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example_acquisition_settings.yaml
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example_acquisition_settings.yaml
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# This is an example settings file for combined label-free and light--sheet
# acquisition on the mantis microscope.
# Here we define variables (YAML anchors) which will be used later, for
# convenience
LCA_DAC: &LCA_DAC 'TS1_DAC01'
LCB_DAC: &LCB_DAC 'TS1_DAC02'
MCL_DAC: &MCL_DAC 'TS1_DAC06'
AP_GALVO_DAC: &AP_GALVO_DAC 'TS2_DAC03'
# The label-free and the light-sheet acquisition share the same time settings
# which are controlled by the mantis acquisition engine. Data are acquired in
# TPCZYX order. `time_interval_s` is the minimum time between positions, i.e.
# the acquisition will continue immediately if the elapsed time to acquire all
# positions is greater
time_settings:
num_timepoints: 10
time_interval_s: 60
# Define channel settings for the label-free acquisition. All channels must be
# within the same config group. `default_exposure_times_ms` must be a float
# which will be used for all channels or a list of length equal to the number of
# channels. Currently, however, the acquisition software does not support
# different exposure times for the label-free channels.
lf_channel_settings:
default_exposure_times_ms: 10
channel_group: 'Channel - LF'
channels: ['State0', 'State1', 'State2', 'State3', 'State4']
use_sequencing: True
# Define slice (i.e. z-stack) settings for the label-free acquisition.
lf_slice_settings:
z_stage_name: 'MCL Piezo'
z_start: -10 # in sample-space micrometers
z_end: 15
# When using 0.52 NA transmission light illumination, Nyquist sampling of the
# axial dimension will be achieved by using (450*1.4)/(1.35^2 + 0.52^2) = 300 nm
# steps in sample space. We can achieve this by using (300 nm)*1.4/2 = 210 nm
# steps of the mirror due to the 1.4x magnification of the remote volume and the
# fact that the optical path length is extended by twice the mirror's motion.
#
# Here we choose to oversample the data to match the light-sheet axial
# sampling. After deskewing and 3x binning, the light-sheet samples are spaced
# by ~205 nm. We chose a matching sample-space sampling, which corresponds to
# (205 nm)*1.4/2 = 143 nm motion of the mirror or (0.143 um)*(10 V / 65 um) =
# 22 mV DAC steps
z_step: 0.205 # equivalent to 22 mV
use_sequencing: True
# Define channel settings for the light-sheet acquisition. Channels may have
# different exposure times. Exposure times may be updated by the autoexposure
# algorithm. `default_laser_powers` may be a float, a list of length equal to
# the number of channels, or null / blank in which case the laser power will not
# be changed unless updated by the autoexposure algorithm. `use_autoexposure`
# may be bool or a list
ls_channel_settings:
default_exposure_times_ms: [10, 10]
default_laser_powers:
channel_group: 'Channel - LS'
channels: ['GFP EX488 EM525-45', 'mCherry EX561 EM600-37']
use_sequencing: False
use_autoexposure: [True, False]
# Define slice (i.e. z-stack) settings for the light-sheet acquisition.
ls_slice_settings:
z_stage_name: 'AP Galvo'
# 185 um scan range covers the label-free field of view. Corresponds to
# ~5.9 V based on 31.3 um/V conversion factor
z_start: -100 # in sample-space micrometers
z_end: 85
# Nyquist sampling of this dimensions will be achieved by using ~116 nm steps.
# When imaging live cells we chose to undersample this dimension to decrease
# photobleaching and photodamage.
z_step: 0.313 # equivalent to 10 mV
use_sequencing: True
# Microscope settings which will be applied when the label-free acquisition is
# initialized
lf_microscope_settings:
# ROI may be omitted or blank; in this case the ROI will not be changed
roi:
# Config group settings to apply. Must be a list of
# [config_group, config_name] pairs
config_group_settings:
- ['Imaging Path', 'Label-free']
- ['Channel - LS', 'External Control']
# need to set first channel for falling edge sequencing
- ['Channel - LF', 'State0']
# Device property settings to apply. Must be a list of
# [device_name, property_name, property_value] sets
device_property_settings:
- ['Oryx', 'Line Selector', 'Line5']
- ['Oryx', 'Line Mode', 'Output']
- ['Oryx', 'Line Source', 'ExposureActive']
- ['Oryx', 'Line Selector', 'Line2']
- ['Oryx', 'Line Mode', 'Input']
- ['Oryx', 'Trigger Source', 'Line2']
- ['Oryx', 'Trigger Mode', 'On']
# required for external triggering at max fps
- ['Oryx', 'Trigger Overlap', 'ReadOut']
- ['Oryx', 'Frame Rate Control Enabled', '0']
# Device property settings which will be applied when the acquisition is
# finished.
reset_device_properties:
- ['Oryx', 'Trigger Mode', 'Off']
- ['XYStage:XY:31', 'MotorSpeedX-S(mm/s)', 5.75]
- ['XYStage:XY:31', 'MotorSpeedY-S(mm/s)', 5.75]
# Device property settings which enable z sequencing
z_sequencing_settings:
- [*MCL_DAC, 'Sequence', 'On']
# Device property settings which enable channel sequencing
channel_sequencing_settings:
- [*LCA_DAC, 'Sequence', 'On']
- [*LCB_DAC, 'Sequence', 'On']
# Autofocus properties. `autofocus_stage` is the coarse stage which will be
# moved between positions to ensure that the autofocus mechanism is within
# range
use_autofocus: True
autofocus_stage: 'ZDrive'
autofocus_method: 'PFS'
# Microscope settings which will be applied when the light-sheet acquisition is
# initialized
ls_microscope_settings:
roi: [0, 896, 2048, 256]
device_property_settings:
- ['Prime BSI Express', 'ReadoutRate', '200MHz 11bit']
- ['Prime BSI Express', 'Gain', '1-Full well']
- ['Prime BSI Express', 'TriggerMode', 'Edge Trigger']
- ['Prime BSI Express', 'ExposeOutMode', 'Rolling Shutter']
# Illuminate sample only when all rows are exposing, aka pseudo global shutter
- ['TS2_TTL1-8', 'Blanking', 'On']
reset_device_properties:
- ['Prime BSI Express', 'TriggerMode', 'Internal Trigger']
- ['TS2_TTL1-8', 'Blanking', 'Off']
z_sequencing_settings:
- [*AP_GALVO_DAC, 'Sequence', 'On']
use_o3_refocus: True
o3_refocus_config: ['Channel - LS', 'GFP EX488 EM525-45']
o3_refocus_interval_min: 10
ls_autoexposure_settings:
autoexposure_method: 'manual'
rerun_each_timepoint: True