codex-v1.1.yaml

# A dataset consists of a single CODEX experimental run
files:
  -
    example: 'NAV.tif'
    pattern: '[^/]*NAV[^/]*\.tif'
    description: 'Navigational Image showing Region of Interest (Keyance Microscope only)'
    required: False
  -
    example: 'summary.pdf'
    pattern: '[^/]*\.pdf'
    description: 'PDF export of Powerpoint slide deck containing the Image Analysis Report'
    is_qa_qc: True
    required: False
  - 
    pattern: '(raw|processed)/config\.txt|(src_[^/]*|drv_[^/]*|extras)/[sS]egmentation\.json' 
    description: 'Sanity check that verifies the existence of at least one of these files. This is required for the HuBMAP processing pipeline' 
    required: False 
  -
    example: 'raw/reg_00.png'
    pattern: 'raw/reg_[^/]*\.png'
    description: 'Region overviews'
    required: False
  -
    pattern: '(raw|src_[^/]*)/[Ee]xperiment\.json'
    description: 'JSON file produced by the Akoya software which contains the metadata for the experiment, including the software version used, microscope parameters, channel names, pixel dimensions, etc. (required for HuBMAP pipeline)'
    required: False
  -
    example: 'raw/dataset.json'
    pattern: '(raw|src_[^/]*)/dataset\.json'
    description: 'Additional CODEX specific metadata file'
    required: True
  -
    pattern: 'processed/HandE\.tif'
    description: 'HandE image'
    required: False
  -
    pattern: 'processed/HandE_RGB\.tif'
    description: 'HandE RGB image'
    required: False
  -
    pattern: 'processed/HandE_RGB_thumbnail.jpg'
    description: 'HandE RGB thumbnail'
    required: False
  -
    pattern: '(raw|processed)/config\.txt'
    description: 'Configuration file with information needed for the HuBMAP processing pipeline'
    required: False
  -
    pattern: '(raw|src_.*)/[cC]yc.*_reg.*/.*_Z.*_CH.*\.tif'
    description: 'TIFF files produced by the experiment. General folder format: Cycle(n)_Region(n)_date; General file format: name_tileNumber(n)_zplaneNumber(n)_channelNumber(n)'
    required: True
  -
    pattern: 'src_.*/cyc.*_reg.*_.*/.*\.gci'
    description: 'Group Capture Information File (Keyance Microscope only)'
    required: False
  -
    pattern: '(raw|src_.*)/.*'
    description: 'Raw data directory.'
    required: True
  -
    pattern: '(processed|drv_[^/]*)/.*'
    description: 'Processed files produced by the Akoya software or alternative software.'
    required: True
  -
    pattern: 'extras/dir-schema-v1-with-dataset-json'
    description: 'Empty file whose presence indicates the version of the directory schema in use'
  -
    pattern: extras\/.*
    required: False
    description: Folder for general lab-specific files related to the dataset. [Exists in all assays]