Year: 2026
Type: preprint
Abstract: Objectives Hierarchical Phase-Contrast Tomography (HiP-CT) enables non-destructive, multi-scale imaging of whole human organs. We describe how HiP-CT is utilized for biomedical research within the Human Organ Atlas Hub through three case studies: mapping the enteric nervous system (ENS) of the human colon, analysing myocardial and AV conduction architecture in Tetralogy of Fallot (TOF), and characterizing ductal organization in breast carcinoma. The challenges we faced with this novel biomedical data are discussed. Methods Whole-organ and region-of-interest scans of three types of human organs were acquired at the European Synchrotron Radiation Facility (ESRF) with isotropic voxel sizes ranging from 20 µm to 0.8 µm. For the colon, voxel binning and RootPainter were employed to tackle data size to segment the ENS. For the heart, voxel-wise myocyte orientation mapping was calculated in terabyte-scale datasets with a high-performance computational framework (Cardiotensor). Breast carcinoma samples were correlated with histopathology for structure validation. Results HiP-CT revealed the large-scale organization of the ENS in the colon, enabling visualisation of the 3D structures of the ENS across the colon In TOF hearts, analysis uncovered abnormal myocardial structure and heterogeneous conduction system morphology. In breast carcinoma, HiP-CT resolved the full hierarchy of ductal structures and vascular relationships within tumour and peritumoral regions. Conclusions HiP-CT provides unprecedented, hierarchical insight into intact human organ structure, bridging the gap between histology and radiology. Advances in knowledge HiP-CT establishes a new ex vivo radiological modality capable of linking microscale pathology to whole-organ context, advancing translational research in neurogastroenterology, cardiology, and oncology
Authors: Daniel Docter, Joseph Brunet, Vaishnavi Sabarigirivasan, Giel Lemmens, Birger Tielemans, Jon Sporring, Hector Dejea, Theresa Urban, Joanna Purzycka, Ramon Gorter, Judith Huirne, Veerle Michels, Jermo Hanemaaijer-van der Veer, Alexandre Bellier, David Stansby, Maximilian Ackermann, Roman Buelow, Danny Jonigk, Joseph Jacob, Jaco Hagoort, Stijn Verleden, Andrew C. Cook, Claire L. Walsh, Paul Tafforeau, Peter D. Lee, Bernadette S. de Bakker
Institutions: Amsterdam UMC Location University of Amsterdam, Emma Kinderziekenhuis, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam Reproduction Development, European Synchrotron Radiation Facility, University College London, Universitätsklinikum Aachen, KU Leuven, University of Copenhagen, Inserm, Université Grenoble Alpes, Helios Universitätsklinikum Wuppertal, German Center for Lung Research, Amsterdam University Medical Centers, University of Amsterdam, University of Antwerp
Subfield: Radiation
Field: Physics and Astronomy
Domain: Physical Sciences
Open Access status: green
OpenAlex ID: W7124692283