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Reichmann J, Sarrazin C, Schmale S, Blaurock C, Balkema-Buschmann A, Schmitzer B, Salditt T. 3D imaging of SARS-CoV-2 infected hamster lungs by X-ray phase contrast tomography enables drug testing. Sci Rep 2024; 14:12348. [PMID: 38811688 PMCID: PMC11137149 DOI: 10.1038/s41598-024-61746-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/09/2024] [Indexed: 05/31/2024] Open
Abstract
X-ray Phase Contrast Tomography (XPCT) based on wavefield propagation has been established as a high resolution three-dimensional (3D) imaging modality, suitable to reconstruct the intricate structure of soft tissues, and the corresponding pathological alterations. However, for biomedical research, more is needed than 3D visualisation and rendering of the cytoarchitecture in a few selected cases. First, the throughput needs to be increased to cover a statistically relevant number of samples. Second, the cytoarchitecture has to be quantified in terms of morphometric parameters, independent of visual impression. Third, dimensionality reduction and classification are required for identification of effects and interpretation of results. To address these challenges, we here design and implement a novel integrated and high throughput XPCT imaging and analysis workflow for 3D histology, pathohistology and drug testing. Our approach uses semi-automated data acquisition, reconstruction and statistical quantification. We demonstrate its capability for the example of lung pathohistology in Covid-19. Using a small animal model, different Covid-19 drug candidates are administered after infection and tested in view of restoration of the physiological cytoarchitecture, specifically the alveolar morphology. To this end, we then use morphometric parameter determination followed by a dimensionality reduction and classification based on optimal transport. This approach allows efficient discrimination between physiological and pathological lung structure, thereby providing quantitative insights into the pathological progression and partial recovery due to drug treatment. Finally, we stress that the XPCT image chain implemented here only used synchrotron radiation for validation, while the data used for analysis was recorded with laboratory μ CT radiation, more easily accessible for pre-clinical research.
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Affiliation(s)
- Jakob Reichmann
- Georg-August-University of Göttingen, Institute for X-Ray Physics, Friedrich-Hund-Platz 1, 37077, Göttingen, Germany
| | - Clement Sarrazin
- Georg-August-University of Göttingen, Institute of Computer Science, Goldschmidtstraße 7, 37077, Göttingen, Germany
- Equipe RAPSODI, Centre INRIA de l'université de Lille, F-59000, Lille, France
| | - Sebastian Schmale
- Georg-August-University of Göttingen, Institute of Computer Science, Goldschmidtstraße 7, 37077, Göttingen, Germany
| | - Claudia Blaurock
- Friedrich-Loeffler-Institute, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | | | - Bernhard Schmitzer
- Georg-August-University of Göttingen, Institute of Computer Science, Goldschmidtstraße 7, 37077, Göttingen, Germany.
| | - Tim Salditt
- Georg-August-University of Göttingen, Institute for X-Ray Physics, Friedrich-Hund-Platz 1, 37077, Göttingen, Germany.
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Duan X, Ding XF, Li N, Wu FX, Chen X, Zhu N. Sparse2Noise: Low-dose synchrotron X-ray tomography without high-quality reference data. Comput Biol Med 2023; 165:107473. [PMID: 37690288 DOI: 10.1016/j.compbiomed.2023.107473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/12/2023]
Abstract
BACKGROUND Synchrotron radiation computed tomography (SR-CT) holds promise for high-resolution in vivo imaging. Notably, the reconstruction of SR-CT images necessitates a large set of data to be captured with sufficient photons from multiple angles, resulting in high radiation dose received by the object. Reducing the number of projections and/or photon flux is a straightforward means to lessen the radiation dose, however, compromises data completeness, thus introducing noises and artifacts. Deep learning (DL)-based supervised methods effectively denoise and remove artifacts, but they heavily depend on high-quality paired data acquired at high doses. Although algorithms exist for training without high-quality references, they struggle to effectively eliminate persistent artifacts present in real-world data. METHODS This work presents a novel low-dose imaging strategy namely Sparse2Noise, which combines the reconstruction data from paired sparse-view CT scan (normal-flux) and full-view CT scan (low-flux) using a convolutional neural network (CNN). Sparse2Noise does not require high-quality reconstructed data as references and allows for fresh training on data with very small size. Sparse2Noise was evaluated by both simulated and experimental data. RESULTS Sparse2Noise effectively reduces noise and ring artifacts while maintaining high image quality, outperforming state-of-the-art image denoising methods at same dose levels. Furthermore, Sparse2Noise produces impressive high image quality for ex vivo rat hindlimb imaging with the acceptable low radiation dose (i.e., 0.5 Gy with the isotropic voxel size of 26 μm). CONCLUSIONS This work represents a significant advance towards in vivo SR-CT imaging. It is noteworthy that Sparse2Noise can also be used for denoising in conventional CT and/or phase-contrast CT.
