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Lin Q, Wu Z, Huang M, Dang Z, Tian L, Guan Y, Liu G, Lu Y, Tian Y. Detection of early pulmonary emphysema by multi-contrast x-ray Talbot-Lau interferometer. Med Phys 2024; 51:4133-4142. [PMID: 38578373 DOI: 10.1002/mp.17053] [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: 10/16/2023] [Revised: 03/14/2024] [Accepted: 03/24/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Pulmonary emphysema is a part of chronic obstructive pulmonary disease, which is an irreversible chronic respiratory disease. In order to avoid further damage to lung tissue, early diagnosis and treatment of pulmonary emphysema is essential. PURPOSE Early pulmonary emphysema diagnosis is difficult with conventional radiographic imaging. Recently, x-ray phase contrast imaging has proved to be an effective and promising imaging strategy for soft tissue, due to its high sensitivity and multi-contrast. The aim of this study is to diagnose pulmonary emphysema early utilizing an x-ray Talbot-Lau interferometer (TLI). METHODS We successfully established the mouse model of emphysema by porcine pancreatic elastase treatment, and then used the established x-ray TLI to perform imaging experiments on the mice with different treatment time. The traditional absorption CT and phase contrast CT were obtained simultaneously through TLI. The CT results and histopathology of mice lung in different treatment time were quantitatively analyzed. RESULTS By imaging mice lungs, it can be found that phase contrast has higher sensitivity than absorption contrast in early pulmonary emphysema. The results show that the phase contrast signal could distinguish the pulmonary emphysema earlier than the conventional attenuation signal, which can be consistent with histological images. Through the quantitative analysis of pathological section and phase contrast CT, it can be found that there is a strong linear correlation. CONCLUSIONS In this study, we quantitatively analyze mean linear intercept of histological sections and CT values of mice. The results show that the phase contrast signal has higher imaging sensitivity than the attenuation signal. X-ray TLI multi-contrast imaging is proved as a potential diagnostic method for early pulmonary emphysema in mice.
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Affiliation(s)
- Qisi Lin
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China
| | - Zhao Wu
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China
| | - Meng Huang
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China
- Ultrasonic Department, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zheng Dang
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China
| | - Lijiao Tian
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China
| | - Yong Guan
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China
| | - Gang Liu
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China
| | - Yalin Lu
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
| | - Yangchao Tian
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China
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2
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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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3
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Donato S, Arana Peña LM, Arfelli F, Brombal L, Colmo L, Longo R, Martellani F, Tromba G, Zanconati F, Bonazza D. Integrating X-ray phase-contrast imaging and histology for comparative evaluation of breast tissue malignancies in virtual histology analysis. Sci Rep 2024; 14:5831. [PMID: 38461221 PMCID: PMC10924917 DOI: 10.1038/s41598-024-56341-6] [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: 10/20/2023] [Accepted: 03/05/2024] [Indexed: 03/11/2024] Open
Abstract
Detecting breast tissue alterations is essential for cancer diagnosis. However, inherent bidimensionality limits histological procedures' effectiveness in identifying these changes. Our study applies a 3D virtual histology method based on X-ray phase-contrast microtomography (PhC μ CT), performed at a synchrotron facility, to investigate breast tissue samples including different types of lesions, namely intraductal papilloma, micropapillary intracystic carcinoma, and invasive lobular carcinoma. One-to-one comparisons of X-ray and histological images explore the clinical potential of 3D X-ray virtual histology. Results show that PhC μ CT technique provides high spatial resolution and soft tissue sensitivity, while being non-destructive, not requiring a dedicated sample processing and being compatible with conventional histology. PhC μ CT can enhance the visualization of morphological characteristics such as stromal tissue, fibrovascular core, terminal duct lobular unit, stromal/epithelium interface, basement membrane, and adipocytes. Despite not reaching the (sub) cellular level, the three-dimensionality of PhC μ CT images allows to depict in-depth alterations of the breast tissues, potentially revealing pathologically relevant details missed by a single histological section. Compared to serial sectioning, PhC μ CT allows the virtual investigation of the sample volume along any orientation, possibly guiding the pathologist in the choice of the most suitable cutting plane. Overall, PhC μ CT virtual histology holds great promise as a tool adding to conventional histology for improving efficiency, accessibility, and diagnostic accuracy of pathological evaluation.
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Affiliation(s)
- Sandro Donato
- Department of Physics, University of Calabria, 87036, Rende, CS, Italy.
- Division of Frascati, INFN, 00044, Frascati, RM, Italy.
