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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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2
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Lioliou G, Buchanan I, Astolfo A, Endrizzi M, Bate D, Hagen CK, Olivo A. Framework to optimize fixed-length micro-CT systems for propagation-based phase-contrast imaging. OPTICS EXPRESS 2024; 32:4839-4856. [PMID: 38439226 DOI: 10.1364/oe.510317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/11/2024] [Indexed: 03/06/2024]
Abstract
A laboratory X-ray imaging system with a setup that closely resembles commercial micro-CT systems with a fixed source-to-detector distance of ∼90 cm is investigated for single distance propagation-based phase-contrast imaging and computed tomography (CT). The system had a constant source-to-detector distance, and the sample positions were optimized. Initially, a PTFE wire was imaged, both in 2D and 3D, to characterize fringe contrast and spatial resolution for different X-ray source settings and source-to-sample distances. The results were compared to calculated values based on theoretical models and to simulated (wave-optics based) results, with good agreement being found. The optimization of the imaging system is discussed. CT scans of two biological samples, a tissue-engineered esophageal scaffold and a rat heart, were then acquired at the optimum parameters, demonstrating that significant image quality improvements can be obtained with widely available components placed inside fixed-length cabinets through proper optimization of propagation-based phase-contrast.
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3
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Leatham TA, Paganin DM, Morgan KS. X-ray phase and dark-field computed tomography without optical elements. OPTICS EXPRESS 2024; 32:4588-4602. [PMID: 38297656 DOI: 10.1364/oe.509604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/07/2023] [Indexed: 02/02/2024]
Abstract
X-ray diffusive dark-field imaging, which allows spatially unresolved microstructure to be mapped across a sample, is an increasingly popular tool in an array of settings. Here, we present a new algorithm for phase and dark-field computed tomography based on the x-ray Fokker-Planck equation. Needing only a coherent x-ray source, sample, and detector, our propagation-based algorithm can map the sample density and dark-field/diffusion properties of the sample in 3D. Importantly, incorporating dark-field information in the density reconstruction process enables a higher spatial resolution reconstruction than possible with previous propagation-based approaches. Two sample exposures at each projection angle are sufficient for the successful reconstruction of both the sample density and dark-field Fokker-Planck diffusion coefficients. We anticipate that the proposed algorithm may be of benefit in biomedical imaging and industrial settings.
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Häggmark I, Hoshino M, Uesugi K, Sasaki T. X-ray phase contrast reveals soft tissue and shell growth lines in mollusks. Commun Biol 2024; 7:17. [PMID: 38172227 PMCID: PMC10764734 DOI: 10.1038/s42003-023-05457-y] [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: 03/22/2023] [Accepted: 10/13/2023] [Indexed: 01/05/2024] Open
Abstract
High-resolution 3D imaging of species with exoskeletons such as shell-bearing mollusks typically involves destructive steps. Nondestructive alternatives are desirable since samples can be rare and valuable, and destructive steps are time-consuming and may distort the tissue. Here, we show for the first time that propagation-based phase-contrast X-ray imaging can significantly increase contrast in mollusks with intact shells. By using the recently upgraded monochromator at the SPring-8 BL20B2 synchrotron beamline, we imaged six species of mollusks, showing that X-ray phase contrast enhances soft-tissue contrast. Features that are almost invisible in conventional attenuation-based micro-computed tomography (micro-CT) are clearly reproduced with phase-contrast imaging under the same scan conditions. Furthermore, this method can reveal features such as growth rings in the shell and differentiate between calcite and aragonite crystal forms. Phase-contrast imaging can thus serve as a compelling alternative when destructive methods are not an option.
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Affiliation(s)
- Ilian Häggmark
- The University Museum, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Masato Hoshino
- Japan Synchrotron Radiation Research Institute (JASRI/SPring-8), 1-1-1 Kouto, Sayo, Hyogo, 679-5198, Japan
| | - Kentaro Uesugi
- Japan Synchrotron Radiation Research Institute (JASRI/SPring-8), 1-1-1 Kouto, Sayo, Hyogo, 679-5198, Japan
| | - Takenori Sasaki
- The University Museum, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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5
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Østergaard M, Naver EB, Kaestner A, Willendrup PK, Brüel A, Sørensen HO, Thomsen JS, Schmidt S, Poulsen HF, Theil Kuhn L, Birkedal H. Polychromatic neutron phase-contrast imaging of weakly absorbing samples enabled by phase retrieval. J Appl Crystallogr 2023; 56:673-682. [PMID: 37284268 PMCID: PMC10241042 DOI: 10.1107/s1600576723003011] [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: 09/30/2022] [Accepted: 04/01/2023] [Indexed: 06/08/2023] Open
Abstract
The use of a phase-retrieval technique for propagation-based phase-contrast neutron imaging with a polychromatic beam is demonstrated. This enables imaging of samples with low absorption contrast and/or improving the signal-to-noise ratio to facilitate e.g. time-resolved measurements. A metal sample, designed to be close to a phase pure object, and a bone sample with canals partially filled with D2O were used for demonstrating the technique. These samples were imaged with a polychromatic neutron beam followed by phase retrieval. For both samples the signal-to-noise ratios were significantly improved and, in the case of the bone sample, the phase retrieval allowed for separation of bone and D2O, which is important for example for in situ flow experiments. The use of deuteration contrast avoids the use of chemical contrast enhancement and makes neutron imaging an interesting complementary method to X-ray imaging of bone.
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Affiliation(s)
- Maja Østergaard
- Department of Chemistry and iNANO, Aarhus University, Gustav Wieds Vej 14, Aarhus, Denmark
| | - Estrid Buhl Naver
- Department of Energy Conversion and Storage, Technical University of Denmark, Fysikvej 310, Kongens Lyngby, Denmark
| | - Anders Kaestner
- Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institute, Villigen, Switzerland
| | - Peter K. Willendrup
- Department of Physics, Technical University of Denmark, Fysikvej 307, Kongens Lyngby, Denmark
- European Spallation Source ERIC, PO Box 176, Lund, Sweden
| | - Annemarie Brüel
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Aarhus, Denmark
| | - Henning Osholm Sørensen
- Department of Physics, Technical University of Denmark, Fysikvej 307, Kongens Lyngby, Denmark
- Xnovo Technology ApS, Galoche Alle 15, 1, Køge, Denmark
| | | | - Søren Schmidt
- European Spallation Source ERIC, PO Box 176, Lund, Sweden
| | - Henning Friis Poulsen
- Department of Physics, Technical University of Denmark, Fysikvej 307, Kongens Lyngby, Denmark
| | - Luise Theil Kuhn
- Department of Energy Conversion and Storage, Technical University of Denmark, Fysikvej 310, Kongens Lyngby, Denmark
| | - Henrik Birkedal
- Department of Chemistry and iNANO, Aarhus University, Gustav Wieds Vej 14, Aarhus, Denmark
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6
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Thompson DA, Nesterets YI, Pavlov KM, Gureyev TE. Three-dimensional contrast-transfer-function approach in phase-contrast tomography. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2023; 40:1249-1259. [PMID: 37706779 DOI: 10.1364/josaa.494293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 09/15/2023]
Abstract
A new method is developed for 3D reconstruction of multimaterial objects using propagation-based x-ray phase-contrast tomography (PB-CT) with phase retrieval via contrast-transfer-function (CTF) formalism. The approach differs from conventional PB-CT algorithms, which apply phase retrieval to individual 2D projections. Instead, this method involves performing phase retrieval to the CT-reconstructed volume in 3D. The CTF formalism is further extended to the cases of partially coherent illumination and strongly absorbing samples. Simulated results demonstrate that the proposed post-reconstruction CTF method provides fast and stable phase retrieval, producing results equivalent to conventional pre-reconstruction 2D CTF phase retrieval. Moreover, it is shown that application can be highly localized to isolated objects of interest, without a significant loss of quality, thus leading to increased computational efficiency. Combined with the extended validity of the CTF to greater propagation distances, this method provides additional advantages over approaches based on the transport-of-intensity equation.