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Affiliation(s)
- Xiaoman Duan
- Division of Biomedical Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada
| | - Xiao Fan Ding
- Division of Biomedical Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada
| | - Naitao Li
- Division of Biomedical Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada
| | - Fang-Xiang Wu
- Division of Biomedical Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada; Department of Computer Science, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada; Department of Mechanical Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada
| | - Xiongbiao Chen
- Division of Biomedical Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada; Department of Mechanical Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada.
| | - Ning Zhu
- Division of Biomedical Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada; Canadian Light Source, Saskatoon, S7N 2V3, SK, Canada; Department of Chemical and Biological Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada.
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Ahookhosh K, Vanoirbeek J, Vande Velde G. Lung function measurements in preclinical research: What has been done and where is it headed? Front Physiol 2023; 14:1130096. [PMID: 37035677 PMCID: PMC10073442 DOI: 10.3389/fphys.2023.1130096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/10/2023] [Indexed: 04/11/2023] Open
Abstract
Due to the close interaction of lung morphology and functions, repeatable measurements of pulmonary function during longitudinal studies on lung pathophysiology and treatment efficacy have been a great area of interest for lung researchers. Spirometry, as a simple and quick procedure that depends on the maximal inspiration of the patient, is the most common lung function test in clinics that measures lung volumes against time. Similarly, in the preclinical area, plethysmography techniques offer lung functional parameters related to lung volumes. In the past few decades, many innovative techniques have been introduced for in vivo lung function measurements, while each one of these techniques has their own advantages and disadvantages. Before each experiment, depending on the sensitivity of the required pulmonary functional parameters, it should be decided whether an invasive or non-invasive approach is desired. On one hand, invasive techniques offer sensitive and specific readouts related to lung mechanics in anesthetized and tracheotomized animals at endpoints. On the other hand, non-invasive techniques allow repeatable lung function measurements in conscious, free-breathing animals with readouts related to the lung volumes. The biggest disadvantage of these standard techniques for lung function measurements is considering the lung as a single unit and providing only global readouts. However, recent advances in lung imaging modalities such as x-ray computed tomography and magnetic resonance imaging opened new doors toward obtaining both anatomical and functional information from the same scan session, without the requirement for any extra pulmonary functional measurements, in more regional and non-invasive manners. Consequently, a new field of study called pulmonary functional imaging was born which focuses on introducing new techniques for regional quantification of lung function non-invasively using imaging-based techniques. This narrative review provides first an overview of both invasive and non-invasive conventional methods for lung function measurements, mostly focused on small animals for preclinical research, including discussions about their advantages and disadvantages. Then, we focus on those newly developed, non-invasive, imaging-based techniques that can provide either global or regional lung functional readouts at multiple time-points.