| | - Lucia Mariel Arana Peña
- Department of Physics, University of Trieste, 34127, Trieste, Italy
- Division of Trieste, INFN, 34127, Trieste, Italy
- Elettra-Sincrotrone Trieste S.C.p.A, 34149, Trieste, Italy
| | - Fulvia Arfelli
- Department of Physics, University of Trieste, 34127, Trieste, Italy
- Division of Trieste, INFN, 34127, Trieste, Italy
| | - Luca Brombal
- Department of Physics, University of Trieste, 34127, Trieste, Italy
- Division of Trieste, INFN, 34127, Trieste, Italy
| | - Luisella Colmo
- Unit of Surgical Pathology of the Cattinara Hospital, Azienda Sanitaria Universitaria Giuliana Isontina (ASUGI), 34149, Trieste, Italy
| | - Renata Longo
- Department of Physics, University of Trieste, 34127, Trieste, Italy
- Division of Trieste, INFN, 34127, Trieste, Italy
| | - Fulvia Martellani
- Unit of Surgical Pathology of the Cattinara Hospital, Azienda Sanitaria Universitaria Giuliana Isontina (ASUGI), 34149, Trieste, Italy
| | | | - Fabrizio Zanconati
- Unit of Surgical Pathology of the Cattinara Hospital, Azienda Sanitaria Universitaria Giuliana Isontina (ASUGI), 34149, Trieste, Italy
| | - Deborah Bonazza
- Unit of Surgical Pathology of the Cattinara Hospital, Azienda Sanitaria Universitaria Giuliana Isontina (ASUGI), 34149, Trieste, Italy
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4
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Brahimetaj R, Cornelis J, Van Ongeval C, De Mey J, Jansen B. The impact of (simulated) resolution on breast cancer diagnosis based on high-resolution 3D micro-CT microcalcification images. Med Phys 2024; 51:1754-1762. [PMID: 37698346 DOI: 10.1002/mp.16708] [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: 02/01/2023] [Revised: 08/09/2023] [Accepted: 08/23/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Breast microcalcifications (MCs) are considered to be a robust marker of breast cancer. A machine learning model can provide breast cancer diagnosis based on properties of individual MCs - if their characteristics are captured at high resolution and in 3D. PURPOSE The main purpose of the study was to explore the impact of image resolution (8 µm, 16 µm, 32 µm, 64 µm) when diagnosing breast cancer using radiomics features extracted from individual high resolution 3D micro-CT MC images. METHODS Breast MCs extracted from 86 female patients were analyzed at four different spatial resolutions: 8 µm (original resolution) and 16 µm, 32 µm, 64 µm (simulated image resolutions). Radiomic features were extracted at each image resolution in an attempt, to find a compact feature signature allowing to distinguish benign and malignant MCs. Machine learning algorithms were used for classifying individual MCs and samples (i.e., patients). For sample diagnosis, a custom-based thresholding approach was used to combine individual MC results into sample results. We conducted classification experiments when using (a) the same MCs visible in 8 µm, 16 µm, 32 µm, and 64 µm resolution; (b) the same MCs visible in 8 µm, 16 µm, and 32 µm resolution; (c) the same MCs visible in 8 µm and 16 µm resolution; (d) all MCs visible in 8 µm, 16 µm, 32 µm, and 64 µm resolution. Accuracy, sensitivity, specificity, AUC, and F1 score were computed for each experiment. RESULTS The individual MC results yielded an accuracy of 77.27%, AUC of 83.83%, F1 score of 77.25%, sensitivity of 80.86%, and specificity of 72.2% at 8 µm resolution. For the individual MC classifications we report for the F1 scores: a 2.29% drop when using 16 µm instead of 8 µm, a 4.01% drop when using 32 µm instead of 8 µm, a 10.69% drop when using 64 µm instead of 8 µm. The sample results yielded an accuracy and F1 score of 81.4%, sensitivity of 80.43%, and specificity value of 82.5% at 8 µm. For the sample classifications we report for F1 score values: a 6.3% drop when using 16 µm instead of 8 µm, a 4.91% drop when using 32 µm instead of 8 µm, and a 6.3% drop when using 64 µm instead of 8 µm. CONCLUSIONS The highest classification results are obtained at the highest resolution (8 µm). If breast MCs characteristics could be visualized/captured in 3D at a higher resolution compared to what is used nowadays in digital mammograms (approximately 70 µm), breast cancer diagnosis will be improved.
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Affiliation(s)
- Redona Brahimetaj
- Department of Electronics and Informatics (ETRO), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Jan Cornelis
- Department of Electronics and Informatics (ETRO), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Chantal Van Ongeval
- Department of Radiology, Universitair Ziekenhuis Leuven, KU Leuven, Leuven, Belgium
| | - Johan De Mey
- Department of Radiology, Universitair Ziekenhuis Brussel, Brussels, Belgium
| | - Bart Jansen
- Department of Electronics and Informatics (ETRO), Vrije Universiteit Brussel (VUB), Brussels, Belgium
- IMEC, Leuven, Belgium
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5
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Dizbay Sak S, Sevim S, Buyuksungur A, Kayı Cangır A, Orhan K. The Value of Micro-CT in the Diagnosis of Lung Carcinoma: A Radio-Histopathological Perspective. Diagnostics (Basel) 2023; 13:3262. [PMID: 37892083 PMCID: PMC10606474 DOI: 10.3390/diagnostics13203262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/12/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Micro-computed tomography (micro-CT) is a relatively new imaging modality and the three-dimensional (3D) images obtained via micro-CT allow researchers to collect both quantitative and qualitative information on various types of samples. Micro-CT could potentially be used to examine human diseases and several studies have been published on this topic in the last decade. In this study, the potential uses of micro-CT in understanding and evaluating lung carcinoma and the relevant studies conducted on lung and other tumors are summarized. Currently, the resolution of benchtop laboratory micro-CT units has not reached the levels that can be obtained with light microscopy, and it is not possible to detect the histopathological features (e.g., tumor type, adenocarcinoma pattern, spread through air spaces) required for lung cancer management. However, its ability to provide 3D images in any plane of section, without disturbing the integrity of the specimen, suggests that it can be used as an auxiliary technique, especially in surgical margin examination, the evaluation of tumor invasion in the entire specimen, and calculation of primary and metastatic tumor volume. Along with future developments in micro-CT technology, it can be expected that the image resolution will gradually improve, the examination time will decrease, and the relevant software will be more user friendly. As a result of these developments, micro-CT may enter pathology laboratories as an auxiliary method in the pathological evaluation of lung tumors. However, the safety, performance, and cost effectiveness of micro-CT in the areas of possible clinical application should be investigated. If micro-CT passes all these tests, it may lead to the convergence of radiology and pathology applications performed independently in separate units today, and the birth of a new type of diagnostician who has equal knowledge of the histological and radiological features of tumors.
