The HTAN data model for imaging data is based upon the Minimum Information about Tissue Imaging (MITI) reporting guidelines. These comprise minimal metadata for highly multiplexed tissue images and were developed in consultation with methods developers, experts in imaging metadata (e.g., DICOM and OME) and multiple large-scale atlasing projects; they are guided by existing standards and accommodate most multiplexed imaging technologies and both centralized and distributed data storage.
For further information on the MITI guidelines, please see the MITI website, specification on Github, and Nature Methods publication.
The HTAN data model for imaging was intended primarily for multiplexed imaging, such as CODEX, CyCIF, and IMC, in addition to brightfield imaging of H&E stained tissues.
As with sequencing data, the imaging data model is split into data levels as follows:
| Level | Description |
|---|---|
| 1 | Raw imaging data requiring tiling, stitching, illumination correction, registration or other pre-processing. |
| 2 | Imaging data compiled into a single file format, preferably a tiled and pyramidal OME-TIFF. Accompanied by a csv file containing channel metadata. |
| 3 | Segmentation mask, Validated channel metadata, QC checked image. |
| 4 | An object-by-feature table (typically cell-by-marker) generated from the segmentation mask and image. |
WARNING: Manifests provided on this page are for reference only. DO NOT USE THESE MANIFESTS FOR DATA SUBMISSION.
The interactive tables below are provided to help users understand the HTAN Data Model. The tables allow a user to view, search or download attributes either:
To view a specific manifest, click on the link in the Manifests tab. The manifest will appear in a new tab on the page. Navigate to the new tab to search for attributes or download the manifest.
To search for attributes among all manifests, navigate to the All Attributes tab and use the search box provided at the top of the tab. All attributes can also be downloaded as a csv file.