Overview

This page describes the assays and data levels for the HTAN imaging data model.

Description of Standard

The HTAN imaging data model captures attributes from all HTAN experiments for which imaging data is generated, including:

  • H&E
  • t-CyCif
  • MxIF
  • Clinical and Multiplex IHC
  • SABER
  • IMC
  • MIBI
  • CODEX
  • GeoMx-DSP
  • MERFISH
  • Metadata Levels

The HTAN data model currently supports Level 2 image data:

Level Number DefinitionAllowed file types
2Pre-processed image data OME-TIFF*

* OME-TIFF files are required to contain image pyramids (unless the full image is relatively small, or a pyramid representation is not appropriate, for example for a segmentation mask), conforming to BioFormats 6.0.0 (or later), with compression strongly suggested.

Metadata elements have been collected from the OME-XML metadata standard, as well as the extension proposed by the 4D Nucleosome Imaging Standards Working Group, which divides fluorescence microscopy data provenance metadata into categories:

  • biospecimen preparation — eg fixation, staining, and mounting conditions
  • experimental — eg tissue culture conditions, number of conditions and/or replicates
  • image acquisition — eg microscope specification, imaging settings
  • image data structure — eg number of focal planes, targets (aka channels), and/or time points, dimensions (including order), resolution/pixel size
  • data analysis — ie details regarding algorithms (including versions and parameters) used for any processing steps used to generate an image file
Data Schema:
Attribute
Label
Description
Imaging
Imaging
TBD
Imaging Level 2
ImagingLevel2
Raw and pre-processed image data