Human Organ Atlas now online!

The Human Organ Atlas is now online, with data on studies using the new technique Hierarchical Phase-Contrast Tomography (HIP-CT), an X-ray tomography technology, for imaging whole human bodies at multiple anatomical levels, from organs to cells.

Histology using optical and electron microscopy images cells and other structures with sub-micron accuracy but only on small biopsies of tissue from an organ, while clinical CT and MRI scans can image whole organs, but with a resolution only down to just below a millimetre. HiP-CT bridges these scales in 3D, imaging intact organs with ca. 20 micron voxels, and locally down to microns.

It is expected that the open access Atlas, enabled by the ESRF-EBS (Extremely Brilliant Source) will act as a reference to provide new insights into our biological makeup in health and disease.

The portal frontend is based on the PaNOSC search portal and API

Nature article’s abstract

Imaging intact human organs from the organ to the cellular scale in three dimensions is a goal of biomedical imaging. To meet this challenge, we developed hierarchical phase-contrast tomography (HiP-CT), an X-ray phase propagation technique using the European Synchrotron Radiation Facility (ESRF)’s Extremely Brilliant Source (EBS). The spatial coherence of the ESRF-EBS combined with our beamline equipment, sample preparation and scanning developments enabled us to perform non-destructive, three-dimensional (3D) scans with hierarchically increasing resolution at any location in whole human organs. We applied HiP-CT to image five intact human organ types: brain, lung, heart, kidney and spleen. HiP-CT provided a structural overview of each whole organ followed by multiple higher-resolution volumes of interest, capturing organotypic functional units and certain individual specialized cells within intact human organs. We demonstrate the potential applications of HiP-CT through quantification and morphometry of glomeruli in an intact human kidney and identification of regional changes in the tissue architecture in a lung from a deceased donor with coronavirus disease 2019 (COVID-19).


Walsh, C.L., Tafforeau, P., Wagner, W.L. et al. Imaging intact human organs with local resolution of cellular structures using hierarchical phase-contrast tomography. Nat Methods (2021).

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