stained-v1.0.yaml

files:
  #   A dataset consists of a stained microscopy run, and
  #   a set of transformation files that are useful for other
  #   related datasets. (Vanderbilt)
  -
    pattern: '(processedMicroscopy|processed_microscopy)/[^/]+_images/[^/]+ome\.(tif|tiff)'
    description: 'OME TIFF files (multichannel, multi-layered, image pyramids) produced by the PAS microscopy experiment'
  -
    pattern: '(processedMicroscopy|processed_microscopy)/[^/]+_transformations/[^/]+\.txt'
    description: 'Transformations to PAS (related) data'
    required: False
  -
    pattern: '(rawMicroscopy|raw_microscopy)/[^/]+\.xml'
    description: 'XML metadata file from the autofluorescence microscopy experiments'

  # Note: extension might change depending on the microscope used. This is just for
  # Leica .scn which is a container with tiled scan images (bigtiff)
  # which is the only type that we are currently receiving.
  -
    pattern: '(rawMicroscopy|raw_microscopy)/[^/]+\.(scn|czi|tif|tiff)'
    description: 'Raw microscope file for the experiment'
  -
    pattern: extras\/.*
    required: False
    description: Folder for general lab-specific files related to the dataset. [Exists in all assays]