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7
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Alloo SJ, Morgan KS, Paganin DM, Pavlov KM. Multimodal intrinsic speckle-tracking (MIST) to extract images of rapidly-varying diffuse X-ray dark-field. Sci Rep 2023; 13:5424. [PMID: 37012270 PMCID: PMC10070351 DOI: 10.1038/s41598-023-31574-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/14/2023] [Indexed: 04/05/2023] Open
Abstract
Speckle-based phase-contrast X-ray imaging (SB-PCXI) can reconstruct high-resolution images of weakly-attenuating materials that would otherwise be indistinguishable in conventional attenuation-based X-ray imaging. The experimental setup of SB-PCXI requires only a sufficiently coherent X-ray source and spatially random mask, positioned between the source and detector. The technique can extract sample information at length scales smaller than the imaging system's spatial resolution; this enables multimodal signal reconstruction. "Multimodal Intrinsic Speckle-Tracking" (MIST) is a rapid and deterministic formalism derived from the paraxial-optics form of the Fokker-Planck equation. MIST simultaneously extracts attenuation, refraction, and small-angle scattering (diffusive dark-field) signals from a sample and is more computationally efficient compared to alternative speckle-tracking approaches. Hitherto, variants of MIST have assumed the diffusive dark-field signal to be spatially slowly varying. Although successful, these approaches have been unable to well-describe unresolved sample microstructure whose statistical form is not spatially slowly varying. Here, we extend the MIST formalism such that this restriction is removed, in terms of a sample's rotationally-isotropic diffusive dark-field signal. We reconstruct multimodal signals of two samples, each with distinct X-ray attenuation and scattering properties. The reconstructed diffusive dark-field signals have superior image quality-as measured by the naturalness image quality evaluator, signal-to-noise ratio, and azimuthally averaged power-spectrum-compared to our previous approaches which assume the diffusive dark-field to be a slowly varying function of transverse position. Our generalisation may assist increased adoption of SB-PCXI in applications such as engineering and biomedical disciplines, forestry, and palaeontology, and is anticipated to aid the development of speckle-based diffusive dark-field tensor tomography.
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Affiliation(s)
- Samantha J Alloo
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand.
| | - Kaye S Morgan
- School of Physics and Astronomy, Monash University, Clayton, VIC, Australia
| | - David M Paganin
- School of Physics and Astronomy, Monash University, Clayton, VIC, Australia
| | - Konstantin M Pavlov
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand
- School of Physics and Astronomy, Monash University, Clayton, VIC, Australia
- School of Science and Technology, University of New England, Armidale, NSW, Australia
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8
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Deshpande R, Avachat A, Brooks FJ, Anastasio MA. Investigating the robustness of a deep learning-based method for quantitative phase retrieval from propagation-based x-ray phase contrast measurements under laboratory conditions. Phys Med Biol 2023; 68:10.1088/1361-6560/acc2aa. [PMID: 36889005 PMCID: PMC10405978 DOI: 10.1088/1361-6560/acc2aa] [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: 10/18/2022] [Accepted: 03/08/2023] [Indexed: 03/10/2023]
Abstract
Objective.Quantitative phase retrieval (QPR) in propagation-based x-ray phase contrast imaging of heterogeneous and structurally complicated objects is challenging under laboratory conditions due to partial spatial coherence and polychromaticity. A deep learning-based method (DLBM) provides a nonlinear approach to this problem while not being constrained by restrictive assumptions about object properties and beam coherence. The objective of this work is to assess a DLBM for its applicability under practical scenarios by evaluating its robustness and generalizability under typical experimental variations.Approach.Towards this end, an end-to-end DLBM was employed for QPR under laboratory conditions and its robustness was investigated across various system and object conditions. The robustness of the method was tested via varying propagation distances and its generalizability with respect to object structure and experimental data was also tested.Main results.Although the end-to-end DLBM was stable under the studied variations, its successful deployment was found to be affected by choices pertaining to data pre-processing, network training considerations and system modeling.Significance.To our knowledge, we demonstrated for the first time, the potential applicability of an end-to-end learning-based QPR method, trained on simulated data, to experimental propagation-based x-ray phase contrast measurements acquired under laboratory conditions with a commercial x-ray source and a conventional detector. We considered conditions of polychromaticity, partial spatial coherence, and high noise levels, typical to laboratory conditions. This work further explored the robustness of this method to practical variations in propagation distances and object structure with the goal of assessing its potential for experimental use. Such an exploration of any DLBM (irrespective of its network architecture) before practical deployment provides an understanding of its potential behavior under experimental settings.
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Affiliation(s)
- Rucha Deshpande
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, United States of America
| | - Ashish Avachat
- Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh, PA, United States of America
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, United States of America
| | - Frank J Brooks
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, United States of America
| | - Mark A Anastasio
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, United States of America
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9
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Vommaro ML, Donato S, Lo LK, Brandmayr P, Giglio A. Anatomical study of the red flour beetle using synchrotron radiation X-ray phase-contrast micro-tomography. J Anat 2023; 242:510-524. [PMID: 36417320 PMCID: PMC9919503 DOI: 10.1111/joa.13796] [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: 07/31/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 11/24/2022] Open
Abstract
Synchrotron X-ray phase-contrast microtomography (SR-PhC micro-CT) is well established, fast and non-destructive imaging technique for data acquisition that is currently being used to obtain new insights into insect anatomy and function in physiological, morphological and phylogenetic studies. In this study, we described in situ the internal organs of the red flour beetle Tribolium castaneum Herbst 1797, a widespread pest of cereals and stored food causing serious damage to the human economy. Two-dimensional virtual sections and volumetric reconstructions of the nervous, alimentary and reproductive systems were carried out in both sexes. The results provided a comprehensive overview of the morphological characteristics of this species, such as the different maturation stages of ovarioles and the realistic location, size and shape of internal organs. Given the great interest in this model species in experimental biology and forensic entomology, complete knowledge of the general anatomy is required for future functional applications in pest control and experimental studies. In addition, this study confirms SR-PhC micro-CT as a powerful and innovative tool in entomology, particularly suitable for small species and chitinized structures that are difficult to analyse using conventional dissection and histological methods.
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Affiliation(s)
- Maria Luigia Vommaro
- Department of Biology, Ecology and Earth Science, University of Calabria, Cosenza, Italy
| | - Sandro Donato
- Department of Physics, University of Calabria, Cosenza, Italy.,Division of Frascati, Istituto Nazionale di Fisica Nucleare, Rome, Italy
| | - Lai Ka Lo
- Animal Evolutionary Ecology Group, Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Pietro Brandmayr
- Department of Biology, Ecology and Earth Science, University of Calabria, Cosenza, Italy
| | - Anita Giglio
- Department of Biology, Ecology and Earth Science, University of Calabria, Cosenza, Italy
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10
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Precise phase retrieval for propagation-based images using discrete mathematics. Sci Rep 2022; 12:18469. [PMID: 36323686 PMCID: PMC9630448 DOI: 10.1038/s41598-022-19940-9] [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: 04/05/2022] [Accepted: 09/06/2022] [Indexed: 11/17/2022] Open
Abstract
The ill-posed problem of phase retrieval in optics, using one or more intensity measurements, has a multitude of applications using electromagnetic or matter waves. Many phase retrieval algorithms are computed on pixel arrays using discrete Fourier transforms due to their high computational efficiency. However, the mathematics underpinning these algorithms is typically formulated using continuous mathematics, which can result in a loss of spatial resolution in the reconstructed images. Herein we investigate how phase retrieval algorithms for propagation-based phase-contrast X-ray imaging can be rederived using discrete mathematics and result in more precise retrieval for single- and multi-material objects and for spectral image decomposition. We validate this theory through experimental measurements of spatial resolution using computed tomography (CT) reconstructions of plastic phantoms and biological tissues, using detectors with a range of imaging system point spread functions (PSFs). We demonstrate that if the PSF substantially suppresses high spatial frequencies, the potential improvement from utilising the discrete derivation is limited. However, with detectors characterised by a single pixel PSF (e.g. direct, photon-counting X-ray detectors), a significant improvement in spatial resolution can be obtained, demonstrated here at up to 17%.
