Imaging Mass Spectrometry (IMS)


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:

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 2.0 (use this one)
pattern required? description
extras\/.* βœ“ Folder for general lab-specific files related to the dataset.
extras\/mass-spec_environment\.(?:json|tsv) Β  JSON or TSV file containing the machine parameters/settings. This is akin to the microscope_environment.json file that’s used to describe the imaging equipment.
raw\/.* βœ“ Raw data files for the experiment.
raw\/imzML\/.* βœ“ Raw mass spec data.
raw\/imzML\/[^\/]+\.ibd βœ“ Mass spec data saved in a binary format.
raw\/imzML\/[^\/]+\.imzML βœ“ Mass spec metadata saved in XML format. Index to .ibd file.
lab_processed\/.* βœ“ Experiment files that were processed by the lab generating the data.
lab_processed\/images\/.* βœ“ Processed image files
lab_processed\/images\/[^\/]+\.ome\.tiff βœ“ 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.
lab_processed\/images\/[^\/]*ome-tiff\.channels\.csv βœ“ 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
lab_processed\/transformations\/.* Β  Directory containing image transformations.
lab_processed\/transformations\/[^\/]+\.txt Β  Transformations/map back to autofluorescence microscopy (related) data
lab_processed\/annotations\/.* βœ“ Directory containing annotations
lab_processed\/annotations\/[^\/]+_MolecularAssignments\.tsv βœ“ TSV file containing the m/z, molecular assignment, etc.