protocol_offline.yml

# For offline testing (demo mode only)
demo_mode: true
system:
  ip_address: localhost # IP address to connect to the microscope.
  application_file_rectangle: 'Si' # Application file for rectangle milling.
  application_file_cleaning_cross_section: 'Si'
imaging: # Ion beam imaging parameters
  horizontal_field_width: 50e-6 # In meters. Horizontal field of view
  dwell_time: 1e-7 # In seconds. Dwell time of ion beam for imaging.
  resolution: '1536x1024' # Must be one of the set resolutions available.
  autocontrast: false # whether to automatically run auto contrast adjustment
  full_field_ib_images: false # Whether to acquire multiple intermediate full field ion beam images (warning: high dose)
fiducial: # Fiducial marker parameters
  reduced_area_resolution: '3072x2048'
  fiducial_length: 5e-7 # In meters. Fiducial cross stroke length.
  fiducial_width:  1e-7 # In meters. Fiducial cross stroke width.
  fiducial_image_size_x: 15e-7 # In meters. Field of view for fiducial in x.
  fiducial_image_size_y: 15e-7 # In meters. Field of view for fiducial in y.
  fiducial_milling_depth: 100e-9 # In meters. Milling depth of fiducial.
  fiducial_milling_current: 3e-10 # In Amperes. Milling current for fiducial marker.
  min_distance_from_lamella: 1e-7 # In meters. Buffer distance separating lamella from fiducial image.
lamella: # Lamella parameters
  lamella_width:  5e-7 # In meters. Width of lamella.
  lamella_height: 1e-7 # In meters. Thickness of lamella.
  total_cut_height: 5e-7 # In meters. Combined milling region above & below.
  milling_depth: 1e-6 # In meters. Default milling depth.
  milling_current: 3e-10 # In Amperes. Default milling current.
  # Protocol stages are milled in the order they appear here.
  # Stages may override the default parmeters above Eg: current, depth, etc.
  protocol_stages:
  # Rough cut, stage 1
  - percentage_roi_height: 0.5 # Milling size as fraction of total_cut_height.
    percentage_from_lamella_surface: 0.5 # Fraction from surface of lamella.
    milling_current: 3e-10 # In Amperes. Overrides the default current.
    milling_depth: 5e-7 # In meters. Overrides the default miling depth.
  # Regular cut, stage 2
  - percentage_roi_height: 0.3 # Milling size as fraction of total_cut_height.
    percentage_from_lamella_surface: 0.2 # Fraction from surface of lamella.
    milling_current: 3e-10 # In Amperes. Overrides the default current.
  # Polishing cut, stage 3
  - percentage_roi_height: 0.2 # Milling size as fraction of total_cut_height.
    percentage_from_lamella_surface: 0. # Fraction from surface of lamella.
    milling_current: 3e-10 # In Amperes. Overrides the default current.
    overtilt_degrees: 2 # offset to stage tilt (ignore sample pre-tilt)