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Affiliation(s)
- Serpil Dizbay Sak
- Department of Pathology, Faculty of Medicine, Ankara University, Ankara 06230, Turkey
| | - Selim Sevim
- Department of Pathology, Faculty of Medicine, Ankara University, Ankara 06230, Turkey
| | - Arda Buyuksungur
- Department of Basic Medical Sciences, Faculty of Dentistry, Ankara University, Ankara 06560, Turkey
| | - Ayten Kayı Cangır
- Department of Thoracic Surgery Ankara, Faculty of Medicine, Ankara University, Ankara 06230, Turkey
| | - Kaan Orhan
- Department of Dentomaxillofacial Radiology, Faculty of Dentistry, Ankara University, Ankara 06560, Turkey
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6
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Arana Peña LM, Donato S, Bonazza D, Brombal L, Martellani F, Arfelli F, Tromba G, Longo R. Multiscale X-ray phase-contrast tomography: From breast CT to micro-CT for virtual histology. Phys Med 2023; 112:102640. [PMID: 37441823 DOI: 10.1016/j.ejmp.2023.102640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/31/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
Phase-contrast imaging techniques address the issue of poor soft-tissue contrast encountered in traditional X-ray imaging. This can be accomplished with the propagation-based phase-contrast technique by employing a coherent photon beam, which is available at synchrotron facilities, as well as long sample-to-detector distances. This study demonstrates the optimization of propagation-based phase-contrast computed tomography (CT) techniques for multiscale X-ray imaging of the breast at the Elettra synchrotron facility (Trieste, Italy). Two whole breast mastectomy samples were acquired with propagation-based breast-CT using a monochromatic synchrotron beam at a pixel size of 60 µm. Paraffin-embedded blocks sampled from the same tissues were scanned with propagation-based micro-CT imaging using a polychromatic synchrotron beam at a pixel size of 4 µm. Images of both methodologies and of the same sample were spatially registered. The resulting images showed the transition from whole breast imaging with propagation-based breast-CT methodology to virtual histology with propagation-based micro-CT imaging of the same sample. Additionally, conventional histological images were matched to virtual histology images. Phase-contrast images offer a high resolution with low noise, which allows for a highly precise match between virtual and conventional histology. Furthermore, those techniques allow a clear discernment of breast structures, lesions, and microcalcifications, being a promising clinically-compatible tool for breast imaging in a multiscale approach, to either assist in the detection of cancer in full volume breast samples or to complement structure identification in paraffin-embedded breast tissue samples.
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Affiliation(s)
- L M Arana Peña
- Department of Physics, University of Trieste, Via Alfonso Valerio 2, Trieste I-34127, Italy; INFN Division of Trieste, 34127 Trieste, Italy; Elettra-Sincrotrone Trieste, SS 14 Km 163,5, AREA Science Park, 34149 Basovizza, (Trieste), Italy
| | - S Donato
- Department of Physics and STAR Lab, University of Calabria, Via P. Bucci 31C, Rende, (CS), I-87036, Italy; INFN Division of Frascati, Via E. Fermi 54, Frascati I-00044, Italy.
| | - D Bonazza
- Unit of Surgical Pathology, Cattinara Hospital, Azienda Sanitaria Universitaria Giuliana Isontina (ASUGI), Strada di Fiume, 447, Trieste I-34149, Italy
| | - L Brombal
- Department of Physics, University of Trieste, Via Alfonso Valerio 2, Trieste I-34127, Italy; INFN Division of Trieste, 34127 Trieste, Italy
| | - F Martellani
- Unit of Surgical Pathology, Cattinara Hospital, Azienda Sanitaria Universitaria Giuliana Isontina (ASUGI), Strada di Fiume, 447, Trieste I-34149, Italy
| | - F Arfelli
- Department of Physics, University of Trieste, Via Alfonso Valerio 2, Trieste I-34127, Italy; INFN Division of Trieste, 34127 Trieste, Italy
| | - G Tromba
- Elettra-Sincrotrone Trieste, SS 14 Km 163,5, AREA Science Park, 34149 Basovizza, (Trieste), Italy
| | - R Longo
- Department of Physics, University of Trieste, Via Alfonso Valerio 2, Trieste I-34127, Italy; INFN Division of Trieste, 34127 Trieste, Italy
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7
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Polikarpov M, Vila-Comamala J, Wang Z, Pereira A, van Gogh S, Gasser C, Jefimovs K, Romano L, Varga Z, Lång K, Schmeltz M, Tessarini S, Rawlik M, Jermann E, Lewis S, Yun W, Stampanoni M. Towards virtual histology with X-ray grating interferometry. Sci Rep 2023; 13:9049. [PMID: 37270642 DOI: 10.1038/s41598-023-35854-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 05/24/2023] [Indexed: 06/05/2023] Open
Abstract
Breast cancer is the most common type of cancer worldwide. Diagnosing breast cancer relies on clinical examination, imaging and biopsy. A core-needle biopsy enables a morphological and biochemical characterization of the cancer and is considered the gold standard for breast cancer diagnosis. A histopathological examination uses high-resolution microscopes with outstanding contrast in the 2D plane, but the spatial resolution in the third, Z-direction, is reduced. In the present paper, we propose two high-resolution table-top systems for phase-contrast X-ray tomography of soft-tissue samples. The first system implements a classical Talbot-Lau interferometer and allows to perform ex-vivo imaging of human breast samples with a voxel size of 5.57 μm. The second system with a comparable voxel size relies on a Sigray MAAST X-ray source with structured anode. For the first time, we demonstrate the applicability of the latter to perform X-ray imaging of human breast specimens with ductal carcinoma in-situ. We assessed image quality of both setups and compared it to histology. We showed that both setups made it possible to target internal features of breast specimens with better resolution and contrast than previously achieved, demonstrating that grating-based phase-contrast X-ray CT could be a complementary tool for clinical histopathology.
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Affiliation(s)
- M Polikarpov
- Swiss Light Source, Paul Scherrer Institut, 5232, Villigen-PSI, Switzerland.
