Prepare your metadata based on the latest metadata schema using one of the template files below. See the instructions in the Metadata Validation Workflow document for more information on preparing and validating your metadata.tsv file prior to submission.

Related files:

• 📝 Excel template: For metadata entry.
• 📝 TSV template: Alternative for metadata entry.

Metadata schema

Version 0 (use this one)

Directory schemas

Version 2 (use this one)

pattern	required?	description
extras\/.*	✓	Folder for general lab-specific files related to the dataset.
extras\/microscope_hardware\.json$	✓	[QA/QC] 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.
extras\/microscope_settings\.json$		[QA/QC] 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.
raw\/.*	✓	All raw data files for the experiment.
lab_processed\/.*	✓	Experiment files that were processed by the lab generating the data.
lab_processed\/alignment\.json$	✓	JSON file for the manual tissue alignment created using Loupe browser and used as input to Space Ranger.
lab_processed\/images\/.*	✓	Processed image files
lab_processed\/images\/[^\/]+\.ome\.tiff$ (example: lab_processed/images/HBM892.MDXS.293.ome.tiff)	✓	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
lab_processed\/images\/[^\/]*ome-tiff\.channels\.csv$	✓	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
lab_processed\/dragen\/.*	✓	Output from the Illumina Spatial Transcriptome pipeline.
lab_processed\/dragen\/pipeline-manifest\.json$	✓	The pipeline execution parameter file
lab_processed\/dragen\/.*contour\.*\.csv$	✓	The coordinate matrices containing the machine-learning-derived cell or nuclei boundaries.
lab_processed\/dragen\/.*_cell_binned_normalized\.h5ad$	✓	Normalized Dragen AnnData object containing cell-binned spatial gene expression and cell metadata.
lab_processed\/dragen\/.*_cell_binned_pca\.h5ad$	✓	AnnData object containing cell-binned spatial gene expression, cell metadata and PCA embeddings.
lab_processed\/dragen\/.*_cell_binned_umap\.h5ad$	✓	AnnData object containing cell-binned spatial gene expression, cell metadata and PCA UMAP.
lab_processed\/dragen\/.*_cell_binned\.h5ad$	✓	AnnData object containing cell-binned spatial gene expression and cell metadata.
lab_processed\/dragen\/.*_grid_binned_normalized\.h5ad$	✓	Normalized AnnData object containing grid-binned spatial gene expression and cell metadata.
lab_processed\/dragen\/.*_grid_binned_pca\.h5ad$	✓	AnnData object containing grid-binned spatial gene expression, cell metadata and PCA embeddings.
lab_processed\/dragen\/.*_grid_binned_umap\.h5ad$	✓	AnnData object containing grid-binned spatial gene expression, cell metadata and PCA UMAP.
lab_processed\/dragen\/.*_grid_binned\.h5ad$	✓	AnnData object containing grid-binned spatial gene expression and cell metadata.