lightsheet-v0.0.yaml

files:
  # Level0/
  -
    pattern: 'Level0/Channel[^/]+/[^/]+\.csv'
    description: 'Contains metadata and channel info.'
    required: True
    is_qa_qc: True
  -
    pattern: 'Level0/Channel[^/]+/[^/]+\.czi'
    description: 'Zeiss raw image file. File is optional.'
    required: False
    is_qa_qc: False
  -
    pattern: 'Level0/Channel[^/]+/[^/]+\.ome.tiff'
    description: 'Raw image file.'
    required: True
    is_qa_qc: False

  # Level1/
  -
    pattern: 'Level1/Channel[^/]+/[^/]+\.tif'
    description: 'Stitched image. File is optional.'
    required: False
    is_qa_qc: False
  -
    pattern: 'Level1/Channel[^/]+/[^/]+\.mp4'
    description: 'Stitched image. File is optional.'
    required: False
    is_qa_qc: False

  # Level2/
  -
    pattern: 'Level2/Channel[^/]+/[^/]+\.csv'
    description: 'Contains file, parent and bounds. Required when level 2 is populated. File is optional.'
    required: False
    is_qa_qc: True
  -
    pattern: 'Level2/Channel[^/]+/[^/]+\.obj'
    description: 'Segmentation mask. File is optional.'
    required: False
    is_qa_qc: False
  -
    pattern: 'Level2/Channel[^/]+/[^/]+\.stl'
    description: 'Segmentation mask. File is optional.'
    required: False
    is_qa_qc: False
  -
    pattern: 'Level2/Channel[^/]+/[^/]+\.ome.tiff'
    description: 'Segmentation mask. File is optional.'
    required: False
    is_qa_qc: False

  # Level3/
  -
    pattern: 'Level3/Channel[^/]+/[^/]+\.csv'
    description: 'Contains file, parent and bounds. Required when level 3 is populated. File is optional.'
    required: False
    is_qa_qc: True
  -
    pattern: 'Level3/Channel[^/]+/[^/]+\.obj'
    description: 'Annotation file. File is optional.'
    required: False
    is_qa_qc: False
  -
    pattern: 'Level3/Channel[^/]+/[^/]+\.stl'
    description: 'Annotation file. File is optional.'
    required: False
    is_qa_qc: False
  -
    pattern: 'Level3/Channel[^/]+/[^/]+\.ome.tiff'
    description: 'Annotation file. File is optional.'
    required: False
    is_qa_qc: False
  -
    pattern: extras\/.*
    required: False
    description: Folder for general lab-specific files related to the dataset. [Exists in all assays]