- Institute for Biomedical Engineering, ETH Zurich, 8092, Zurich, Switzerland.
| | - J Vila-Comamala
- Swiss Light Source, Paul Scherrer Institut, 5232, Villigen-PSI, Switzerland
| | - Z Wang
- Swiss Light Source, Paul Scherrer Institut, 5232, Villigen-PSI, Switzerland
- Institute for Biomedical Engineering, ETH Zurich, 8092, Zurich, Switzerland
- Department of Engineering Physics, Tsinghua University, Haidian District, Beijing, 100080, China
| | - A Pereira
- Swiss Light Source, Paul Scherrer Institut, 5232, Villigen-PSI, Switzerland
- Institute for Biomedical Engineering, ETH Zurich, 8092, Zurich, Switzerland
| | - S van Gogh
- Swiss Light Source, Paul Scherrer Institut, 5232, Villigen-PSI, Switzerland
- Institute for Biomedical Engineering, ETH Zurich, 8092, Zurich, Switzerland
| | - C Gasser
- Institute for Biomedical Engineering, ETH Zurich, 8092, Zurich, Switzerland
| | - K Jefimovs
- Swiss Light Source, Paul Scherrer Institut, 5232, Villigen-PSI, Switzerland
| | - L Romano
- Swiss Light Source, Paul Scherrer Institut, 5232, Villigen-PSI, Switzerland
- Institute for Biomedical Engineering, ETH Zurich, 8092, Zurich, Switzerland
| | - Z Varga
- Department of Pathology and Molecular Pathology, University Hospital Zürich, 8091, Zurich, Switzerland
| | - K Lång
- Department of Diagnostic Radiology, Translational Medicine, Lund University, Lund, Sweden
- Unilabs Mammography Unit, Skåne University Hospital, Malmö, Sweden
| | - M Schmeltz
- Swiss Light Source, Paul Scherrer Institut, 5232, Villigen-PSI, Switzerland
| | - S Tessarini
- Swiss Light Source, Paul Scherrer Institut, 5232, Villigen-PSI, Switzerland
- Institute for Biomedical Engineering, ETH Zurich, 8092, Zurich, Switzerland
| | - M Rawlik
- Swiss Light Source, Paul Scherrer Institut, 5232, Villigen-PSI, Switzerland
- Institute for Biomedical Engineering, ETH Zurich, 8092, Zurich, Switzerland
| | | | - S Lewis
- Sigray Inc., Concord, CA, 94520, USA
| | - W Yun
- Sigray Inc., Concord, CA, 94520, USA
| | - M Stampanoni
- Swiss Light Source, Paul Scherrer Institut, 5232, Villigen-PSI, Switzerland
- Institute for Biomedical Engineering, ETH Zurich, 8092, Zurich, Switzerland
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8
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Pinkert-Leetsch D, Frohn J, Ströbel P, Alves F, Salditt T, Missbach-Guentner J. Three-dimensional analysis of human pancreatic cancer specimens by phase-contrast based X-ray tomography - the next dimension of diagnosis. Cancer Imaging 2023; 23:43. [PMID: 37131262 PMCID: PMC10152799 DOI: 10.1186/s40644-023-00559-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 04/19/2023] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND The worldwide increase of pancreatic ductal adenocarcinoma (PDAC), which still has one of the lowest survival rates, requires novel imaging tools to improve early detection and to refine diagnosis. Therefore, the aim of this study was to assess the feasibility of propagation-based phase-contrast X-ray computed tomography of already paraffin-embedded and unlabeled human pancreatic tumor tissue to achieve a detailed three-dimensional (3D) view of the tumor sample in its entirety. METHODS Punch biopsies of areas of particular interest were taken from paraffin blocks after initial histological analysis of hematoxylin and eosin stained tumor sections. To cover the entire 3.5 mm diameter of the punch biopsy, nine individual tomograms with overlapping regions were acquired in a synchrotron parallel beam configuration and stitched together after data reconstruction. Due to the intrinsic contrast based on electron density differences of tissue components and a voxel size of 1.3 μm achieved PDAC and its precursors were clearly identified. RESULTS Characteristic tissue structures for PDAC and its precursors, such as dilated pancreatic ducts, altered ductal epithelium, diffuse immune cell infiltrations, increased occurrence of tumor stroma and perineural invasion were clearly identified. Certain structures of interest were visualized in three dimensions throughout the tissue punch. Pancreatic duct ectasia of different caliber and atypical shape as well as perineural infiltration could be contiguously traced by viewing serial tomographic slices and by applying semi-automatic segmentation. Histological validation of corresponding sections confirmed the former identified PDAC features. CONCLUSION In conclusion, virtual 3D histology via phase-contrast X-ray tomography visualizes diagnostically relevant tissue structures of PDAC in their entirety, preserving tissue integrity in label-free, paraffin embedded tissue biopsies. In the future, this will not only enable a more comprehensive diagnosis but also a possible identification of new 3D imaging tumor markers.
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Affiliation(s)
- Diana Pinkert-Leetsch
- Department of Diagnostic and Interventional Radiology, University Medical Center, Goettingen, Germany.
| | - Jasper Frohn
- Institute for X-ray Physics, Georg-August-University, Goettingen, Germany
| | - Philipp Ströbel
- Department of Pathology, University Medical Center, Goettingen, Germany
| | - Frauke Alves
- Department of Diagnostic and Interventional Radiology, University Medical Center, Goettingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany
- Department of Hematology and Medical Oncology, University Medical Center, Goettingen, Germany
- Translational Molecular Imaging, Max-Planck-Institute for Multidisciplinary Sciences, Goettingen, Germany
| | - Tim Salditt
- Institute for X-ray Physics, Georg-August-University, 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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9
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Zhao Y, Zheng M, Li Y, Han S, Li F, Qi B, Liu D, Hu C. Suppressing multi-material and streak artifacts with an accelerated 3D iterative image reconstruction algorithm for in-line X-ray phase-contrast computed tomography. OPTICS EXPRESS 2022; 30:19684-19704. [PMID: 36221738 DOI: 10.1364/oe.459924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/09/2022] [Indexed: 06/16/2023]
Abstract
In-line X-ray phase-contrast computed tomography typically contains two independent procedures: phase retrieval and computed tomography reconstruction, in which multi-material and streak artifacts are two important problems. To address these problems simultaneously, an accelerated 3D iterative image reconstruction algorithm is proposed. It merges the above-mentioned two procedures into one step, and establishes the data fidelity term in raw projection domain while introducing 3D total variation regularization term in image domain. Specifically, a transport-of-intensity equation (TIE)-based phase retrieval method is updated alternately for different areas of the multi-material sample. Simulation and experimental results validate the effectiveness and efficiency of the proposed algorithm.
