cosmx-v2.0.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\/[^\/]*_exprMat_file\.csv
    required: True
    description: 'Cell expression matrix with raw counts of genes for each identified cell. Apart from the gene specific columns, additional columns include: the origin of the cell (fov, unique cell id); negative probes; probes associated with the fiducial frame (SystemControl)'
  -
    pattern: raw\/[^\/]*_fov_positions_file\.csv
    required: True
    description: FOV Positions file that provides an overview of the tissue locations and to help specify separate regions and/or tissues on the slide. This contains information about the Slide - slide number it comes from; FOV - field of view; X_mm/Y_mm - x/y coordinates of FOV positions in mm (previously in px)
  -
    pattern: raw\/[^\/]*_metadata_file\.csv
    required: True
    description: Cell metadata file containing the following information - the origin of the cell (fov, unique cell id); physical properties of the cell (area, aspect ratio, width, height); location of the cell centroid within each FOV (center X/Y local) and global position (center X/Y global); information about the protein staining (min/max intensity); type of protein, which may be specific to each experiment but generally includes DAPI, Membrane, PanCK, CD45; other (e.g. Seurat information if that pipeline was used within AtoMx, some data quality information)
  -
    pattern: raw\/[^\/]*_tx_file\.csv
    required: True
    description: Cell transcript file
  -
    pattern: raw\/[^\/]*_config\.ini
    required: True
    description: Needed to generate the DCC file from the fastq file. Contains pipeline processing parameters.  Generated by DSP run, prior to sequencing.
  -
    pattern: raw\/markers\.csv
    required: True
    description: A csv file describing any morphology markers used to guide ROI and/or AOI selection.
  -
    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. The expected format is: gene_id (ensembl ID), gene_name.'
  -
    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\/transcript_locations\.csv
    required: True
    description: 'The origin of the coordinate is 0,0 at the top left corner of the image. The file should include: gene name, x, y, z (optional), quality score (optional). It is expected that the first row in the file contains the column header.'
  -
    pattern: raw\/custom_gene_list\.csv
    required: False
    description: 'This describes the target genes profiled by the assay. For advanced design, this can be probes sequences for splicing or other analysis for any target of interest. The format should minimally contain: gene name, ensemble ID'
  -
    pattern: raw\/probes\.csv
    required: False
    description: A CSV file describing the probe panel used. This is typically what's used to specifiy the probe set when ordering a probe panel for a Xenium run.
  -
    pattern: raw\/images\/overlay\.(?:jpeg|tiff)
    required: False
    description: State whether an overlay image was used to guide ROI selection. If an overlay is used, then the overlay details will be provided in the protocols.io protocol. If used, this needs to be uploaded. It is not included in the OME TIFF. This can be a JPEG or TIFF file
  -
    pattern: raw\/images\/preview_scan\.png
    required: True
    description: Assists in selection of regions of FOVs using the grid FOV placement tool.
  -
    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. 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