experiment.yaml

name: 'Cellular Marker (Small)'
date: '2019-01-01 00:00:00'
environment:
  path_formats: keyence_multi_cycle_v01
acquisition:
  per_cycle_channel_names: [DAPI, FITC]
  channel_names: [DAPI1, MEMB, DAPI2, CELL]
  emission_wavelengths: [425, 525]
  axial_resolution: 1000.0
  lateral_resolution: 377.442
  magnification: 20
  num_cycles: 2
  num_z_planes: 3
  numerical_aperture: 0.75
  objective_type: air
  region_names: [Region1]
  region_height: 1
  region_width: 1
  tile_height: 128
  tile_overlap_x: 0
  tile_overlap_y: 0
  tile_width: 128
  tiling_mode: snake
operator:
  - extract:
      name: best_z_segm
      channels:
        - proc_DAPI1
        - proc_MEMB
        - proc_DAPI2
        - proc_CELL
        - cyto_cell_boundary
        - cyto_nucleus_boundary
        - cyto_cell_mask
        - cyto_nucleus_mask
  - montage: {name: best_z_segm, extract_name: best_z_segm}
analysis:
  - aggregate_cytometry_statistics: {mode: best_z_plane}
processor:
  args:
    gpus: [0,1]
    run_deconvolution: true
    run_cytometry: true
    run_best_focus: true
    run_drift_comp: true
  tile_generator: {raw_file_type: keyence_mixed}
  drift_compensation: {channel: DAPI1}
  best_focus: {channel: DAPI1}
  deconvolution: {n_iter: 10, scale_factor: 0.5}
  cytometry:
    nuclei_channel_name: DAPI1
    membrane_channel_name: MEMB
    segmentation_params:
      memb_sigma: 1
      memb_hole_size: 48
      memb_min_dist: 3
      memb_max_dist: null
      memb_propagation_regularization: .25
    quantification_params: {nucleus_intensity: true, cell_graph: true, morphology_features: true}