template.yaml

name: DatasetName

# Define an arbitrary number of layers
layers:
  SomeImages: # unique layer name
    type: image # 'image' for image data and for label data one of: 'semseg' | 'multilabel'
    path: some/path/to/data # directory
    file_type: .png # required extension incl. dot (e.g., .png | .nii.gz | .b2nd)
    pattern: # optional regex to filter files relative to 'path' without file_type
    backend: # optional backend to load/write the data (e.g., sitk | nib) for .nii.gz, etc.
    channels: 3 # number of channels, required for image
    file_stack: False # True if each channel is a separate file: *_0000, *_0001, ...

  SomeLabels:
    type: semseg # semseg --> Semantic Segmentation | multilabel --> Multilabel Segmentation
    path: some/path/to/data
    file_type: .png|.nii.gz|.b2nd|...
    pattern:
    backend:
    classes: 19 # number of classes, required for semseg/multilabel
    file_stack: False # for multilabel: true if each class is a separate file: *_0000, *_0001, ...
    ignore_bg: null # optional bool for labels; if true, class 0 is ignored in metrics and analysis
    ignore_index: 255 # optional int for labels; label value to ignore in loss/eval

# Splitting (optional)
splits:
  splits_file: some/path/splits_final.json # optional: use a file to define splits, content can be:
  # 1) per-split, per-layer: {"train": {"Images": [...], "Labels": [...]}, "val": {"Images": [...], "Labels": [...]}, "test": {...}}
  # 2) cross-validation per split: {"train": [{"Images": [...], "Labels": [...]}, {...}], "val": [{"Images": [...], "Labels": [...]}, {...}]}
  # IDs must be exact names relative to each layer path, without file_type extension (stacked: use stack root, e.g. "train_001")
  # Empty splits are allowed, e.g. "val": []
  # optional: Per-layer overrides for paths/patterns by split.
  train:
    SomeImages: # empty -> use defaults
    SomeLabels: # empty -> use defaults
  val:
    SomeImages:
      pattern: some_pattern # optional: example override for pattern parameter for layer and split
      path: some/path/to/data # optional: example override for path parameter for layer and split
    SomeLabels:
      pattern: some_pattern
      path: some/path/to/data
  test: # empty --> split is not defined