haadf_projection_export:
  source: "50-frame HAADF series in each Velox EMD"
  source_shape_per_tilt: [400, 300, 50]
  source_dtype: uint16
  output: derived/haadf/HAADF_stack.tif
  frame_selection: UNKNOWN
  rejected_frames: UNKNOWN
  combination: UNKNOWN
  drift_correction: UNKNOWN
  normalization: UNKNOWN
  crop: UNKNOWN
  binning: UNKNOWN

haadf_alignment:
  input: derived/haadf/HAADF_stack.tif
  output: derived/haadf/HAADF_aligned.tiff
  parameters: derived/haadf/alignment/ali_haadf.json
  reference_angle_deg: 0
  parameter_count: 16
  parameter_shape: [16, 2]
  parameter_units: pixels
  parameter_meaning: "translation used to align each HAADF projection to the 0-degree acquisition"
  zero_degree_entry: [0, 0]
  component_order: UNKNOWN
  sign_convention: UNKNOWN
  interpolation: UNKNOWN
  boundary_handling: UNKNOWN

eds_map_extraction:
  source: "50-frame EDS spectrum stream in each Velox EMD"
  detector: "Super-X, four SDDs"
  map_mode: NetIntensity
  lines:
    Ge: "Kα"
    Te: "Lα"
    Sb: "Lα"
    Ti: "Kα"
  embedded_additional_elements: [N, O, Si]
  rendered_map_filter:
    enabled: true
    type: Mean
    kernel_size: 3
  spectral_filter:
    enabled: false
    type: Gaussian
  absorption_correction:
    enabled: false

publication_elemental_alignment:
  software: Fiji
  plugin: MultiStackReg
  transform: translation-only
  reference_channel_for_transform_estimation: Ge
  applied_to_channels: [Ge, Te, Sb, Ti]
  later_output_shape: [176, 112]
  binning_factor: 2
  normalization: "independent maximum normalization per channel"
  note: "The distributed 400x300 TIFFs precede this later reconstruction preprocessing."