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11
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Hodge DS, Leong AFT, Pandolfi S, Kurzer-Ogul K, Montgomery DS, Aluie H, Bolme C, Carver T, Cunningham E, Curry CB, Dayton M, Decker FJ, Galtier E, Hart P, Khaghani D, Ja Lee H, Li K, Liu Y, Ramos K, Shang J, Vetter S, Nagler B, Sandberg RL, Gleason AE. Multi-frame, ultrafast, x-ray microscope for imaging shockwave dynamics. OPTICS EXPRESS 2022; 30:38405-38422. [PMID: 36258406 DOI: 10.1364/oe.472275] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Inertial confinement fusion (ICF) holds increasing promise as a potential source of abundant, clean energy, but has been impeded by defects such as micro-voids in the ablator layer of the fuel capsules. It is critical to understand how these micro-voids interact with the laser-driven shock waves that compress the fuel pellet. At the Matter in Extreme Conditions (MEC) instrument at the Linac Coherent Light Source (LCLS), we utilized an x-ray pulse train with ns separation, an x-ray microscope, and an ultrafast x-ray imaging (UXI) detector to image shock wave interactions with micro-voids. To minimize the high- and low-frequency variations of the captured images, we incorporated principal component analysis (PCA) and image alignment for flat-field correction. After applying these techniques we generated phase and attenuation maps from a 2D hydrodynamic radiation code (xRAGE), which were used to simulate XPCI images that we qualitatively compare with experimental images, providing a one-to-one comparison for benchmarking material performance. Moreover, we implement a transport-of-intensity (TIE) based method to obtain the average projected mass density (areal density) of our experimental images, yielding insight into how defect-bearing ablator materials alter microstructural feature evolution, material compression, and shock wave propagation on ICF-relevant time scales.
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12
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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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13
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Donato S, Brombal L, Arana Peña LM, Arfelli F, Contillo A, Delogu P, Di Lillo F, Di Trapani V, Fanti V, Longo R, Oliva P, Rigon L, Stori L, Tromba G, Golosio B. Optimization of a customized simultaneous algebraic reconstruction technique algorithm for phase-contrast breast computed tomography. Phys Med Biol 2022; 67. [DOI: 10.1088/1361-6560/ac65d4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 04/08/2022] [Indexed: 12/22/2022]
Abstract
Abstract
Objective. To introduce the optimization of a customized GPU-based simultaneous algebraic reconstruction technique (cSART) in the field of phase-contrast breast computed tomography (bCT). The presented algorithm features a 3D bilateral regularization filter that can be tuned to yield optimal performance for clinical image visualization and tissues segmentation. Approach. Acquisitions of a dedicated test object and a breast specimen were performed at Elettra, the Italian synchrotron radiation (SR) facility (Trieste, Italy) using a large area CdTe single-photon counting detector. Tomographic images were obtained at 5 mGy of mean glandular dose, with a 32 keV monochromatic x-ray beam in the free-space propagation mode. Three independent algorithms parameters were optimized by using contrast-to-noise ratio (CNR), spatial resolution, and noise texture metrics. The results obtained with the cSART algorithm were compared with conventional SART and filtered back projection (FBP) reconstructions. Image segmentation was performed both with gray scale-based and supervised machine-learning approaches. Main results. Compared to conventional FBP reconstructions, results indicate that the proposed algorithm can yield images with a higher CNR (by 35% or more), retaining a high spatial resolution while preserving their textural properties. Alternatively, at the cost of an increased image ‘patchiness’, the cSART can be tuned to achieve a high-quality tissue segmentation, suggesting the possibility of performing an accurate glandularity estimation potentially of use in the realization of realistic 3D breast models starting from low radiation dose images. Significance. The study indicates that dedicated iterative reconstruction techniques could provide significant advantages in phase-contrast bCT imaging. The proposed algorithm offers great flexibility in terms of image reconstruction optimization, either toward diagnostic evaluation or image segmentation.
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14
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Alloo SJ, Paganin DM, Morgan KS, Gureyev TE, Mayo SC, Mohammadi S, Lockie D, Menk RH, Arfelli F, Zanconati F, Tromba G, Pavlov KM. Tomographic phase and attenuation extraction for a sample composed of unknown materials using x-ray propagation-based phase-contrast imaging. OPTICS LETTERS 2022; 47:1945-1948. [PMID: 35427307 DOI: 10.1364/ol.445802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
Propagation-based phase-contrast x-ray imaging (PB-PCXI) generates image contrast by utilizing sample-imposed phase-shifts. This has proven useful when imaging weakly attenuating samples, as conventional attenuation-based imaging does not always provide adequate contrast. We present a PB-PCXI algorithm capable of extracting the x-ray attenuation β and refraction δ, components of the complex refractive index of distinct materials within an unknown sample. The method involves curve fitting an error-function-based model to a phase-retrieved interface in a PB-PCXI tomographic reconstruction, which is obtained when Paganin-type phase retrieval is applied with incorrect values of δ and β. The fit parameters can then be used to calculate true δ and β values for composite materials. This approach requires no a priori sample information, making it broadly applicable. Our PB-PCXI reconstruction is single-distance, requiring only one exposure per tomographic angle, which is important for radiosensitive samples. We apply this approach to a breast-tissue sample, recovering the refraction component δ, with 0.6-2.4% accuracy compared with theoretical values.
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15
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Wu Y, Zhang L, Guo S, Zhang L, Gao F, Jia M, Zhou Z. Enhanced phase retrieval via deep concatenation networks for in-line X-ray phase contrast imaging. Phys Med 2022; 95:41-49. [DOI: 10.1016/j.ejmp.2021.12.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/19/2021] [Accepted: 12/28/2021] [Indexed: 12/18/2022] Open
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16
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Ghani MU, Yan A, Fajardo LL, Wu X, Liu H. Dual-energy phase retrieval algorithm for inline phase sensitive x-ray imaging system. OPTICS EXPRESS 2021; 29:26538-26552. [PMID: 34615087 PMCID: PMC8687111 DOI: 10.1364/oe.431623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/16/2021] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
Phase retrieval is vital for quantitative x-ray phase contrast imaging. This work presents an iterative method to simultaneously retrieve the x-ray absorption and phase images from a single x-ray exposure. The proposed approach uses the photon-counting detectors' energy-resolving capability in providing multiple spectrally resolved phase contrast images from a single x-ray exposure. The retrieval method is derived, presented, and experimentally tested with a multi-material phantom in an inline phase contrast imaging setup. By separating the contributions of photoelectric absorption and Compton scattering to the attenuation, the authors divide the phase contrast image into two portions, the attenuation map arises from photoelectric absorption and a pseudo phase contrast image generated by electron density. This way one can apply the Phase Attenuation Dualiby (PAD) algorithm and Fresnel propagation for the iteration. The retrieval results from the experimental images show that this iterative method is fast, accurate, robust against noise, and thus yields noticeable enhancement in contrast to noise ratios.
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Affiliation(s)
- Muhammad U. Ghani
- Advanced Medical Imaging Center and School of Electrical and Computer Engineering, University of Oklahoma, Norman, OK 73019, USA
| | - Aimin Yan
- Advanced Medical Imaging Center and School of Electrical and Computer Engineering, University of Oklahoma, Norman, OK 73019, USA
| | - Laurie. L. Fajardo
- Department of Radiology and Imaging Sciences, University of Utah, Salt Lake City, UT 84132, USA
| | - Xizeng Wu
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL 35249, USA
| | - Hong Liu
- Advanced Medical Imaging Center and School of Electrical and Computer Engineering, University of Oklahoma, Norman, OK 73019, USA
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17
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Olivo A. Edge-illumination x-ray phase-contrast imaging. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:363002. [PMID: 34167096 PMCID: PMC8276004 DOI: 10.1088/1361-648x/ac0e6e] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 06/07/2021] [Accepted: 06/24/2021] [Indexed: 05/08/2023]
Abstract
Although early demonstration dates back to the mid-sixties, x-ray phase-contrast imaging (XPCI) became hugely popular in the mid-90s, thanks to the advent of 3rd generation synchrotron facilities. Its ability to reveal object features that had so far been considered invisible to x-rays immediately suggested great potential for applications across the life and the physical sciences, and an increasing number of groups worldwide started experimenting with it. At that time, it looked like a synchrotron facility was strictly necessary to perform XPCI with some degree of efficiency-the only alternative being micro-focal sources, the limited flux of which imposed excessively long exposure times. However, new approaches emerged in the mid-00s that overcame this limitation, and allowed XPCI implementations with conventional, non-micro-focal x-ray sources. One of these approaches showing particular promise for 'real-world' applications is edge-illumination XPCI: this article describes the key steps in its evolution in the context of contemporary developments in XPCI research, and presents its current state-of-the-art, especially in terms of transition towards practical applications.
