer documentation for more details.
# # https://imagej.net/BigDataViewer
# shear:
# shear_data: True
# shear_dimension: YZ # XZ, YZ, or XY
# shear_angle: 45
# rotate:
# rotate_data: False
# rotate_dimension: X # X, Y, Z
# rotate_angle: 0

389
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# 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

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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

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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

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# Only one microscope can be active in the GUI at a time, but all microscopes will be accessible
microscopes:
CTASLMv2:
daq:
hardware:
type: NI
sample_rate: 100000
# triggers
master_trigger_out_line: PCI6738/port0/line1 #3
camera_trigger_out_line: /PCI6738/ctr0 #9/42
trigger_source: /PCI6738/PFI0 #4
camera:
# -
hardware:
type: HamamatsuOrca
serial_number: 100803
defect_correct_mode: 2.0
delay: 20 #ms
settle_down: 0.0 #ms
# -
# hardware:
# name: camera
# type: HamamatsuOrca
# serial_number: 003054
# 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: 2.0
# 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: 20
# pulse_percent: 1
# line_interval: 0.000075
# display_acquisition_subsampling: 4
# display_acquisition_subsampling: 4
# average_frame_rate: 4.969
# frames_to_average: 1
# exposure_time_range:
# min: 1
# max: 1000
# step: 1
remote_focus_device:
hardware:
type: NI #synthetic #EquipmentSolutions # NI
channel: PCI6738/ao2 #45/46
port: COM700
min: -5
max: 5
galvo:
-
hardware:
type: NI
channel: PCI6738/ao0 #10/11
min: -5
max: 5
waveform: sawtooth
phase: 1.57079 # pi/2
filter_wheel:
hardware:
type: SutterFilterWheel
wheel_number: 1
port: COM1
baudrate: 9600
filter_wheel_delay: .030 # in seconds
available_filters:
647-LP: 0
600-50: 1
525-50: 2
480-40: 3
Empty-1: 4
Empty-2: 5
Empty-3: 6
Empty-4: 7
stage:
hardware:
-
name: stage1
type: synthetic #MP285
serial_number: 0001
port: COM6
timeout: 0.25
baudrate: 9600
axes: [y, x, f]
axes_mapping: [z, y, x]
max: 25000
min: 0
-
name: stage2
type: syntheticstage
serial_number: 0000
axes: [theta]
axes_mapping: [theta]
max: 360
min: 0
-
name: PIFOC
type: GalvoNIStage
serial_number: 0000
axes: [z]
axes_mapping: [PCI6738/ao6] #48/49
volts_per_micron: 0.1*x
max: 10
min: 0
x_max: 12500
x_min: -12500
y_max: 12500
y_min: -12500
z_max: 200
z_min: 0
f_max: 12500
f_min: -12500
theta_max: 360
theta_min: 0
x_offset: 0
y_offset: 0
z_offset: 0
theta_offset: 0
f_offset: 0
zoom:
hardware:
type: synthetic
servo_id: 1
port: COM18
baudrate: 10000
position:
62.5X: 0.104
pixel_size:
62.5X: 0.104
stage_positions:
BABB:
f:
62.5X: 0
shutter:
hardware:
type: SyntheticShutter
channel: PCI6738/port0/line10
min: 0
max: 5
lasers:
- wavelength: 405
onoff:
hardware:
type: NI
channel: PCI6738/port1/line5 # 7/41
min: 0
max: 5
power:
hardware:
type: NI
channel: PCI6738/ao8 # 16/50
min: 0
max: 5
type: Obis
- wavelength: 445
onoff:
hardware:
type: NI
channel: PCI6738/port1/line2 # 5/39
min: 0
max: 5
power:
hardware:
type: NI
channel: PCI6738/ao9 # 17/50
min: 0
max: 5
type: Obis
- wavelength: 488
onoff:
hardware:
type: NI
channel: PCI6738/port1/line3 # 6/39
min: 0
max: 5
power:
hardware:
type: NI
channel: PCI6738/ao10 # 51/50
min: 0
max: 5
type: Obis
- wavelength: 514
onoff:
hardware:
type: NI
channel: PCI6738/port1/line4 #40/41
min: 0
max: 5
power:
hardware:
type: NI
channel: PCI6738/ao11 #52/18
min: 0
max: 5
type: Obis
- wavelength: 561
onoff:
hardware:
type: NI
channel: PCI6738/port1/line6 # 8/42
min: 0
max: 5
power:
hardware:
type: NI
channel: PCI6738/ao12 #53/20
min: 0
max: 5
type: Obis
- wavelength: 640
onoff:
hardware:
type: NI
channel: PCI6738/port0/line0 #9/42
min: 0
max: 5
power:
hardware:
type: NI
channel: PCI6738/ao13 #54/20
min: 0
max: 5
type: Obis
gui:
channels:
count: 5