Hierarchical Phase-Contrast Tomography Imaging: Applicability in biomedical research
bioRxiv (Cold Spring Harbor Laboratory)
Abstract
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 26
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Daniël Docter corresponding
Amsterdam UMC Location University of Amsterdam · Emma Kinderziekenhuis · Amsterdam Gastroenterology Endocrinology Metabolism · Amsterdam Reproduction Development
Affiliation as printed
Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
Amsterdam UMC location University of Amsterdam, Department of Obstetrics and Gynecology, Meibergdreef 9, Amsterdam, the Netherlands
Amsterdam UMC location University of Amsterdam, Department of Pediatric Surgery, Emma’s children hospital, Meibergdreef 9, Amsterdam, the Netherlands
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European Synchrotron Radiation Facility · University College London
Affiliation as printed
Department of Mechanical Engineering, University College London, London, UK
ESRF – The European Synchrotron, Grenoble, France
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Affiliation as printed
Division of Medicine, University College London, London, UK
Institute of Cardiovascular Science, University College London, London, UK
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Affiliation as printed
Institute of Pathology, Uniklinik RWTH Aachen, Aachen, Germany
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Universitätsklinikum Aachen · KU Leuven
Affiliation as printed
Institute of Pathology, Uniklinik RWTH Aachen, Aachen, Germany
Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium
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Affiliation as printed
Department of Computer Science, University of Copenhagen, Universitetsparker1, DK-2100 Copenhagen, Denmark
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European Synchrotron Radiation Facility
Affiliation as printed
ESRF – The European Synchrotron, Grenoble, France
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European Synchrotron Radiation Facility
Affiliation as printed
ESRF – The European Synchrotron, Grenoble, France
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European Synchrotron Radiation Facility
Affiliation as printed
ESRF – The European Synchrotron, Grenoble, France
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Amsterdam UMC Location University of Amsterdam · Emma Kinderziekenhuis · Amsterdam Gastroenterology Endocrinology Metabolism · Amsterdam Reproduction Development
Affiliation as printed
Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
Amsterdam UMC location University of Amsterdam, Department of Pediatric Surgery, Emma’s children hospital, Meibergdreef 9, Amsterdam, the Netherlands
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Amsterdam UMC Location University of Amsterdam · Amsterdam Reproduction Development
Affiliation as printed
Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
Amsterdam UMC location University of Amsterdam, Department of Obstetrics and Gynecology, Meibergdreef 9, Amsterdam, the Netherlands
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Amsterdam UMC Location University of Amsterdam · Amsterdam Reproduction Development
Affiliation as printed
Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
Amsterdam UMC location University of Amsterdam, Department of Obstetrics and Gynecology, Meibergdreef 9, Amsterdam, the Netherlands
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Amsterdam UMC Location University of Amsterdam
Affiliation as printed
Amsterdam UMC location University of Amsterdam, Department of Obstetrics and Gynecology, Meibergdreef 9, Amsterdam, the Netherlands
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Inserm · Université Grenoble Alpes
Affiliation as printed
Univ. Grenoble Alpes, Department of Anatomy (LADAF), CIC INSERM 1406, Grenoble, France
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Affiliation as printed
Centre for Advanced Research Computing, UCL, London, United Kingdom
Department of Mechanical Engineering, University College London, London, UK
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Helios Universitätsklinikum Wuppertal · Universitätsklinikum Aachen
Affiliation as printed
Institute of Pathology and Department of Molecular Pathology, Helios University Clinic Wuppertal, Wuppertal, Germany
Institute of Pathology, Uniklinik RWTH Aachen, Aachen, Germany
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Affiliation as printed
Institute of Pathology, Uniklinik RWTH Aachen, Aachen, Germany
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Universitätsklinikum Aachen · German Center for Lung Research
Affiliation as printed
Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover, Germany
Institute of Pathology, Uniklinik RWTH Aachen, Aachen, Germany
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Affiliation as printed
Satsuma Lab, UCL Hawkes Institute, University College London, London, UK
UCL Respiratory, University College London, London, UK
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Amsterdam University Medical Centers · University of Amsterdam
Affiliation as printed
Amsterdam UMC, University of Amsterdam, Department of Medical Biology, Meibergdreef 9, Amsterdam, the Netherlands
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Affiliation as printed
Antwerp Surgical Training, Anatomy and Research Centre (ASTARC), University of Antwerp, Wilrijkn, Belgium
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Affiliation as printed
Division of Medicine, University College London, London, UK
Institute of Cardiovascular Science, University College London, London, UK
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Affiliation as printed
Department of Mechanical Engineering, University College London, London, UK
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European Synchrotron Radiation Facility
Affiliation as printed
ESRF – The European Synchrotron, Grenoble, France
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Affiliation as printed
Department of Mechanical Engineering, University College London, London, UK
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Amsterdam UMC Location University of Amsterdam · Amsterdam Reproduction Development
Affiliation as printed
Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
Amsterdam UMC location University of Amsterdam, Department of Obstetrics and Gynecology, Meibergdreef 9, Amsterdam, the Netherlands
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