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Affiliation(s)
- Alessandro Olivo
- Department of Medical Physics and Biomedical Engineering, UCL, London, United Kingdom
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18
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Parodi B, Sanna A, Cedola A, Uccelli A, Kerlero de Rosbo N. Hydroxycarboxylic Acid Receptor 2, a Pleiotropically Linked Receptor for the Multiple Sclerosis Drug, Monomethyl Fumarate. Possible Implications for the Inflammatory Response. Front Immunol 2021; 12:655212. [PMID: 34084164 PMCID: PMC8167049 DOI: 10.3389/fimmu.2021.655212] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/06/2021] [Indexed: 12/12/2022] Open
Abstract
Monomethyl fumarate (MMF), metabolite of dimethyl fumarate (DMF), an immunosuppressive drug approved for the treatment of multiple sclerosis (MS), is a potent agonist for hydroxycarboxylic acid receptor 2 (HCAR2), eliciting signals that dampen cell activation or lead to inflammation such as the skin flushing reaction that is one of the main side effects of the treatment, together with gastrointestinal inflammation. Our aim is to further understand the molecular basis underlying these differential effects of the drug. We have used wild-type and HCAR2 knock-out mice to investigate, in vitro and ex vivo under steady-state and pathological conditions, the HCAR2-mediated signaling pathways activated by MMF in dendritic cells (DC), which promote differentiation of T cells, and in intestinal epithelial cells (IEC) where activation of a pro-inflammatory pathway, such as the cyclooxygenase-2 pathway involved in skin flushing, could underlie gastrointestinal side effects of the drug. To understand how DMF treatment might impact on gut inflammation induced by experimental autoimmune encephalomyelitis (EAE), the animal model for MS, we have used 3D X-ray phase contrast tomography and flow cytometry to monitor possible intestinal alterations at morphological and immunological levels, respectively. We show that HCAR2 is a pleiotropically linked receptor for MMF, mediating activation of different pathways leading to different outcomes in different cell types, depending on experimental in-vitro and in-vivo conditions. In the small intestine of EAE-affected mice, DMF treatment affected migration of tolerogenic DC from lamina propria to mesenteric lymph nodes, and/or reverted their profile to pro-inflammatory, probably as a result of reduced expression of aldehyde dehydrogenase and transforming growth factor beta as well as the inflammatory environment. Nevertheless, DMF treatment did not amplify the morphological alterations induced by EAE. On the basis of our further understanding of MMF signaling through HCAR2, we suggest that the pleiotropic signaling of fumarate via HCAR2 should be addressed for its pharmaceutical relevance in devising new lead compounds with reduced inflammatory side effects.
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Affiliation(s)
- Benedetta Parodi
- Neuroimmunology Laboratory, DINOGMI, University of Genoa, Genoa, Italy
| | | | | | - Antonio Uccelli
- Neuroimmunology Laboratory, DINOGMI, University of Genoa, Genoa, Italy.,IRCCS Ospedale Policlinico San Martino, Genoa, Italy
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19
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Levine ZH, Garboczi EJ, Peskin AP, Ekman AA, Mansfield E, Holm JD. X-ray computed tomography using partially coherent Fresnel diffraction with application to an optical fiber. OPTICS EXPRESS 2021; 29:1788-1804. [PMID: 33726385 PMCID: PMC7920526 DOI: 10.1364/oe.414398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 05/17/2023]
Abstract
A reconstruction algorithm for partially coherent x-ray computed tomography (XCT) including Fresnel diffraction is developed and applied to an optical fiber. The algorithm is applicable to a high-resolution tube-based laboratory-scale x-ray tomography instrument. The computing time is only a few times longer than the projective counterpart. The algorithm is used to reconstruct, with projections and diffraction, a tilt series acquired at the micrometer scale of a graded-index optical fiber using maximum likelihood and a Bayesian method based on the work of Bouman and Sauer. The inclusion of Fresnel diffraction removes some reconstruction artifacts and use of a Bayesian prior probability distribution removes others, resulting in a substantially more accurate reconstruction.
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Affiliation(s)
- Zachary H. Levine
- Quantum Metrology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Edward J. Garboczi
- Applied Chemicals and Materials Division, National Institute of Standards and Technology, Boulder, CO 80305, USA
| | - Adele P. Peskin
- Software and Systems Division, National Institute of Standards and Technology, Boulder, CO 80305, USA
| | - Axel A. Ekman
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94158, USA
| | - Elisabeth Mansfield
- Applied Chemicals and Materials Division, National Institute of Standards and Technology, Boulder, CO 80305, USA
| | - Jason D. Holm
- Applied Chemicals and Materials Division, National Institute of Standards and Technology, Boulder, CO 80305, USA
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20
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Chalmers MC, Kitchen MJ, Uesugi K, Falzon G, Quin P, Pavlov KM. Tomographic reconstruction using tilted Laue analyser-based X-ray phase-contrast imaging. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:283-291. [PMID: 33399579 DOI: 10.1107/s1600577520013995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/20/2020] [Indexed: 06/12/2023]
Abstract
Analyser-based phase-contrast imaging (ABPCI) is a highly sensitive phase-contrast imaging method that produces high-contrast images of weakly absorbing materials. However, it is only sensitive to phase gradient components lying in the diffraction plane of the analyser crystal [i.e. in one dimension (1-D)]. In order to accurately account for and measure phase effects produced by the wavefield-sample interaction, ABPCI and other 1-D phase-sensitive methods must achieve 2-D phase gradient sensitivity. An inclined geometry method was applied to a Laue geometry setup for X-ray ABPCI through rotation of the detector and object about the optical axis. This allowed this traditionally 1-D phase-sensitive phase-contrast method to possess 2-D phase gradient sensitivity. Tomographic datasets were acquired over 360° of a multi-material phantom with the detector and sample tilted by 8°. The real and imaginary parts of the refractive index were reconstructed for the phantom.
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Affiliation(s)
- M C Chalmers
- University of Canterbury, 20 Kirkwood Avenue, Upper Riccarton, Christchurch 8041, New Zealand
| | - M J Kitchen
- Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - K Uesugi
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - G Falzon
- College of Science and Engineering, Flinders University, Adelaide, South Australia 5001, Australia
| | - P Quin
- University of New England, Armidale, NSW 2351, Australia
| | - K M Pavlov
- University of Canterbury, 20 Kirkwood Avenue, Upper Riccarton, Christchurch 8041, New Zealand
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21
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Abstract
Nanotechnology has been widely applied to medical interventions for prevention, diagnostics, and therapeutics of diseases, and the application of nanotechnology for medical purposes, which is called as a term "nanomedicine" has received tremendous attention. In particular, the design and development of nanoparticle for biosensors have received a great deal of attention, since those are most impactful area of clinical translation showing potential breakthrough in early diagnosis of diseases such as cancers and infections. For example, the nanoparticles that have intrinsic unique features such as magnetic responsive characteristics or photoluminescence can be utilized for noninvasive visualization of inner body. Drug delivery that makes use of drug-containing nanoparticles as a carrier is another field of study, in which the particulate form nanomedicine is given by parenteral administration for further systemic targeting to pathological tissues. In addition, encapsulation into nanoparticles gives the opportunity to secure the sensitive therapeutic payloads that are readily degraded or deactivated until reached to the target in biological environments, or to provide sufficient solubilization (e.g., to deliver compounds which have physicochemical properties that strongly limit their aqueous solubility and therefore systemic bioavailability). The nanomedicine is further intended to enhance the targeting index such as increased specificity and reduced false binding, thus improve the diagnostic and therapeutic performances. In this chapter, principles of nanomaterials for medicine will be thoroughly covered with applications for imaging-based diagnostics and therapeutics.
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Affiliation(s)
- Jinmyoung Joo
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, South Korea.
