merfish-v2.1.yaml

files:
  -
    pattern: extras\/.*
    required: True
    description: Folder for general lab-specific files related to the dataset.
  -
    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: All raw data files for the experiment.
  -
    pattern: raw\/additional_panels_used\.csv
    required: False
    description: If multiple commercial probe panels were used, then the primary probe panel should be selected in the "oligo_probe_panel" metadata field. The additional panels must be included in this file. Each panel record should include:manufacturer, model/name, product code.
  -
    pattern: raw\/gene_panel\.csv
    required: True
    description: The list of target genes.
  -
    pattern: raw\/custom_probe_set\.csv
    required: False
    description: This file should contain any custom probes used and must be included if the metadata field "is_custom_probes_used" is "Yes". The file should minimally include:target gene id, probe seq, probe id. The contents of this file are modeled after the 10x Genomics probe set file (see <https://support.10xgenomics.com/spatial-gene-expression-ffpe/probe-sets/probe-set-file-descriptions/probe-set-file-descriptions#probe_set_csv_file>).
  -
    pattern: raw\/micron_to_mosaic_pixel_transform\.csv
    required: False
    description: Matrix used to transform from pixels to physical distance.
  -
    pattern: raw\/manifest\.json
    required: True
    description: This file contains stain by channel details and pixel details.
  -
    pattern: raw\/codebook\.csv
    required: True
    description: CSV containing codebook information for the experiment. Rows are barcodes and columns are imaging rounds. The first column is the barcode target, and the following column IDs are expected to be sequential, and round identifiers are expected to be integers (not roman numerals).
  -
    pattern: raw\/positions\.csv
    required: True
    description: File that includes the top left coordinate of each tiled image. This is required to stitch the images.
  -
    pattern: raw\/dataorganization\.csv
    required: True
    description: Necessary image definitions
  -
    pattern: raw\/data\/.*
    required: True
    description: All raw stack data files for the MERFISH experiment.
  -
    pattern: raw\/data\/[^\/]+\.dax
    required: True
    description: The raw image stack.
  -
    pattern: raw\/data\/[^\/]+\.inf
    required: True
    description: Information file with dax image format specifications. Variable expected for downstream processing with PIPEFISH are frame dimensions, number of frames, little/big endian, stage X and Y locations, lock target, scalemin, and scalemax.
  -
    pattern: raw\/images\/.*
    required: True
    description: Directory containing raw image files. This directory should include at least one raw file.
  -
    pattern: raw\/images\/[^\/]+\.tif
    required: True
    description: Raw microscope file for the experiment.
  -
    pattern: lab_processed\/.*
    required: True
    description: Experiment files that were processed by the lab generating the data.
  -
    pattern: lab_processed\/detected_transcripts\.csv
    required: True
    description: A file containing the locations of each RNA target.
  -
    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. For Visium this stitched file should only include the single capture area relevant to the current dataset. For GeoMx there will be one OME TIFF file per slide, with each slide including multiple AOIs. 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