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10
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Improved automated early detection of breast cancer based on high resolution 3D micro-CT microcalcification images. BMC Cancer 2022; 22:162. [PMID: 35148703 PMCID: PMC8832731 DOI: 10.1186/s12885-021-09133-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 12/20/2021] [Indexed: 11/10/2022] Open
Abstract
Background The detection of suspicious microcalcifications on mammography represents one of the earliest signs of a malignant breast tumor. Assessing microcalcifications’ characteristics based on their appearance on 2D breast imaging modalities is in many cases challenging for radiologists. The aims of this study were to: (a) analyse the association of shape and texture properties of breast microcalcifications (extracted by scanning breast tissue with a high resolution 3D scanner) with malignancy, (b) evaluate microcalcifications’ potential to diagnose benign/malignant patients. Methods Biopsy samples of 94 female patients with suspicious microcalcifications detected during a mammography, were scanned using a micro-CT scanner at a resolution of 9 μm. Several preprocessing techniques were applied on 3504 extracted microcalcifications. A high amount of radiomic features were extracted in an attempt to capture differences among microcalcifications occurring in benign and malignant lesions. Machine learning algorithms were used to diagnose: (a) individual microcalcifications, (b) samples. For the samples, several methodologies to combine individual microcalcification results into sample results were evaluated. Results We could classify individual microcalcifications with 77.32% accuracy, 61.15% sensitivity and 89.76% specificity. At the sample level diagnosis, we achieved an accuracy of 84.04%, sensitivity of 86.27% and specificity of 81.39%. Conclusions By studying microcalcifications’ characteristics at a level of details beyond what is currently possible by using conventional breast imaging modalities, our classification results demonstrated a strong association between breast microcalcifications and malignancies. Microcalcification’s texture features extracted in transform domains, have higher discriminating power to classify benign/malignant individual microcalcifications and samples compared to pure shape-features.
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11
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Zhu Y, O'Connell AM, Ma Y, Liu A, Li H, Zhang Y, Zhang X, Ye Z. Dedicated breast CT: state of the art-Part II. Clinical application and future outlook. Eur Radiol 2021; 32:2286-2300. [PMID: 34476564 DOI: 10.1007/s00330-021-08178-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 06/19/2021] [Accepted: 06/29/2021] [Indexed: 12/17/2022]
Abstract
Dedicated breast CT is being increasingly used for breast imaging. This technique provides images with no compression, removal of tissue overlap, rapid acquisition, and available simultaneous assessment of microcalcifications and contrast enhancement. In this second installment in a 2-part review, the current status of clinical applications and ongoing efforts to develop new imaging systems are discussed, with particular emphasis on how to achieve optimized practice including lesion detection and characterization, response to therapy monitoring, density assessment, intervention, and implant evaluation. The potential for future screening with breast CT is also addressed. KEY POINTS: • Dedicated breast CT is an emerging modality with enormous potential in the future of breast imaging by addressing numerous clinical needs from diagnosis to treatment. • Breast CT shows either noninferiority or superiority with mammography and numerical comparability to MRI after contrast administration in diagnostic statistics, demonstrates excellent performance in lesion characterization, density assessment, and intervention, and exhibits promise in implant evaluation, while potential application to breast cancer screening is still controversial. • New imaging modalities such as phase-contrast breast CT, spectral breast CT, and hybrid imaging are in the progress of R & D.
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Affiliation(s)
- Yueqiang Zhu
- Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Huan-Hu-Xi Road, Ti-Yuan-Bei, Hexi District, 300060, Tianjin, China
| | - Avice M O'Connell
- Department of Imaging Sciences, University of Rochester Medical Center, 601 Elmwood Avenue, Box 648, Rochester, NY, 14642, USA
| | - Yue Ma
- Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Huan-Hu-Xi Road, Ti-Yuan-Bei, Hexi District, 300060, Tianjin, China
| | - Aidi Liu
- Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Huan-Hu-Xi Road, Ti-Yuan-Bei, Hexi District, 300060, Tianjin, China
| | - Haijie Li
- Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Huan-Hu-Xi Road, Ti-Yuan-Bei, Hexi District, 300060, Tianjin, China
| | - Yuwei Zhang
- Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Huan-Hu-Xi Road, Ti-Yuan-Bei, Hexi District, 300060, Tianjin, China
| | - Xiaohua Zhang
- Koning Corporation, Lennox Tech Enterprise Center, 150 Lucius Gordon Drive, Suite 112, West Henrietta, NY, 14586, USA
| | - Zhaoxiang Ye
- Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Huan-Hu-Xi Road, Ti-Yuan-Bei, Hexi District, 300060, Tianjin, China.
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12
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Wu C, Xing Y, Zhang L, Li X, Zhu X, Zhang X, Gao H. Fourier-based interpretation and noise analysis of the moments of small-angle x-ray scattering in grating-based x-ray phase contrast imaging. OPTICS EXPRESS 2021; 29:21902-21920. [PMID: 34265967 DOI: 10.1364/oe.426129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/15/2021] [Indexed: 06/13/2023]
Abstract
In grating-based x-ray phase contrast imaging, Fourier component analysis (FCA) is usually recognized as a gold standard to retrieve the contrasts including attenuation, phase and dark-field, since it is well-established on wave optics and is of high computational efficiency. Meanwhile, an alternative approach basing on the particle scattering theory is being developed and can provide similar contrasts with FCA by calculating multi-order moments of deconvolved small-angle x-ray scattering, so called as multi-order moment analysis (MMA). Although originated from quite different physics theories, the high consistency between the contrasts retrieved by FCA and MMA implies us that there may be some intrinsic connections between them, which has not been fully revealed to the best of our knowledge. In this work, we present a Fourier-based interpretation of MMA and conclude that the contrasts retrieved by MMA are actually the weighted compositions of Fourier coefficients, which means MMA delivers similar physical information as FCA. Based on the recognized cosine model, we also provide a truncated analytic MMA method, and its computational efficiency can be hundreds of times faster than the original deconvolution-based MMA method. Moreover, a noise analysis for our proposed truncated method is also conducted to further evaluate its performances. The results of numerical simulation and physical experiments support our analyses and conclusions.
