example_config.yaml

---
io:
  # where your hdf5 and layout file are
  input-directory: "/home/gerhard/test/yaml_r"
  # where you want the output from the script
  output-directory: "/home/gerhard/test/yaml_r/H5CP_output"
# select which modules to run
run:
  - extract-hdf5
  - tracking
# number of cpu cores to use    
cores: 16
# module configuration
modules:
  # extract information from hdf5 (block 1)
  extract-hdf5:
    show-results: TRUE
    input:
      hdf5:
        - "20160403_GB01_03_cp_output_hcc38.h5"
      layout: "20160401_GB01_03_layout.tsv"
    metadata:
      location-id:
        - "Image/Metadata_well_name"
      plate-id:
        - "20121120_hs"
      image-id:
        - "Image/Metadata_well_name"
      time-id:
        - "Image/Metadata_Time"
      replicate-id: []
      exposure-delay:
        - "00:00"
      time-between-frame:
        - "00:06:00"
      objects:
        parent-object: "obj_cell"
        # child-objects: use [] for no objects, otherwise use - on the next line (like in features)
        child-objects: []
        tertiary-object:
      # features: #do not define displacement and parent object, these are automatically included
      features:
        - "obj_cell/Intensity_MeanIntensity_raw_img_nuclei_cropped"
        - "obj_cell/TrackObjects_Displacement_30"
        - "obj_cell/TrackObjects_DistanceTraveled_30"
        - "obj_cell/TrackObjects_IntegratedDistance_30"
        - "obj_cell/TrackObjects_Linearity_30"
  # tracking module (block 4)
  tracking:
    reconnect-tracks: true
    reconnect-over-frames: 2
    max-pixel-reconnect:
      - 20
      - 20
      - 20
    min-tracked-frames: 20
    # Can be "disconnect_all" (recommended) or "min_distance"
    parent-resolve-strategy: "disconnect_all"
    write:
      unique-parents-no-rec: true
      before-combine-tracks: true
      after-first-connect: true
      after-second-connect: true
      after-third-connect: true
...