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Affiliation(s)
- Kaveh Ahookhosh
- Biomedical MRI, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Jeroen Vanoirbeek
- Centre of Environment and Health, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Greetje Vande Velde
- Biomedical MRI, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
- *Correspondence: Greetje Vande Velde,
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Dullin C, Svetlove A, Zschüntzsch J, Alves F. Simultaneous assessment of lung morphology and respiratory motion in retrospectively gated in-vivo microCT of free breathing anesthetized mice. Sci Rep 2022; 12:13299. [PMID: 35918439 PMCID: PMC9345384 DOI: 10.1038/s41598-022-17335-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 07/25/2022] [Indexed: 11/26/2022] Open
Abstract
Retrospective gating (RG) is a well established technique in preclinical computed tomography (CT) to assess 3D morphology of the lung. In RG additional angular projections are recorded typically by performing multiple rotations. Consequently, the projections are sorted according to the expansion state of the chest and those sets are then reconstructed separately. Thus, the breathing motion artefacts are suppressed at a cost of strongly elevated X-ray dose levels. Here we propose to use the entire raw data to assess respiratory motion in addition to retrospectively gated 3D reconstruction that visualize anatomical structures of the lung. Using this RG based X-ray respiratory motion measurement approach, which will be referred to as RG based X-ray lung function measurement (rgXLF) on the example of the mdx mouse model of Duchenne muscle dystrophy (mdx) we accurately obtained both the 3D anatomical morphology of the lung and the thoracic bones as well as functional temporal parameters of the lung. Thus, rgXLF will remove the necessity for separate acquisition procedures by being able to reproduce comparable results to the previously established planar X-ray based lung function measurement approach in a single low dose CT scan.
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Affiliation(s)
- Christian Dullin
- Institute for Diagnostic and Interventional Radiology, University Medical Center Goettingen, Goettingen, Germany. .,Max-Plank-Institute for Multidisciplinary Sciences, Translational Molecular Imaging, Goettingen, Germany. .,Institute for Diagnostic and Interventional Radiology, University Hospital Heidelberg, Heidelberg, Germany.
| | - Angelika Svetlove
- Max-Plank-Institute for Multidisciplinary Sciences, Translational Molecular Imaging, Goettingen, Germany
| | - Jana Zschüntzsch
- Clinic for Neurology, University Medical Center Goettingen, Göettingen, Germany
| | - Frauke Alves
- Institute for Diagnostic and Interventional Radiology, University Medical Center Goettingen, Goettingen, Germany.,Max-Plank-Institute for Multidisciplinary Sciences, Translational Molecular Imaging, Goettingen, Germany.,Clinic for Haematology and Medical Oncology, University Medical Center Goettingen, Goettingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany
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Synchrotron X-ray Radiation (SXR) in Medical Imaging: Current Status and Future Prospects. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12083790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Synchrotron X-ray radiation (SXR) has been widely studied to explore the structure of matter. Recently, there has been an intense focus on the medical application of SXR in imaging. This review is intended to explore the latest applications of SXR in medical imaging and to shed light on the advantages and drawbacks of this modality. The article highlights the latest developments in other fields that can greatly enhance the capability and applicability of SXR. The potentials of using machine and deep learning (DL)-based methods to generate synthetic images to use in regular clinics along with the use of photon counting X-ray detectors for spectral medical imaging with SXR are also discussed.
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Bayat S, Fardin L, Cercos-Pita JL, Perchiazzi G, Bravin A. Imaging Regional Lung Structure and Function in Small Animals Using Synchrotron Radiation Phase-Contrast and K-Edge Subtraction Computed Tomography. Front Physiol 2022; 13:825433. [PMID: 35350681 PMCID: PMC8957951 DOI: 10.3389/fphys.2022.825433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
Synchrotron radiation offers unique properties of coherence, utilized in phase-contrast imaging, and high flux as well as a wide energy spectrum which allow the selection of very narrow energy bands of radiation, used in K-edge subtraction imaging (KES) imaging. These properties extend X-ray computed tomography (CT) capabilities to quantitatively assess lung morphology, and to map regional lung ventilation, perfusion, inflammation, aerosol particle distribution and biomechanical properties, with microscopic spatial resolution. Four-dimensional imaging, allows the investigation of the dynamics of regional lung functional parameters simultaneously with structural deformation of the lung as a function of time. These techniques have proven to be very useful for revealing the regional differences in both lung structure and function which is crucial for better understanding of disease mechanisms as well as for evaluating treatment in small animal models of lung diseases. Here, synchrotron radiation imaging methods are described and examples of their application to the study of disease mechanisms in preclinical animal models are presented.
