celldive-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: raw\/images\/.*
    required: True
    description: Raw image files. Using this subdirectory allows for harmonization with other more complex assays, like Visium that includes both raw imaging and sequencing data.
  -
    pattern: raw\/images\/round_info_[^\/]+\.dat
    required: True
    description: Metadata file for the capture item-value tab separated format. This contains various instrument and acquisition details for each acquisition cycle.
    is_qa_qc: False
    example: raw/images/round_info_002.dat
  -
    pattern: lab_processed\/.*
    required: True
    description: Experiment files that were processed by the lab generating the data.
  -
    pattern: lab_processed\/images\/.*
    required: True
    description: This is a directory containing processed image files
  -
    pattern: lab_processed\/images\/region_[^\/]+\/[^\/]+_region_[^\/]+\.ome\.(?:tif|tiff)
    required: True
    description: OME TIFF Files for the corresponding region (e.g. region_001) by slide (e.g S20030077), organized into subdirectories based on their region.
    is_qa_qc: False
    example: lab_processed/images/region_001/S20030092_region_011.ome.tif
  -
    pattern: lab_processed\/images\/region_[^\/]+\/[^\/]*ome-tiff\.channels\.csv
    required: True
    description: This file provides essential documentation pertaining to each channel of the accommpanying OME TIFF. The file should contain one row per OME TIFF channel. The required fields are detailed <https://docs.google.com/spreadsheets/d/1xEJSb0xn5C5fB3k62pj1CyHNybpt4-YtvUs5SUMS44o/edit#gid=0>
  -
    pattern: lab_processed\/annotations\/.*
    required: True
    description: This is a directory containing annotations.
  -
    pattern: lab_processed\/annotations\/slide_list\.txt
    required: True
    description: Information about the slides used by the experiment- each line corresponds to a slide name (begins with S - e.g. S20030077) - used in filenames.
  -
    pattern: lab_processed\/virtual_histology\/.*
    required: True
    description: This is a directory containing annotations for virtual histology images
  -
    pattern: lab_processed\/virtual_histology\/HandE_RGB_thumbnail\.jpg
    required: True
    description: Virtual H&E RGB thumbnail
  -
    pattern: lab_processed\/virtual_histology\/HandE_RGB\.tif
    required: True
    description: Virtual H&E RGB image
  -
    pattern: lab_processed\/virtual_histology\/[^\/]+_VHE_region_[^\/]+\.tif
    required: True
    description: Virtual H&E image