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13
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Zhao Y, Zhao Q, Zheng M, Yang T, Liu D, Sun L, Lv W, Li Y, Liu Y, Hu C. Comparison of microstructural imaging of the root canal isthmus using propagation-based X-ray phase-contrast and absorption micro-computed tomography. J Microsc 2021; 284:74-82. [PMID: 34143441 DOI: 10.1111/jmi.13042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 06/04/2021] [Accepted: 06/16/2021] [Indexed: 11/30/2022]
Abstract
Clear and complete microstructural imaging of the root canal isthmus is an important part of pathological investigations in research and clinical practice. X-ray micro-computed tomography (μCT) is a widely used non-destructive imaging technique, which allows for distortion-free three-dimensional (3D) visualisation. While absorption μCT typically has poor contrast resolution for observing the root canal isthmus, especially for weak-absorbing tissues, propagation-based X-ray phase-contrast imaging (PBI) is a powerful imaging method, which in its combination with μCT (PB-PCμCT) enables high-resolution and high-contrast microstructural imaging of the weak-absorbing tissues in samples. To investigate the feasibility and ability of PB-PCμCT in microstructural imaging of the root canal isthmus, conventional absorption μCT and PB-PCμCT experiments were performed. The two-dimensional (2D) and 3D comparison results demonstrated that, compared to absorption μCT, PB-PCμCT has the ability to image the root canal isthmus more clearly and completely, and thus, it has great potential to serve as a valuable tool for biomedical and preclinical studies on the root canal isthmus.
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Affiliation(s)
- Yuqing Zhao
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, People's Republic of China
| | - Qi Zhao
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, People's Republic of China
| | - Mengting Zheng
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, People's Republic of China
| | - Tingting Yang
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, People's Republic of China
| | - Dayong Liu
- Tianjin Medical University School of Stomatology, Tianjin, People's Republic of China
| | - Lianlian Sun
- Department of Stomatology, Fifth Central of Tianjin, Tianjin, People's Republic of China
| | - Wenjuan Lv
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, People's Republic of China
| | - Yimin Li
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, People's Republic of China
| | - Yongchao Liu
- Department of Radiation Oncology, Fifth Central of Tianjin, Tianjin, People's Republic of China
| | - Chunhong Hu
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, People's Republic of China
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14
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Lwin TT, Yoneyama A, Maruyama H, Takeda T. Visualization Ability of Phase-Contrast Synchrotron-Based X-Ray Imaging Using an X-Ray Interferometer in Soft Tissue Tumors. Technol Cancer Res Treat 2021; 20:15330338211010121. [PMID: 33896273 PMCID: PMC8085371 DOI: 10.1177/15330338211010121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Phase-contrast synchrotron-based X-ray imaging using an X-ray interferometer provides high sensitivity and high spatial resolution, and it has the ability to depict the fine morphological structures of biological soft tissues, including tumors. In this study, we quantitatively compared phase-contrast synchrotron-based X-ray computed tomography images and images of histopathological hematoxylin-eosin-stained sections of spontaneously occurring rat testicular tumors that contained different types of cells. The absolute densities measured on the phase-contrast synchrotron-based X-ray computed tomography images correlated well with the densities of the nuclear chromatin in the histological images, thereby demonstrating the ability of phase-contrast synchrotron-based X-ray imaging using an X-ray interferometer to reliably identify the characteristics of cancer cells within solid soft tissue tumors. In addition, 3-dimensional synchrotron-based phase-contrast X-ray computed tomography enables screening for different structures within tumors, such as solid, cystic, and fibrous tissues, and blood clots, from any direction and with a spatial resolution down to 26 μm. Thus, phase-contrast synchrotron-based X-ray imaging using an X-ray interferometer shows potential for being useful in preclinical cancer research by providing the ability to depict the characteristics of tumor cells and by offering 3-dimensional information capabilities.
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Affiliation(s)
- Thet-Thet Lwin
- School of Allied Health Sciences, Kitasato University, Sagamihara, Kanagawa, Japan.,Graduate School of Medical Sciences, Kitasato University, Sagamihara, Kanagawa, Japan
| | | | - Hiroko Maruyama
- School of Allied Health Sciences, Kitasato University, Sagamihara, Kanagawa, Japan.,Graduate School of Medical Sciences, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Tohoru Takeda
- School of Allied Health Sciences, Kitasato University, Sagamihara, Kanagawa, Japan.,Graduate School of Medical Sciences, Kitasato University, Sagamihara, Kanagawa, Japan
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15
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Fidalgo G, Paiva K, Mendes G, Barcellos R, Colaço G, Sena G, Pickler A, Mota CL, Tromba G, Nogueira LP, Braz D, Silva HR, Colaço MV, Barroso RC. Synchrotron microtomography applied to the volumetric analysis of internal structures of Thoropa miliaris tadpoles. Sci Rep 2020; 10:18934. [PMID: 33144603 PMCID: PMC7641268 DOI: 10.1038/s41598-020-75993-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
Amphibians are models for studying applied ecological issues such as habitat loss, pollution, disease, and global climate change due to their sensitivity and vulnerability to changes in the environment. Developmental series of amphibians are informative about their biology, and X-ray based 3D reconstruction holds promise for quantifying morphological changes during growth—some with a direct impact on the possibility of an experimental investigation on several of the ecological topics listed above. However, 3D resolution and discrimination of their soft tissues have been difficult with traditional X-ray computed tomography, without time-consuming contrast staining. Tomographic data were initially performed (pre-processing and reconstruction) using the open-source software tool SYRMEP Tomo Project. Data processing and analysis of the reconstructed tomography volumes were conducted using the segmentation semi-automatic settings of the software Avizo Fire 8, which provide information about each investigated tissues, organs or bone elements. Hence, volumetric analyses were carried out to quantify the development of structures in different tadpole developmental stages. Our work shows that synchrotron X-ray microtomography using phase-contrast mode resolves the edges of the internal tissues (as well as overall tadpole morphology), facilitating the segmentation of the investigated tissues. Reconstruction algorithms and segmentation software played an important role in the qualitative and quantitative analysis of each target structure of the Thoropa miliaris tadpole at different stages of development, providing information on volume, shape and length. The use of the synchrotron X-ray microtomography setup of the SYRMEP beamline of Elettra Synchrotron, in phase-contrast mode, allows access to volumetric data for bone formation, eye development, nervous system and notochordal changes during the development (ontogeny) of tadpoles of a cycloramphid frog Thoropa miliaris. As key elements in the normal development of these and any other frog tadpole, the application of such a comparative ontogenetic study, may hold interest to researchers in experimental and environmental disciplines.