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Affiliation(s)
- Sam Bayat
- Univ. Grenoble Alpes, Inserm UA07 STROBE Laboratory, University of Grenoble Alpes, Grenoble, France.,Department of Pulmonology and Clinical Physiology, Grenoble University Hospital, Grenoble, France
| | - Luca Fardin
- European Synchrotron Radiation Facility, Grenoble, France
| | - José Luis Cercos-Pita
- Hedenstierna Laboratory, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Gaetano Perchiazzi
- Hedenstierna Laboratory, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Alberto Bravin
- Department of Physics, University of Milano-Bicocca, Milan, Italy
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Ruaro B, Salton F, Braga L, Wade B, Confalonieri P, Volpe MC, Baratella E, Maiocchi S, Confalonieri M. The History and Mystery of Alveolar Epithelial Type II Cells: Focus on Their Physiologic and Pathologic Role in Lung. Int J Mol Sci 2021; 22:2566. [PMID: 33806395 PMCID: PMC7961977 DOI: 10.3390/ijms22052566] [Citation(s) in RCA: 126] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/27/2021] [Accepted: 02/28/2021] [Indexed: 12/13/2022] Open
Abstract
Alveolar type II (ATII) cells are a key structure of the distal lung epithelium, where they exert their innate immune response and serve as progenitors of alveolar type I (ATI) cells, contributing to alveolar epithelial repair and regeneration. In the healthy lung, ATII cells coordinate the host defense mechanisms, not only generating a restrictive alveolar epithelial barrier, but also orchestrating host defense mechanisms and secreting surfactant proteins, which are important in lung protection against pathogen exposure. Moreover, surfactant proteins help to maintain homeostasis in the distal lung and reduce surface tension at the pulmonary air-liquid interface, thereby preventing atelectasis and reducing the work of breathing. ATII cells may also contribute to the fibroproliferative reaction by secreting growth factors and proinflammatory molecules after damage. Indeed, various acute and chronic diseases are associated with intensive inflammation. These include oedema, acute respiratory distress syndrome, fibrosis and numerous interstitial lung diseases, and are characterized by hyperplastic ATII cells which are considered an essential part of the epithelialization process and, consequently, wound healing. The aim of this review is that of revising the physiologic and pathologic role ATII cells play in pulmonary diseases, as, despite what has been learnt in the last few decades of research, the origin, phenotypic regulation and crosstalk of these cells still remain, in part, a mystery.
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Affiliation(s)
- Barbara Ruaro
- Pulmonology Department, University Hospital of Cattinara, 34128 Trieste, Italy; (F.S.); (P.C.); (M.C.)
| | - Francesco Salton
- Pulmonology Department, University Hospital of Cattinara, 34128 Trieste, Italy; (F.S.); (P.C.); (M.C.)
| | - Luca Braga
- ICGEB, Area Science Park, Padriciano, 34128 Trieste, Italy;
| | - Barbara Wade
- City of Health and Science of Turin, Department of Science of Public Health and Pediatrics, University of Torino, 34128 Trieste, Italy;
| | - Paola Confalonieri
- Pulmonology Department, University Hospital of Cattinara, 34128 Trieste, Italy; (F.S.); (P.C.); (M.C.)
| | - Maria Concetta Volpe
- Life Sciences Department, University of Trieste, 34128 Trieste, Italy; (M.C.V.); (S.M.)
| | - Elisa Baratella
- Department of Radiology, Department of Medicine, Surgery and Health Science, University of Trieste, 34128 Trieste, Italy;
| | - Serena Maiocchi
- Life Sciences Department, University of Trieste, 34128 Trieste, Italy; (M.C.V.); (S.M.)
| | - Marco Confalonieri
- Pulmonology Department, University Hospital of Cattinara, 34128 Trieste, Italy; (F.S.); (P.C.); (M.C.)
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Editorial. Phys Med 2020; 79:ii-v. [DOI: 10.1016/j.ejmp.2020.11.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/20/2020] [Indexed: 11/20/2022] Open
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