Computed Tomography (CT)#

While the OME community comes from the bioimaging and microscopy world, the OME-NGFF specification is also applicable to other imaging modalities. There are several kinds of tomography that can benefit from the OME-NGFF specification, including x-ray computed tomography (CT-scan).

The value of the specification includes the metadata for mapping voxels to physical space, and the ability to store large datasets in a chunked and compressed format, with multiscale support, that is suitable for cloud storage and analysis.

Example#

Datasets#

  • The Human Organ Atlas - Human organs scanned with Hierarchical Phase-Contrast Tomography (HiP-CT) made available in the OME-Zarr format (paper).

  • Herculaneum Scrolls - Scrolls carbonized by Mount Vesuvius eruptions imaged via X-ray micro-CT, made available in OME-Zarr format. (data, source). Multimillion-dollar awards for teams that “unroll” the scrolls – all starting with processing OME-Zarr data.

  • Open SciVis - A collection of volumetric datasets in OME-Zarr format, including several CT scans. (source)

  • VoDaSuRe - A large-scale dataset covering volumetric super-resolution data with micro-CT (arXiv; dataset)

Tools#

Tools that work on 3D volumetric data (like CT-scans) are sometimes developed for 3D microscopy, but natively work for visualizing other 3D data, such as tomography images:

  • VolE - Allen Institute for Cell Science’s viewer for large-scale volumetric datasets, with native support for OME-Zarr.

  • WebKnossos - A web-based platform for visualizing, annotating, and sharing large-scale volumetric datasets.

  • Neuroglancer - Google’s WebGL-based viewer for volumetric data, with first class support for OME-Zarr.