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Affiliation(s)
- G Fidalgo
- Laboratory of Applied Physics to Biomedical Science, State University of Rio de Janeiro, Rio de Janeiro, Brazil.
| | - K Paiva
- Laboratory of Applied Physics to Biomedical Science, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - G Mendes
- Laboratory of Applied Physics to Biomedical Science, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - R Barcellos
- Laboratory of Applied Physics to Biomedical Science, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - G Colaço
- Laboratory of Herpetology, Federal Rural University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - G Sena
- Laboratory of Applied Physics to Biomedical Science, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - A Pickler
- Laboratory of Applied Physics to Biomedical Science, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - C L Mota
- Laboratory of Applied Physics to Biomedical Science, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - G Tromba
- Elettra/Sincrotrone Trieste S.C.P.a., Trieste, Italy
| | - L P Nogueira
- Oral Research Laboratory, Institute of Clinical Dentistry, University of Oslo, Oslo, Norway
| | - D Braz
- Nuclear Engineering Program/COPPE, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - H R Silva
- Laboratory of Herpetology, Federal Rural University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - M V Colaço
- Laboratory of Applied Physics to Biomedical Science, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - R C Barroso
- Laboratory of Applied Physics to Biomedical Science, State University of Rio de Janeiro, Rio de Janeiro, Brazil
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16
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Zhao Y, Ji D, Li Y, Zhao X, Lv W, Xin X, Han S, Hu C. Three-dimensional visualization of microvasculature from few-projection data using a novel CT reconstruction algorithm for propagation-based X-ray phase-contrast imaging. BIOMEDICAL OPTICS EXPRESS 2020; 11:364-387. [PMID: 32010522 PMCID: PMC6968748 DOI: 10.1364/boe.380084] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/29/2019] [Accepted: 12/12/2019] [Indexed: 05/23/2023]
Abstract
Propagation-based X-ray phase-contrast imaging (PBI) is a powerful nondestructive imaging technique that can reveal the internal detailed structures in weakly absorbing samples. Extending PBI to CT (PBCT) enables high-resolution and high-contrast 3D visualization of microvasculature, which can be used for the understanding, diagnosis and therapy of diseases involving vasculopathy, such as cardiovascular disease, stroke and tumor. However, the long scan time for PBCT impedes its wider use in biomedical and preclinical microvascular studies. To address this issue, a novel CT reconstruction algorithm for PBCT is presented that aims at shortening the scan time for microvascular samples by reducing the number of projections while maintaining the high quality of reconstructed images. The proposed algorithm combines the filtered backprojection method into the iterative reconstruction framework, and a weighted guided image filtering approach (WGIF) is utilized to optimize the intermediate reconstructed images. Notably, the homogeneity assumption on the microvasculature sample is adopted as prior knowledge, and therefore, a prior image of microvasculature structures can be acquired by a k-means clustering approach. Then, the prior image is used as the guided image in the WGIF procedure to effectively suppress streaking artifacts and preserve microvasculature structures. To evaluate the effectiveness and capability of the proposed algorithm, simulation experiments on 3D microvasculature numerical phantom and real experiments with CT reconstruction on the microvasculature sample are performed. The results demonstrate that the proposed algorithm can, under noise-free and noisy conditions, significantly reduce the artifacts and effectively preserve the microvasculature structures on the reconstructed images and thus enables it to be used for clear and accurate 3D visualization of microvasculature from few-projection data. Therefore, for 3D visualization of microvasculature, the proposed algorithm can be considered an effective approach for reducing the scan time required by PBCT.
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Affiliation(s)
- Yuqing Zhao
- School of Biomedical Engineering and
Technology, Tianjin Medical University, Tianjin 300070, China
| | - Dongjiang Ji
- The School of Science, Tianjin University
of Technology and Education, Tianjin 300222, China
| | - Yimin Li
- School of Biomedical Engineering and
Technology, Tianjin Medical University, Tianjin 300070, China
| | - Xinyan Zhao
- Liver Research Center, Beijing Friendship
Hospital, Capital Medical University, Beijing 100050, China
| | - Wenjuan Lv
- School of Biomedical Engineering and
Technology, Tianjin Medical University, Tianjin 300070, China
| | - Xiaohong Xin
- School of Biomedical Engineering and
Technology, Tianjin Medical University, Tianjin 300070, China
| | - Shuo Han
- School of Biomedical Engineering and
Technology, Tianjin Medical University, Tianjin 300070, China
| | - Chunhong Hu
- School of Biomedical Engineering and
Technology, Tianjin Medical University, Tianjin 300070, China
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17
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Tesařová M, Heude E, Comai G, Zikmund T, Kaucká M, Adameyko I, Tajbakhsh S, Kaiser J. An interactive and intuitive visualisation method for X-ray computed tomography data of biological samples in 3D Portable Document Format. Sci Rep 2019; 9:14896. [PMID: 31624273 PMCID: PMC6797759 DOI: 10.1038/s41598-019-51180-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/25/2019] [Indexed: 12/14/2022] Open
Abstract
3D imaging approaches based on X-ray microcomputed tomography (microCT) have become increasingly accessible with advancements in methods, instruments and expertise. The synergy of material and life sciences has impacted biomedical research by proposing new tools for investigation. However, data sharing remains challenging as microCT files are usually in the range of gigabytes and require specific and expensive software for rendering and interpretation. Here, we provide an advanced method for visualisation and interpretation of microCT data with small file formats, readable on all operating systems, using freely available Portable Document Format (PDF) software. Our method is based on the conversion of volumetric data into interactive 3D PDF, allowing rotation, movement, magnification and setting modifications of objects, thus providing an intuitive approach to analyse structures in a 3D context. We describe the complete pipeline from data acquisition, data processing and compression, to 3D PDF formatting on an example of craniofacial anatomical morphology in the mouse embryo. Our procedure is widely applicable in biological research and can be used as a framework to analyse volumetric data from any research field relying on 3D rendering and CT-biomedical imaging.
