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.

This link lists the set of fields that are required in the OME TIFF file XML header. We require both the the raw image file as well as a lab-created image based on the raw one in the open source OME-TIFF format. Our processing pipeline uses the OME-TIFF image to generate an OME-TIFF pyramid for portal visualization. We recommend BioFormats for converting raw image files to OME-TIFF. A relevant guide for converting raw TIFF image files to OME-TIFF using BioFormats can be found here.

Metadata schema

Version 2 (use this one)

Directory schemas

Version 2.0 (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\/.*	✓	Raw data files for the experiment.
raw\/images\/.*	✓	Raw image files. Using this subdirectory allows for harmonization with other more complex assays, like Visium that includes both raw imaging and sequencing data. This directory should include at least one raw file.
raw\/images\/[^\/]+\.(?:xml|scn|vsi|ndpi|svs|czi|tiff|qptiff)	✓	Raw microscope file for the experiment
lab_processed\/.*	✓	Experiment files that were processed by the lab generating the data.
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. 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 here https://docs.google.com/spreadsheets/d/1xEJSb0xn5C5fB3k62pj1CyHNybpt4-YtvUs5SUMS44o/edit#gid=0
lab_processed\/images\/[^\/]+\.tissue-boundary\.geojson		[QA/QC] If the boundaries of the tissue have been identified (e.g., by manual efforts), then the boundary geometry can be included as a GeoJSON file named “*.tissue-boundary.geojson”.
lab_processed\/transformations\/.*		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).
lab_processed\/transformations\/[^\/]+\.txt		Transformation matrices used to overlay images from the exact same tissue section (e.g., MALDI imaging mass spec, autofluorescence microscopy, MxIF, histological stains).
lab_processed\/probabilities\/.*		Directory containing probabilities pertaining to lab processed data (e.g., from Ilastik pixel classification).
lab_processed\/probabilities\/[^\/]+\.tiff		[QA/QC] A TIFF file that contains pixel probabilities.