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 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\/.*	✓	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\/[^\/]+\.czi$	✓	Raw image file in CZI format
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\.(?:tif|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 It is recommended that you confirm you’re using the latest version of Bio-Formats, when generating the OME TIFF, as newer versions have improved XML handling.
lab_processed\/images\/region_[^\/]+\/[^\/]*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\/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).