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22
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Omoumi FH, Ghani MU, Wong MD, Li Y, Zheng B, Yan A, Jenkins PA, Wu X, Liu H. The Potential of Utilizing Mid-Energy X-Rays for In-Line Phase Sensitive Breast Cancer Imaging. BIOMEDICAL SPECTROSCOPY AND IMAGING 2020; 9:89-102. [PMID: 34141562 PMCID: PMC8208526 DOI: 10.3233/bsi-200204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
OBJECTIVE The objective of this study is to demonstrate the potential of utilizing mid-energy x-rays for in-line phase-sensitive breast cancer imaging by phantom studies. METHODS The midenergy (50-80kV) in-line phase sensitive imaging prototype was used to acquire images of the contrast-detail mammography (CDMAM) phantom, an ACR accreditation phantom, and an acrylic edge phantom. The low-dose mid-energy phase-sensitive images were acquired at 60 kV with a radiation dose of 0.9 mGy, while the high-energy phase-sensitive images were acquired at 90 kV with a radiation dose of 1.2 mGy. The Phase-Attenuation Duality (PAD) principle for soft tissue was used for the phase retrieval. A blind observer study was conducted and paired-sample T-test were performed to compare the mean differences in the two imaging systems. RESULTS The correct detection ratio for the CDMAM phantom for phase-contrast images acquired by the low-dose mid-energy system was 56.91%, whereas images acquired by the high-energy system correctly revealed only 40.97% of discs. The correct detection ratios were 57.88% and 43.41% for phase-retrieved images acquired by the low-dose mid-energy and high-energy imaging systems, respectively. The reading scores for all three groups of objects in the ACR phantom were higher for the mid energy imaging system as compared to the high-energy system for both phase-contrast and phase- retrieved images. The calculated edge enhancement index (EEI) from the acrylic edge phantom image for the mid-energy system was higher than that calculated for the high-energy imaging system. The quantitative analyses showed a higher Contrast to Noise Ratio (CNR) as well as a higher Figure of Merit (FOM) in images acquired by the low-dose mid-energy imaging system. CONCLUSION The PAD based retrieval method can be applied in mid-energy system without remarkably affecting the image quality, and in fact, it improves the lesion detectability with a patient dose saving of 25%.
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Affiliation(s)
- F H Omoumi
- Advanced Medical Imaging Center and School of Electrical and Computer Engineering, The University of Oklahoma, Norman, OK 73019, U.S.A
| | - M U Ghani
- Advanced Medical Imaging Center and School of Electrical and Computer Engineering, The University of Oklahoma, Norman, OK 73019, U.S.A
| | - M D Wong
- Advanced Medical Imaging Center and School of Electrical and Computer Engineering, The University of Oklahoma, Norman, OK 73019, U.S.A
| | - Y Li
- Advanced Medical Imaging Center and School of Electrical and Computer Engineering, The University of Oklahoma, Norman, OK 73019, U.S.A
| | - B Zheng
- Advanced Medical Imaging Center and School of Electrical and Computer Engineering, The University of Oklahoma, Norman, OK 73019, U.S.A
| | - A Yan
- Department of Radiology, The University of Alabama at Birmingham, AL 35249, U.S.A
| | - P A Jenkins
- Department of Radiology and Imaging Science, The University of Utah School of Medicine, Salt Lake- City, UT 74132, U.S.A
| | - X Wu
- Department of Radiology, The University of Alabama at Birmingham, AL 35249, U.S.A
| | - H Liu
- Advanced Medical Imaging Center and School of Electrical and Computer Engineering, The University of Oklahoma, Norman, OK 73019, U.S.A
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23
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Schaff F, Morgan KS, Pollock JA, Croton LCP, Hooper SB, Kitchen MJ. Material Decomposition Using Spectral Propagation-Based Phase-Contrast X-Ray Imaging. IEEE TRANSACTIONS ON MEDICAL IMAGING 2020; 39:3891-3899. [PMID: 32746132 DOI: 10.1109/tmi.2020.3006815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Material decomposition in X-ray imaging uses the energy-dependence of attenuation to digitally decompose an object into specific constituent materials, generally at the cost of enhanced image noise. Propagation-based X-ray phase-contrast imaging is a developing technique that can be used to reduce image noise, in particular from weakly attenuating objects. In this paper, we combine spectral phase-contrast imaging with material decomposition to both better visualize weakly attenuating features and separate them from overlying objects in radiography. We derive an algorithm that performs both tasks simultaneously and verify it against numerical simulations and experimental measurements of ideal two-component samples composed of pure aluminum and poly(methyl methacrylate). Additionally, we showcase first imaging results of a rabbit kitten's lung. The attenuation signal of a thorax, in particular, is dominated by the strongly attenuating bones of the ribcage. Combined with the weak soft tissue signal, this makes it difficult to visualize the fine anatomical structures across the whole lung. In all cases, clean material decomposition was achieved, without residual phase-contrast effects, from which we generate an un-obstructed image of the lung, free of bones. Spectral propagation-based phase-contrast imaging has the potential to be a valuable tool, not only in future lung research, but also in other systems for which phase-contrast imaging in combination with material decomposition proves to be advantageous.
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24
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Zboray R. Optimizing and applying high-resolution, in-line laboratory phase-contrast X-ray imaging for low-density material samples. J Microsc 2020; 282:123-135. [PMID: 33219697 DOI: 10.1111/jmi.12986] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/24/2020] [Accepted: 11/18/2020] [Indexed: 11/29/2022]
Abstract
In-line, or propagation-based phase-contrast X-ray imaging (PBI) is an attractive alternative to the attenuation-based modality for low-density, soft samples showing low attenuation contrast. With the growing availability of micro- and nano-focus X-ray tubes, the method is increasingly applied in the laboratory. Here, we discuss the technique and demonstrate its advantages for selected low-density, low attenuation material samples using a lab-based micro- and nano-computed tomography systems Easytom XL Ultra, providing micron and sub-micron range resolution PBI images. We demonstrate a multi-step optimization of the lab-based PBI technique on our scanner that includes choosing the optimal detector-source hardware combination available in the setup, then optimizing the imaging geometry and finally the phase retrieval process through a parametric study. We point out and elaborate on the effect of noise correlation and texturing due to phase retrieval. We demonstrate the overall benefits of using the phase image and the phase retrieval for the selected samples such as improved image quality, increased contrast-to-noise ratio while only marginally influencing the spatial resolution. The improvement in image quality also enables further image processing steps for detailed structural analysis of the samples, which would be much more complicated if not impossible based on the transmission image.
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Affiliation(s)
- Robert Zboray
- Center for X-ray Analytics, Department Materials Meet Life, Swiss Federal Laboratories for Material Science and Technology, Empa, Überlandstrasse 129, Dübendorf, Switzerland
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25
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Schaff F, Morgan KS, Paganin DM, Kitchen MJ. Spectral x-ray imaging: Conditions under which propagation-based phase-contrast is beneficial. Phys Med Biol 2020; 65:205006. [PMID: 32629430 DOI: 10.1088/1361-6560/aba318] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Energy-resolved attenuation data in spectral x-ray imaging enables material decomposition, in which the different materials inside an object can be identified and separated virtually. Material decomposition has the drawback of increased noise in the resulting material images relative to the measured images. Recently, spectral x-ray imaging was combined with propagation-based x-ray phase-contrast imaging, an x-ray technique that has the potential to greatly reduce image noise by utilizing wave-optical effects. The net combined effects on image noise of performing spectral material decomposition with phase-contrast are not yet well understood, and we provide a detailed theoretical investigation of this topic here. In particular, we investigate how the addition of phase-contrast in spectral imaging affects material decomposition compared to using conventional spectral attenuation data. We show how the underlying equations can be rearranged into parts that resemble low- and high-pass filters on the input images, from which we are able to identify different energy-dependent cases where phase-contrast is or is not advantageous. Our results suggest that the benefits of phase-contrast in the context of material decomposition are primarily restricted to x-ray energies under a certain threshold, where that threshold depends on the given material combination, and sits in a region where photoelectric absorption dominates x-ray attenuation. Additionally, we show that decomposition of the electron density using an image basis spanned by functions of the Alvarez-Macovski model benefits from phase-contrast, regardless of the x-ray energies. All our findings are based purely on theoretical considerations, and can, therefore, be used to determine the feasibility and utility of propagation-based phase-contrast in spectral x-ray imaging ahead of any data collection.
