thick-section-multiphoton-mxif-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: Raw data files for the experiment. 
  -  
    pattern: raw\/channel_layout\.tsv
    required: True
    description: Table that includes a dictionary for channel to moiety, which may be a protein given in an OMAP panel or captured in the ASCT+B table. 
    is_qa_qc: False
  -  
    pattern: raw\/lightpath_configuration\.tsv
    required: False
    description: This file documents the light path setttings not captured in the OME-TIFF - will be deprecated upon the implementation of MicroMeta.
  -  
    pattern: raw\/fingerprint_layout\.tsv
    required: False
    description: Table that includes a dictionary for channel to moiety which is determined from spectral clustering and may include lipids, protein, etc. This file is specific to hyper-spectral imaging.
    is_qa_qc: False
  -
    pattern: raw\/images\/.*
    required: True
    description: Raw image files. Using this subdirectory allows for harmonization with other imaging assays. [This directory must include at least one raw file.]
  -
    pattern: raw\/images\/[^\/]+\.(?:xml|nd2|oir|lif|czi|tiff)
    required: True
    description: Raw microscope file for the experiment
    is_qa_qc: False
  -
    pattern: lab_processed\/.*
    required: True
    description: Experiment files that were processed by the lab generating the data.
  -
    pattern: lab_processed\/images\/.*
    required: True
    description: Processed image files
  -
    pattern: lab_processed\/images\/[^\/]+\.ome\.tiff
    required: True
    description: OME-TIFF files (multichannel, multi-layered) produced by the microscopy 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
    example: lab_processed/images/HBM892.MDXS.293.ome.tiff
  -
    pattern: lab_processed\/images\/[^\/]*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>
    is_qa_qc: False
  -
    pattern: lab_processed\/transformations\/.*
    required: False
    description: This directory contains transformation matrices that capture how each modality is aligned with the other and can be used to visualize overlays of multimodal data. This is needed to overlay images from the exact same tissue section (e.g., MALDI imaging mass spec, autofluorescence microscopy, MxIF, histological stains). In these cases data type may have different pixel sizes and slightly different orientations (i.e., one may be rotated relative to another).
  -
    pattern: lab_processed\/transformations\/[^\/]+\.txt
    required: False
    description: Transformation matrices used to overlay images from the exact same tissue section (e.g., MALDI imaging mass spec, autofluorescence microscopy, MxIF, histological stains).   
    is_qa_qc: False
  -
    pattern: qa_qc\/.*
    required: True
    description: Directory containing QA and/or QC information.
  -
    pattern: qa_qc\/resolution_report\/.*
    required: True
    description: Directory containing the results of resolution tests and/or vendor preventative maintenance reports.
  -
    pattern: qa_qc\/resolution_report\/resolution\.txt
    required: False
    description: This file summarizes the results of resolution tests or vendor reports from preventative maintenance visits.
  -
    pattern: qa_qc\/resolution_report\/[^\/]+\.pdf
    required: False
    description: This file is a pdf from a vendor preventative maintenance visit or resolution check tool demonstrating resolution. This file may include illumination test results.
  -
    pattern: qa_qc\/illumination_report\/.*
    required: True
    description: Directory containing the results of illumination tests and/or vendor preventative maintenance reports.
  -
    pattern: qa_qc\/illumination_report\/illumination.txt
    required: False
    description: This file summarizes the results of illumination tests or vendor reports from preventative maintenance visits.
  -
    pattern: qa_qc\/illumination_report\/[^\/]+\.pdf
    required: False
    description: This file is a pdf from a vendor preventative maintenance visit or illumination check tool demonstrating illumination intensity.