protocol_chlanda.yml

system:
  ip_address: '192.168.0.1' # 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: 84e-6 # In meters. Horizontal field of view
  dwell_time: 100e-9  # In seconds. Dwell time of ion beam for imaging.
  resolution: '1536x1024' # Must be one of the set resolutions available.
  autocontrast: true # 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: 10e-6  # In meters. Fiducial cross stroke length.
  fiducial_width: 150e-9  # In meters. Fiducial cross stroke width.
  fiducial_image_size_x: 15e-6  # In meters. Field of view for fiducial in x.
  fiducial_image_size_y: 15e-6  # In meters. Field of view for fiducial in y.
  fiducial_milling_depth: 500e-9 # In meters. Milling depth of fiducial.
  fiducial_milling_current: 1000e-12 # In Amperes. Milling current for fiducial marker.
  min_distance_from_lamella: 300e-12 # In meters. Buffer distance separating lamella from fiducial image.
lamella: # Lamella parameters
  lamella_width: 23e-6  # In meters. Width of lamella + microexpansion joints
  lamella_height: 150e-9  # In meters. Thickness of lamella.
  total_cut_height: 5.5e-6    # In meters. Combined milling region above & below.
  milling_depth: 0.8e-6 # In meters. Default milling depth.
  milling_current: 1000e-12    # In Amperes. Default milling current.
  patterning_mode: 'Parallel'
  # 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: 0.753
      percentage_from_lamella_surface: 0.447
      percentage_roi_height_lower: 1.053
      lamella_width: 15e-6
      milling_current: 1000e-12
      milling_depth: 1.2e-6
      microexpansion_width: 1.0e-6
      microexpansion_distance_from_lamella: 3e-6
      microexpansion_percentage_height: 0.6
    # Regular cut, stage 2
    - percentage_roi_height: 0.276
      percentage_from_lamella_surface: 0.217
      lamella_width: 14e-6
      milling_current: 500e-12
    # Regular cut, stage 3
    - percentage_roi_height: 0.166
      percentage_from_lamella_surface: 0.097
      lamella_width: 13e-6
      milling_current: 300e-12
    # Regular cut, stage 4
    # - percentage_roi_height: 0.083
    #   percentage_from_lamella_surface: 0.032
    #   lamella_width:  12e-6
    #   milling_current: 50e-12
    # Polishing cut, stage 5
    # - percentage_roi_height: 0.055
    #   percentage_from_lamella_surface: 0.00
    #   milling_current: 30e-12
    #   milling_depth: 0.5e-6 # approx. 6 minutes
    #   patterning_mode: 'Serial'
    #   lamella_width_upper:  10.75e-6
    #   lamella_width_lower:  11.25e-6