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Affiliation(s)
- Florian Schaff
- School of Physics and Astronomy, Monash University, Clayton, VIC 3800, Australia
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26
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Li HT, Schaff F, Croton LCP, Morgan KS, Kitchen MJ. Quantitative material decomposition using linear iterative near-field phase retrieval dual-energy x-ray imaging. Phys Med Biol 2020; 65:185014. [PMID: 32946429 DOI: 10.1088/1361-6560/ab9558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This paper expands the linear iterative near-field phase retrieval (LIPR) formalism to achieve quantitative material thickness decomposition. Propagation-based phase contrast x-ray imaging with subsequent phase retrieval has been shown to improve the signal-to-noise ratio (SNR) by factors of up to hundreds compared to conventional x-ray imaging. This is a key step in biomedical imaging, where radiation exposure must be kept low without compromising the SNR. However, for a satisfactory phase retrieval from a single measurement, assumptions must be made about the object investigated. To avoid such assumptions, we use two measurements collected at the same propagation distance but at different x-ray energies. Phase retrieval is then performed by incorporating the Alvarez-Macovski (AM) model, which models the x-ray interactions as being comprised of distinct photoelectric and Compton scattering components. We present the first application of dual-energy phase retrieval with the AM model to monochromatic experimental x-ray projections at two different energies for obtaining split x-ray interactions. Our phase retrieval method allows us to separate the object investigated into the projected thicknesses of two known materials. Our phase retrieval output leads to no visible loss in spatial resolution while the SNR improves by factors of 2 to 10. This corresponds to a possible x-ray dose reduction by a factor of 4 to 100, under the Poisson noise assumption.
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Affiliation(s)
- Heyang Thomas Li
- School of Physics and Astronomy, Monash University, Clayton, VIC 3800, Australia. School of Mathematics and Statistics, College of Engineering, University of Canterbury, Ilam, Christchurch, 8041, New Zealand
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27
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Günther B, Gradl R, Jud C, Eggl E, Huang J, Kulpe S, Achterhold K, Gleich B, Dierolf M, Pfeiffer F. The versatile X-ray beamline of the Munich Compact Light Source: design, instrumentation and applications. JOURNAL OF SYNCHROTRON RADIATION 2020; 27:1395-1414. [PMID: 32876618 PMCID: PMC7467334 DOI: 10.1107/s1600577520008309] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/22/2020] [Indexed: 05/08/2023]
Abstract
Inverse Compton scattering provides means to generate low-divergence partially coherent quasi-monochromatic, i.e. synchrotron-like, X-ray radiation on a laboratory scale. This enables the transfer of synchrotron techniques into university or industrial environments. Here, the Munich Compact Light Source is presented, which is such a compact synchrotron radiation facility based on an inverse Compton X-ray source (ICS). The recent improvements of the ICS are reported first and then the various experimental techniques which are most suited to the ICS installed at the Technical University of Munich are reviewed. For the latter, a multipurpose X-ray application beamline with two end-stations was designed. The beamline's design and geometry are presented in detail including the different set-ups as well as the available detector options. Application examples of the classes of experiments that can be performed are summarized afterwards. Among them are dynamic in vivo respiratory imaging, propagation-based phase-contrast imaging, grating-based phase-contrast imaging, X-ray microtomography, K-edge subtraction imaging and X-ray spectroscopy. Finally, plans to upgrade the beamline in order to enhance its capabilities are discussed.
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Affiliation(s)
- Benedikt Günther
- Department of Physics, Technical University of Munich, James-Franck-Straße 1, 85748 Garching, Germany
- Munich School of BioEngineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Regine Gradl
- Department of Physics, Technical University of Munich, James-Franck-Straße 1, 85748 Garching, Germany
- Munich School of BioEngineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Christoph Jud
- Department of Physics, Technical University of Munich, James-Franck-Straße 1, 85748 Garching, Germany
- Munich School of BioEngineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Elena Eggl
- Department of Physics, Technical University of Munich, James-Franck-Straße 1, 85748 Garching, Germany
- Munich School of BioEngineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Juanjuan Huang
- Department of Physics, Technical University of Munich, James-Franck-Straße 1, 85748 Garching, Germany
- Munich School of BioEngineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Stephanie Kulpe
- Department of Physics, Technical University of Munich, James-Franck-Straße 1, 85748 Garching, Germany
- Munich School of BioEngineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Klaus Achterhold
- Department of Physics, Technical University of Munich, James-Franck-Straße 1, 85748 Garching, Germany
- Munich School of BioEngineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Bernhard Gleich
- Munich School of BioEngineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Martin Dierolf
- Department of Physics, Technical University of Munich, James-Franck-Straße 1, 85748 Garching, Germany
- Munich School of BioEngineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
| | - Franz Pfeiffer
- Department of Physics, Technical University of Munich, James-Franck-Straße 1, 85748 Garching, Germany
- Munich School of BioEngineering, Technical University of Munich, Boltzmannstraße 11, 85748 Garching, Germany
- Department of Diagnostic and Interventional Radiology, Klinikum rechts der Isar, Technical University of Munich, Ismaninger Straße 22, 81675 Munich, Germany
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28
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Hehn L, Gradl R, Dierolf M, Morgan KS, Paganin DM, Pfeiffer F. Model-Based Iterative Reconstruction for Propagation-Based Phase-Contrast X-Ray CT including Models for the Source and the Detector. IEEE TRANSACTIONS ON MEDICAL IMAGING 2020; 39:1975-1987. [PMID: 31880549 DOI: 10.1109/tmi.2019.2962615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Propagation-based phase-contrast X-ray computed tomography is a valuable tool for high-resolution visualization of biological samples, giving distinct improvements in terms of contrast and dose requirements compared to conventional attenuation-based computed tomography. Due to its ease of implementation and advances in laboratory X-ray sources, this imaging technique is increasingly being transferred from synchrotron facilities to laboratory environments. This however poses additional challenges, such as the limited spatial coherence and flux of laboratory sources, resulting in worse resolution and higher noise levels. Here we extend a previously developed iterative reconstruction algorithm for this imaging technique to include models for the reduced spatial coherence and the signal spreading of efficient scintillator-based detectors directly into the physical forward model. Furthermore, we employ a noise model which accounts for the full covariance statistics of the image formation process. In addition, we extend the model describing the interference effects such that it now matches the formalism of the widely-used single-material phase-retrieval algorithm, which is based on the sample-homogeneity assumption. We perform a simulation study as well as an experimental study at a laboratory inverse Compton source and compare our approach to the conventional analytical approaches. We find that the modeling of the source and the detector inside the physical forward model can tremendously improve the resolution at matched noise levels and that the modeling of the covariance statistics reduces overshoots (i.e. incorrect increase / decrease in sample properties) at the sample edges significantly.
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29
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Bukreeva I, Asadchikov V, Buzmakov A, Chukalina M, Ingacheva A, Korolev NA, Bravin A, Mittone A, Biella GEM, Sierra A, Brun F, Massimi L, Fratini M, Cedola A. High resolution 3D visualization of the spinal cord in a post-mortem murine model. BIOMEDICAL OPTICS EXPRESS 2020; 11:2235-2253. [PMID: 32341880 PMCID: PMC7173906 DOI: 10.1364/boe.386837] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/27/2020] [Accepted: 03/02/2020] [Indexed: 05/04/2023]
Abstract
A crucial issue in the development of therapies to treat pathologies of the central nervous system is represented by the availability of non-invasive methods to study the three-dimensional morphology of spinal cord, with a resolution able to characterize its complex vascular and neuronal organization. X-ray phase contrast micro-tomography enables a high-quality, 3D visualization of both the vascular and neuronal network simultaneously without the need of contrast agents, destructive sample preparations or sectioning. Until now, high resolution investigations of the post-mortem spinal cord in murine models have mostly been performed in spinal cords removed from the spinal canal. We present here post-mortem phase contrast micro-tomography images reconstructed using advanced computational tools to obtain high-resolution and high-contrast 3D images of the fixed spinal cord without removing the bones and preserving the richness of micro-details available when measuring exposed spinal cords. We believe that it represents a significant step toward the in-vivo application.
