name: 'src_CX_19-002_spleen_CC2-A'
date: '2018-01-01 00:00:00'
environment:
  path_formats: "get_default_path_formats('cyc{cycle:03d}_reg001/{region:d}_{tile:05d}_Z{z:03d}_CH{channel:d}.tif')"
acquisition:
  per_cycle_channel_names: [CH1, CH2, CH3, CH4]
  channel_names:
  #'get_default_path_formats("Cyc{cycle:d}_reg{region:d}/{region:d}_{tile:05d}_Z{z:03d}_CH{channel:d}.tif")'
    - DAPI-001
    - BLANK
    - BLANK
    - BLANK
    - DAPI-002
    - CD31
    - CD8
    - CD45
    - DAPI-003
    - CD20
    - Ki67
    - CD3e
    - DAPI-004
    - Actin
    - Podoplanin
    - CD68
    - DAPI-005
    - PanCK
    - CD21
    - CD4
    - DAPI-006
    - EMPTY
    - CD45RO
    - CD11c
    - DAPI-007
    - EMPTY
    - E_CAD
    - CD107a
    - DAPI-008
    - EMPTY
    - CD44
    - HistoneH3
    - DAPI-009
    - BLANK
    - BLANK
    - BLANK

  # These are incorrect, since deconvolution isn't really necessary
  # but there have to be as many of them as there are filters
  emission_wavelengths: [358, 488, 550, 650]
  # Each tissue was imaged with a 40x oil immersion objective in a 7x9 tiled acquisition at 1386x1008 pixels per
  # tile and 188 nm/pixel resolution and 11 z-planes per tile (axial resolution 900 nm)
  axial_resolution: 1500.0
  lateral_resolution: 377.4671052631579
  magnification: 20
  num_cycles: 9
  # Paper says 11 z-planes were used but data contains 15 planes
  num_z_planes: 10
  numerical_aperture: 0.75
  objective_type: air
  region_names: [reg1]
  region_height: 7
  region_width: 7
  tile_height: 1007
  tile_width: 1344
  tile_overlap_x: 576
  tile_overlap_y: 432
  tiling_mode: snake
operator:
  - extract:
      name: segm
      channels:
        - proc_DAPI-001
        - proc_CD45
        - cyto_nucleus_boundary
        - cyto_cell_boundary
      z: all
  - montage: {name: segm, extract_name: segm}
  - extract:
      name: full_data
      channels:
        - proc_DAPI-001
        - proc_CD31
        - proc_CD8
        - proc_CD45
        - proc_Ki67
        - proc_CD3e
        - proc_Actin
        - proc_Podoplanin
        - proc_CD68
        - proc_PanCK
        - proc_CD21
        - proc_CD4
        - proc_CD45RO
        - proc_CD11c
        - proc_E_CAD
        - proc_CD107a
        - proc_HistoneH3
      z: all
  - montage: {name: full_data, extract_name: full_data}
analysis:
  - aggregate_cytometry_statistics: {mode: best_z_plane}
  # Uncomment to produce CP exports by default
  # - cellprofiler_quantification: {export_csv: true, export_db: true, export_db_objects_separately: true}
processor:
  args:
    gpus: [0]
    # Tiles are already assembled
    run_crop: false
    run_tile_generator: true
    run_drift_comp: true
    run_cytometry: true
    run_best_focus: true
  best_focus: {channel: DAPI-001}
  drift_compensation: {channel: DAPI-001}
  # Note: Raw data is already deconvolved
  deconvolution: {n_iter: 25, scale_factor: .5}
  tile_generator: {raw_file_type: keyence_mixed}
  cytometry:
    # Downsample by half to get segmentation at 20x
    target_shape: [1024, 1344]
    nuclei_channel_name: DAPI-001
    segmentation_params: {memb_min_dist: 8, memb_sigma: 5, memb_gamma: .25, marker_dilation: 3}
    quantification_params: {nucleus_intensity: true, cell_graph: true}