codex-v2.0.yaml

files:
  -
    pattern: extras\/.*
    required: True
    description: Folder for general lab-specific files related to the dataset. [Exists in all assays]
  -
    pattern: extras\/microscope_hardware\.json
    required: True
    description: A file generated by the micro-meta app that contains a description of the hardware components of the microscope. Email HuBMAP Consortium Help Desk <help@hubmapconsortium.org> if help is required in generating this document.
    is_qa_qc: True
  -
    pattern: extras\/microscope_settings\.json
    required: False
    description: A file generated by the micro-meta app that contains a description of the settings that were used to acquire the image data. Email HuBMAP Consortium Help Desk <help@hubmapconsortium.org> if help is required in generating this document.
    is_qa_qc: True
  -  
    pattern: raw\/.*
    required: True
    description: This is a directory containing raw data.
  -
    pattern: lab_processed\/images\/[^\/]+\.ome\.tiff
    required: True
    description: OME-TIFF file (multichannel, multi-layered) produced by the experiment. If compressed, must use loss-less compression algorithm. See the following link for the set of fields that are required in the OME TIFF file XML header. <https://docs.google.com/spreadsheets/d/1YnmdTAA0Z9MKN3OjR3Sca8pz-LNQll91wdQoRPSP6Q4/edit#gid=0>
    is_qa_qc: False
  -
    pattern: lab_processed\/images\/[^\/]*ome-tiff\.channels\.csv
    required: True
    description: This file should describe any processing that was done to generate the images in each channel of the accompanying OME TIFF. The file should contain one row per OME TIFF channel. Two columns should be booleans "is this a channel to use for nuclei segmentation"  and "is this a channel to use for cell segmentation".
  -
    pattern: '[^\/]*NAV[^\/]*\.tif'
    required: False
    description: Navigational Image showing Region of Interest (Keyance Microscope only)
    is_qa_qc: False
    example: NAV.tif
  -
    pattern: '[^\/]+\.pdf'
    required: False
    description: PDF export of Powerpoint slide deck containing the Image Analysis Report
    is_qa_qc: True
    example: summary.pdf
  -
    pattern: extras\/dir-schema-v2-with-dataset-json
    required: True
    description: Empty file whose presence indicates the version of the directory schema in use
    is_qa_qc: False
  -
    pattern: processed\/drv_[^\/]*\/
    required: True
    description: Processed files produced by the Akoya software or alternative software.
  -
    pattern: raw\/cyc[^\/]*_reg[^\/]*\/.*
    required: True
    description: Intermediary directory
  -
    pattern: raw\/src_[^\/]*\/
    required: True
    description: Intermediary directory
  -
    pattern: raw\/cyc[^\/]*_reg[^\/]*\/[^\/]*_z[^\/]*_CH[^\/]*\.tif
    required: True
    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)'
  -
    pattern: raw\/src_[^\/]*\/cyc[^\/]*_reg[^\/]*_[^\/]*\/[^\/]+\.gci
    required: False
    description: Group Capture Information File (Keyance Microscope only)
  -
    pattern: raw\/dataset\.json
    required: True
    description: Data processing parameters file. This will include additional CODEX specific metadata needed for the HIVE processing workflow. 
    example: raw/dataset.json
  -
    pattern: raw\/reg_[^\/]*\.png
    required: False
    description: Region overviews
    example: raw/reg_00.png
  -
    pattern: raw\/experiment\.json
    required: False
    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) 
    example: raw/experiment.json