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.

Metadata schema

Version 2 (use this one)

Directory schemas

Version 2.1 (use this one)

pattern	required?	description
extras\/.*	✓	Folder for general lab-specific files related to the dataset. [Exists in all assays]
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\/.*	✓	This is a directory containing raw data.
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.
raw\/images\/[^\/]+\.ome\.tiff		Raw image file.
raw\/images\/tiles\.csv		This file contains the approximate coordinates for each of the tiled raw images.
lab_processed\/.*	✓	Experiment files that were processed by the lab generating the data.
lab_processed\/images\/.*	✓	This is a directory containing processed image files
lab_processed\/images\/[^\/]+\.ome\.tiff	✓	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
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

Version 2.0

pattern	required?	description
extras\/.*	✓	Folder for general lab-specific files related to the dataset. [Exists in all assays]
extras\/hardware\.json	✓	JSON file containing the machine parameters/settings. This is akin to the microscope_environment.json file that’s used to describe the imaging equipment.
raw\/.*	✓	This is a directory containing raw data.
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.
raw\/images\/[^\/]+\.ome\.tiff	✓	Raw image file.
raw\/images\/tiles\.csv		This file contains the approximate coordinates for each of the tiled raw images.
lab_processed\/.*	✓	Experiment files that were processed by the lab generating the data.
lab_processed\/images\/.*	✓	This is a directory containing processed image files
lab_processed\/images\/[^\/]+\.ome\.tiff	✓	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
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