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Affiliation(s)
- Inna Bukreeva
- Institute of Nanotechnology- CNR, Rome Unit, Piazzale Aldo Moro 5, Italy
- P. N. Lebedev Physical Institute, RAS, Leninsky pr., 53, Moscow, Russia
| | - Victor Asadchikov
- Shubnikov Institute of Crystallography FSRC “Crystallography and Photonics” RAS, Leninsky prosp., 59, Moscow, Russia
| | - Alexey Buzmakov
- Shubnikov Institute of Crystallography FSRC “Crystallography and Photonics” RAS, Leninsky prosp., 59, Moscow, Russia
| | - Marina Chukalina
- Shubnikov Institute of Crystallography FSRC “Crystallography and Photonics” RAS, Leninsky prosp., 59, Moscow, Russia
- Intitute for Information Transmission Problems RAS, Bolshoi Karetny per, 9, Moscow, Russia
| | - Anastasya Ingacheva
- Intitute for Information Transmission Problems RAS, Bolshoi Karetny per, 9, Moscow, Russia
| | - Nikolay A. Korolev
- National Research Nuclear University /Moscow Engineering Physics Institute, Kashirskoye Highway, 31 Moscow, Russia
| | - Alberto Bravin
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, Grenoble, France
| | - Alberto Mittone
- CELLS - ALBA Synchrotron Light Source, Carrer de la Llum, 2-26, Cerdanyola del Valles, Barcelona, Spain
| | | | - Alejandra Sierra
- Biomedical Imaging Unit, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Francesco Brun
- Department of Engineering and Architecture, University of Trieste, Via A. Valerio, 6/1 Trieste, Italy
| | - Lorenzo Massimi
- Department of Medical Physics and Biomedical Engineering, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Michela Fratini
- Institute of Nanotechnology- CNR, Rome Unit, Piazzale Aldo Moro 5, Italy
- Fondazione Santa Lucia I.R.C.C.S., Via Ardeatina 306, Roma, Italy
| | - Alessia Cedola
- Institute of Nanotechnology- CNR, Rome Unit, Piazzale Aldo Moro 5, Italy
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30
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O'Connell DW, Morgan KS, Ruben G, Schaff F, Croton LCP, Buckley GA, Paganin DM, Uesugi K, Kitchen MJ. Photon-counting, energy-resolving and super-resolution phase contrast X-ray imaging using an integrating detector. OPTICS EXPRESS 2020; 28:7080-7094. [PMID: 32225943 DOI: 10.1364/oe.384928] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 02/10/2020] [Indexed: 06/10/2023]
Abstract
This work demonstrates the use of a scientific-CMOS (sCMOS) energy-integrating detector as a photon-counting detector, thereby eliminating dark current and read-out noise issues, that simultaneously provides both energy resolution and sub-pixel spatial resolution for X-ray imaging. These capabilities are obtained by analyzing visible light photon clouds that result when X-ray photons produce fluorescence from a scintillator in front of the visible light sensor. Using low-fluence monochromatic X-ray projections to avoid overlapping photon clouds, the centroid of individual X-ray photon interactions was identified. This enabled a tripling of the spatial resolution of the detector to 6.71 ± 0.04 µm. By calculating the total charge deposited by this interaction, an energy resolution of 61.2 ± 0.1% at 17 keV was obtained. When combined with propagation-based phase contrast imaging and phase retrieval, a signal-to-noise ratio of up to 15 ± 3 was achieved for an X-ray fluence of less than 3 photons/mm2.
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31
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In vivo monitoring of bone microstructure by propagation-based phase-contrast computed tomography using monochromatic synchrotron light. J Transl Med 2020; 100:72-83. [PMID: 31641229 DOI: 10.1038/s41374-019-0337-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 10/03/2019] [Accepted: 10/03/2019] [Indexed: 11/09/2022] Open
Abstract
Hard X-ray phase-contrast imaging is sensitive to density variation in objects and shows a dose advantage for in vivo observation over absorption-contrast imaging. We examined the capability of propagation-based phase-contrast tomography (PB-PCT) with single-distance phase retrieval for tracking of bone structure and mineral changes using monochromatic synchrotron light. Female mice underwent ovariectomy and drill-hole surgery in the right tibial diaphysis and were divided into two groups: OVX and OVX-E (n = 6 each); the latter group was treated with intraperitoneal administration of 14,15-epoxyeicosatrienoic acid (14,15-EET) for promoting bone repair. Age-matched mice subjected to sham ovariectomy and drill-hole surgery (Sham) were also prepared (n = 6). In vivo CT scans of the drilled defect were acquired 3, 7, and 11 days after surgery, and tomographic images were matched by three-dimensional registration between successive time points for monitoring the process of defect filling. In addition, using absorption-contrast CT as the reference method, the validity of PB-PCT was evaluated in one mouse by comparing images of tibial metaphyseal bone between the two methods in terms of bone geometry as well as the measure of mineralization. Although phase retrieval is strictly valid only for single-material objects, PB-PCT, with its lower radiation dose, could provide a depiction of bone structure similar to that from absorption-contrast CT. There was a significant correlation of linear absorption coefficients between the two methods, indicating the possibility of a rough estimate of the measure of mineralization by PB-PCT. Indeed, delayed bone regeneration (OVX vs. Sham) and the efficacy of 14,15-EET for improving osteoporotic bone repair (OVX-E vs. OVX) could be detected in both bone volume and mineralization by PB-PCT. Thus, in combination with single-distance phase retrieval, PB-PCT would have great potential for providing a valuable tool to track changes in bone structure and mineralization, and for evaluating the effects of therapeutic interventions as well.
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32
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Clark L, Petersen TC, Williams T, Morgan MJ, Paganin DM, Findlay SD. High contrast at low dose using a single, defocussed transmission electron micrograph. Micron 2019; 124:102701. [PMID: 31280007 DOI: 10.1016/j.micron.2019.102701] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 06/03/2019] [Accepted: 06/04/2019] [Indexed: 11/28/2022]
Abstract
For many soft-matter specimens, transmission electron microscopists face the double-bind of low contrast images, due to weakly-scattering specimens, alongside severe limits on the electron dose that can be used before the specimen is damaged by the electron beam. The combination of these effects causes the resultant micrographs to have very low signal-to-noise. It is well known that varying the defocus aberration can enhance image contrast in electron microscopy. For single-material objects where the variation of absorption and phase contrast are functions of one another, since both are governed by the variation in thickness profile, we show that the thickness profile can be reconstructed at very low dose. The algorithm, first established in X-ray imaging, requires some a priori information but only a single defocussed image of the region of interest, making it more dose efficient than either a conventional transport-of-intensity phase reconstruction (which would require two images and tends to amplify noise), or an absorption-contrast analysis of a single in-focus image recorded at the same electron dose (which does not benefit from the significant signal-to-noise enhancement of the present algorithm). These findings are presented through both simulations and experimental data.
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Affiliation(s)
- L Clark
- School of Physics and Astronomy, Monash University, Victoria 3800, Australia.
| | - T C Petersen
- School of Physics and Astronomy, Monash University, Victoria 3800, Australia
| | - T Williams
- Monash Centre for Electron Microscopy, Monash University, Victoria 3800, Australia
| | - M J Morgan
- School of Physics and Astronomy, Monash University, Victoria 3800, Australia
| | - D M Paganin
- School of Physics and Astronomy, Monash University, Victoria 3800, Australia
| | - S D Findlay
- School of Physics and Astronomy, Monash University, Victoria 3800, Australia
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33
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Croton LCP, Ruben G, Morgan KS, Paganin DM, Kitchen MJ. Ring artifact suppression in X-ray computed tomography using a simple, pixel-wise response correction. OPTICS EXPRESS 2019; 27:14231-14245. [PMID: 31163875 DOI: 10.1364/oe.27.014231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
We present a pixel-specific, measurement-driven correction that effectively reduces errors in detector response that give rise to the ring artifacts commonly seen in X-ray computed tomography (CT) scans. This correction is easy to implement, suppresses CT artifacts significantly, and is effective enough for use with both absorption and phase contrast imaging. It can be used as a standalone correction or in conjunction with existing ring artifact removal algorithms to further improve image quality. We validate this method using two X-ray CT data sets acquired using monochromatic sources, showing post-correction signal-to-noise increases of up to 55%, and we define an image quality metric to use specifically for the assessment of ring artifact suppression.
