af-v0.yaml

files:
  # A dataset consists of a single autofluorescence 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 autofluorescence microscopy'
  -
    pattern: '(processedMicroscopy|processed_microscopy)/[^/]+_transformations/[^/]+\.txt'
    description: 'Transformations to IMS (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 Zeiss
  # which is the only type that we are currently receiving.
  -
    pattern: '(rawMicroscopy|raw_microscopy)/[^/]+\.czi'
    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]