chuan/navigate
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

feat: init

Browse Source
This commit is contained in:
chuan
2025-12-04 16:07:30 +08:00
commit 262583a57f
681 changed files with 117578 additions and 0 deletions
Download Patch File Download Diff File Expand all files Collapse all files

389
docs/source/05_reference/implementations/configurations/configuration_multiscale.yaml Normal file
View File

@@ -0,0 +1,389 @@
# 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