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Affiliation(s)
- Markéta Tesařová
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Eglantine Heude
- Department Adaptation du Vivant, Museum national d'Histoire naturelle, CNRS UMR 7221, Paris, France.,Department of Developmental and Stem Cell Biology, Stem Cells and Development Unit, Institut Pasteur, Paris, France.,CNRS UMR, 3738, Paris, France
| | - Glenda Comai
- Department of Developmental and Stem Cell Biology, Stem Cells and Development Unit, Institut Pasteur, Paris, France.,CNRS UMR, 3738, Paris, France
| | - Tomáš Zikmund
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Markéta Kaucká
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden.,Department of Molecular Neurosciences, Medical University of Vienna, Vienna, Austria
| | - Igor Adameyko
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, Sweden.,Department of Molecular Neurosciences, Medical University of Vienna, Vienna, Austria
| | - Shahragim Tajbakhsh
- Department of Developmental and Stem Cell Biology, Stem Cells and Development Unit, Institut Pasteur, Paris, France.,CNRS UMR, 3738, Paris, France
| | - Jozef Kaiser
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic.
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18
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Hellerhoff K, Birnbacher L, Sztrókay-Gaul A, Grandl S, Auweter S, Willner M, Marschner M, Mayr D, Reiser MF, Pfeiffer F, Herzen J. Assessment of intraductal carcinoma in situ (DCIS) using grating-based X-ray phase-contrast CT at conventional X-ray sources: An experimental ex-vivo study. PLoS One 2019; 14:e0210291. [PMID: 30625220 PMCID: PMC6326478 DOI: 10.1371/journal.pone.0210291] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/08/2018] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The extent of intraductal carcinoma in situ (DCIS) is commonly underestimated due to the discontinuous growth and lack of microcalcifications. Specimen radiography has been established to reduce the rate of re-excision. However, the predictive value for margin assessment with conventional specimen radiography for DCIS is low. In this study we assessed the potential of grating-based phase-contrast computed tomography (GBPC-CT) at conventional X-ray sources for specimen tomography of DCIS containing samples. MATERIALS AND METHODS GBPC-CT was performed on four ex-vivo breast specimens containing DCIS and invasive carcinoma of non-specific type. Phase-contrast and absorption-based datasets were manually matched with corresponding histological slices as the standard of reference. RESULTS Matching of CT images and histology was successful. GBPC-CT showed an improved soft tissue contrast compared to absorption-based images revealing more histological details in the same sections. Non-calcifying DCIS exceeding the invasive tumor could be correlated to areas of dilated bright ducts around the tumor. CONCLUSIONS GBPC-CT imaging at conventional X-ray sources offers improved depiction quality for the imaging of breast tissue samples compared to absorption-based imaging, allows the identification of diagnostically relevant tissue details, and provides full three-dimensional assessment of sample margins.
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MESH Headings
- Breast Neoplasms/diagnostic imaging
- Breast Neoplasms/pathology
- Breast Neoplasms/surgery
- Calcinosis/diagnostic imaging
- Calcinosis/pathology
- Carcinoma, Ductal, Breast/diagnostic imaging
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Intraductal, Noninfiltrating/diagnostic imaging
- Carcinoma, Intraductal, Noninfiltrating/pathology
- Carcinoma, Intraductal, Noninfiltrating/surgery
- Female
- Humans
- In Vitro Techniques
- Mammography/methods
- Microscopy, Phase-Contrast/methods
- Prospective Studies
- Tomography, X-Ray Computed/methods
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Affiliation(s)
- Karin Hellerhoff
- Institute for Clinical Radiology, Ludwig-Maximilians-University Hospital Munich, Munich, Germany
- Abteilung für Diagnostische Radiologie, Rotkreuzklinikum München, Munich, Germany
| | - Lorenz Birnbacher
- Chair of Biomedical Physics, Department of Physics & Munich School of BioEngineering, Technical University of Munich, Garching, Germany
- * E-mail:
| | - Anikó Sztrókay-Gaul
- Institute for Clinical Radiology, Ludwig-Maximilians-University Hospital Munich, Munich, Germany
- Abteilung für Diagnostische Radiologie, Rotkreuzklinikum München, Munich, Germany
| | - Susanne Grandl
- Institute for Clinical Radiology, Ludwig-Maximilians-University Hospital Munich, Munich, Germany
- Abteilung für Diagnostische Radiologie, Rotkreuzklinikum München, Munich, Germany
| | - Sigrid Auweter
- Institute for Clinical Radiology, Ludwig-Maximilians-University Hospital Munich, Munich, Germany
| | - Marian Willner
- Chair of Biomedical Physics, Department of Physics & Munich School of BioEngineering, Technical University of Munich, Garching, Germany
| | - Mathias Marschner
- Chair of Biomedical Physics, Department of Physics & Munich School of BioEngineering, Technical University of Munich, Garching, Germany
| | - Doris Mayr
- Institute of Pathology, Ludwig-Maximilians-University Hospital Munich, Munich, Germany
| | - Maximilian F. Reiser
- Institute for Clinical Radiology, Ludwig-Maximilians-University Hospital Munich, Munich, Germany
| | - Franz Pfeiffer
- Chair of Biomedical Physics, Department of Physics & Munich School of BioEngineering, Technical University of Munich, Garching, Germany
- Institute of Diagnostic and Interventional Radiology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Julia Herzen
- Chair of Biomedical Physics, Department of Physics & Munich School of BioEngineering, Technical University of Munich, Garching, Germany
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