mibi-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\/hardware\.json
    required: True
    description: JSON file containing the machine parameters/settings. This is akin to the microscope_environment.json file that's used to describe the imaging equipment.
  -  
    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\/[^\/]+\.ome\.tiff
    required: True
    description: Raw image file.
  -
    pattern: raw\/images\/tiles\.csv
    required: False
    description: This file contains the approximate coordinates for each of the tiled raw images.
  -
    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\/[^\/]+\.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 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>