parameters_axel.yml

general:
  user: Axel_Bisi
  save_dir: M:\analysis\Axel_Bisi\ImagedBrains
bigstitcher:
    xml_file: 
    reader: fast
    fusion: fast
    channel_alignment:
      pairwise_shifts_downsamples:
        x: 4
        y: 4
        z: 2
      filter_min_r: 0.7
    tile_alignment:
      use_channel: 0
      pairwise_shifts_downsamples:
        x: 4
        y: 4
        z: 2
      filter_min_r: 0.7
    icp_refinement:
      icp_refinement_type: Simple (all together)
      downsampling: Downsampling 8/8/4
      interest: Average Threshold
      icp_max_error: Normal Adjustment (<5px)
    reorientation:
      raw_orientation: IAL
      reorient_to_asr: true # Choose false if you do not want to reorient your sample
    fusion:
      fusion_type: bigstitcher
      downsampling: 1
      preserve_original: #preserve_original # Or select nothing, especially if you reorient your sample
      produce: Each timepoint & channel
      fused_image: Save as (compressed) TIFF stacks
      fusion_method: "SMOOTH AVERAGE"
      fuse_dir: fused
brainreg:
    docker_container_name:
    conda_environement_name: brainreg
    conda_activate_path: C:\ProgramData\miniforge3\condabin\conda.bat
    parameters:
        atlas: allen_mouse_bluebrain_barrels_10um
        backend: niftyreg
        affine-n-steps: 6
        affine-use-n-steps: 5
        freeform-n-steps: 6
        freeform-use-n-steps: 4
        bending-energy-weight: 0.8
        grid-spacing: -8
        smoothing-sigma-reference: -1.0
        smoothing-sigma-floating: -1.0
        histogram-n-bins-floating: 128
        histogram-n-bins-reference: 128
        n-free-cpus: 2
        debug: true
        save-original-orientation: true
        brain_geometry: full
        sort-input-file: true
        pre-processing: default