!!ch.epfl.biop.lbw.Config
bigstitcher:
  channel_alignment:
    filter_min_r: 0.7
    pairwise_shifts_downsamples:
      x: 4
      y: 4
      z: 2
  fusion: fast
  fusion_config:
    downsampling: 1
    fuse_dir: fused
    fused_image: Save as (compressed) TIFF stacks
    fusion_method: SMOOTH AVERAGE
    fusion_type: bigstitcher
    preserve_original: null
    produce: Each timepoint & channel
  icp_refinement:
    downsampling: Downsampling 8/8/4
    icp_max_error: Normal Adjustment (<5px)
    icp_refinement_type: Simple (all together)
    interest: Average Threshold
  reader: fast
  reorientation:
    raw_orientation: IAL
    reorient_to_asr: true
  tile_alignment:
    filter_min_r: 0.7
    pairwise_shifts_downsamples:
      x: 4
      y: 4
      z: 2
    use_channel: 0
  xml_file: M:\analysis\Axel_Bisi\ImagedBrains\Axel_Bisi\AB133\AB133.xml
brainreg:
  conda_activate_path: C:\ProgramData\miniforge3\condabin\conda.bat
  conda_environement_name: brainreg
  docker_container_name: null
  parameters:
    affine_n_steps: 6
    affine_use_n_steps: 5
    atlas: allen_mouse_bluebrain_barrels_10um
    backend: niftyreg
    bending_energy_weight: 0.8
    brain_geometry: full
    debug: true
    freeform_n_steps: 6
    freeform_use_n_steps: 4
    grid_spacing: -20
    histogram_n_bins_floating: 128
    histogram_n_bins_reference: 128
    n_free_cpus: 2
    pre_processing: default
    save_original_orientation: true
    smoothing_sigma_floating: -1.0
    smoothing_sigma_reference: -1.0
    sort_input_file: true
general:
  input_file: M:\analysis\Axel_Bisi\ImagedBrains\AB133\AB133.czi
  output_dir: M:\analysis\Axel_Bisi\ImagedBrains\Axel_Bisi\AB133
  save_dir: M:\analysis\Axel_Bisi\ImagedBrains
  user: Axel_Bisi