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34
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Thompson DA, Nesterets YI, Pavlov KM, Gureyev TE. Fast three-dimensional phase retrieval in propagation-based X-ray tomography. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:825-838. [PMID: 31074448 DOI: 10.1107/s1600577519002133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 02/09/2019] [Indexed: 06/09/2023]
Abstract
The following article describes a method for 3D reconstruction of multi-material objects based on propagation-based X-ray phase-contrast tomography (PB-CT) with phase retrieval using the homogeneous form of the transport of intensity equation (TIE-Hom). Unlike conventional PB-CT algorithms that perform phase retrieval of individual projections, the described post-reconstruction phase-retrieval method is applied in 3D to a localized region of the CT-reconstructed volume. This work demonstrates, via numerical simulations, the accuracy and noise characteristics of the method under a variety of experimental conditions, comparing it with both conventional absorption tomography and 2D TIE-Hom phase retrieval applied to projection images. The results indicate that the 3D post-reconstruction method generally achieves a modest improvement in noise suppression over existing PB-CT methods. It is also shown that potentially large computational gains over projection-based phase retrieval for multi-material samples are possible. In particular, constraining phase retrieval to a localized 3D region of interest reduces the overall computational cost and eliminates the need for multiple CT reconstructions and global 2D phase retrieval operations for each material within the sample.
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Affiliation(s)
- Darren A Thompson
- Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria, Australia
| | - Yakov I Nesterets
- Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria, Australia
| | | | - Timur E Gureyev
- Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria, Australia
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35
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Wang Z, Ren K, Shi X, Ren Y, Gao K, Wu Z. Single-image phase retrieval for hard X-ray grating interferometry. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:215-219. [PMID: 30655487 DOI: 10.1107/s1600577518016727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/24/2018] [Indexed: 06/09/2023]
Abstract
A single-image method is proposed for quantitative phase retrieval in hard X-ray grating interferometry. This novel method assumes a quasi-homogeneous sample, with a constant ratio between the real and imaginary parts of its complex refractive index. The method is first theoretically derived and presented, and then validated by synchrotron radiation experiments. Compared with the phase-stepping method, the presented approach abandons grating scanning and multiple image acquisition, and is therefore advantageous in terms of its simplified acquisition procedure and reduced data-collection times, which are especially important for applications such as in vivo imaging and phase tomography. Moreover, the sample's phase image, instead of its first derivative, is directly retrieved. In particular, the stripe artifacts encountered in the integrated phase images are significantly suppressed. The improved quality of the retrieved phase images can be beneficial for image interpretation and subsequent processing. Owing to its requirement for a single image and its robustness against noise, the present method is expected to find use in potential investigations in diverse applications.
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Affiliation(s)
- Zhili Wang
- School of Electronic Science and Applied Physics, Hefei University of Technology, Anhui 230009, People's Republic of China
| | - Kun Ren
- School of Electronic Science and Applied Physics, Hefei University of Technology, Anhui 230009, People's Republic of China
| | - Xiaomin Shi
- School of Electronic Science and Applied Physics, Hefei University of Technology, Anhui 230009, People's Republic of China
| | - Yuqi Ren
- Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201204, People's Republic of China
| | - Kun Gao
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Anhui 230026, People's Republic of China
| | - Zhao Wu
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Anhui 230026, People's Republic of China
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36
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Brombal L, Golosio B, Arfelli F, Bonazza D, Contillo A, Delogu P, Donato S, Mettivier G, Oliva P, Rigon L, Taibi A, Tromba G, Zanconati F, Longo R. Monochromatic breast computed tomography with synchrotron radiation: phase-contrast and phase-retrieved image comparison and full-volume reconstruction. J Med Imaging (Bellingham) 2018; 6:031402. [PMID: 30525064 DOI: 10.1117/1.jmi.6.3.031402] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/18/2018] [Indexed: 11/14/2022] Open
Abstract
A program devoted to performing the first in vivo synchrotron radiation (SR) breast computed tomography (BCT) is ongoing at the Elettra facility. Using the high spatial coherence of SR, phase-contrast (PhC) imaging techniques can be used. The latest high-resolution BCT acquisitions of breast specimens, obtained with the propagation-based PhC approach, are herein presented as part of the SYRMA-3D collaboration effort toward the clinical exam. Images are acquired with a 60 - μ m pixel dead-time-free single-photon-counting CdTe detector. The samples are imaged at 32 and 38 keV in a continuous rotating mode, delivering 5 to 20 mGy of mean glandular dose. Contrast-to-noise ratio (CNR) and spatial resolution performances are evaluated for both PhC and phase-retrieved images, showing that by applying the phase-retrieval algorithm a five-time CNR increase can be obtained with a minor loss in spatial resolution across soft tissue interfaces. It is shown that, despite having a poorer CNR, PhC images can provide a sharper visualization of microcalcifications, thus being complementary to phase-retrieved images. Furthermore, the first full-volume scan of a mastectomy sample ( 9 × 9 × 3 cm 3 ) is reported. This investigation into surgical specimens indicates that SR BCT in terms of CNR, spatial resolution, scan duration, and scan volume is feasible.
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Affiliation(s)
- Luca Brombal
- University of Trieste, Department of Physics, Trieste, Italy.,INFN Division of Trieste, Trieste, Italy
| | - Bruno Golosio
- University of Cagliari, Department of Physics, Cagliari, Italy.,INFN Division of Cagliari, Cagliari, Italy
| | - Fulvia Arfelli
- University of Trieste, Department of Physics, Trieste, Italy.,INFN Division of Trieste, Trieste, Italy
| | - Deborah Bonazza
- University of Trieste, Department of Medical Science, Cattinara Hospital, Trieste, Italy
| | - Adriano Contillo
- University of Ferrara, Department of Physics and Earth Science, Ferrara, Italy.,INFN Division of Ferrara, Ferrara, Italy
| | - Pasquale Delogu
- University of Siena, Department of Physical Sciences, Earth and Environment, Siena, Italy.,INFN Division of Pisa, Pisa, Italy
| | - Sandro Donato
- University of Trieste, Department of Physics, Trieste, Italy.,INFN Division of Trieste, Trieste, Italy
| | - Giovanni Mettivier
- University of Napoli Federico II, Department of Physics, Napoli, Italy.,INFN Division of Napoli, Napoli, Italy
| | - Piernicola Oliva
- University of Sassari, Department of Chemistry and Pharmacy, Sassari, Italy.,INFN Division of Cagliari, Cagliari, Italy
| | - Luigi Rigon
- University of Trieste, Department of Physics, Trieste, Italy.,INFN Division of Trieste, Trieste, Italy
| | - Angelo Taibi
- University of Ferrara, Department of Physics and Earth Science, Ferrara, Italy.,INFN Division of Ferrara, Ferrara, Italy
| | | | - Fabrizio Zanconati
- University of Trieste, Department of Medical Science, Cattinara Hospital, Trieste, Italy
| | - Renata Longo
- University of Trieste, Department of Physics, Trieste, Italy.,INFN Division of Trieste, Trieste, Italy
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37
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Hehn L, Gradl R, Voss A, Günther B, Dierolf M, Jud C, Willer K, Allner S, Hammel JU, Hessler R, Morgan KS, Herzen J, Hemmert W, Pfeiffer F. Propagation-based phase-contrast tomography of a guinea pig inner ear with cochlear implant using a model-based iterative reconstruction algorithm. BIOMEDICAL OPTICS EXPRESS 2018; 9:5330-5339. [PMID: 30460131 PMCID: PMC6238946 DOI: 10.1364/boe.9.005330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/17/2018] [Accepted: 09/08/2018] [Indexed: 06/09/2023]
Abstract
Propagation-based phase-contrast computed tomography has become a valuable tool for visualization of three-dimensional biological samples, due to its high contrast between materials with similar attenuation properties. However, one of the most-widely used phase-retrieval algorithms imposes a homogeneity assumption onto the sample, which leads to artifacts for numerous applications where this assumption is violated. Prominent examples are biological samples with highly-absorbing implants. Using synchrotron radiation, we demonstrate by the example of a guinea pig inner ear with a cochlear implant electrode, how a recently developed model-based iterative algorithm for propagation-based phase-contrast computed tomography yields distinct benefits for such a task. We find that the model-based approach improves the overall image quality, removes the detrimental influence of the implant and accurately visualizes the cochlea.
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Affiliation(s)
- Lorenz Hehn
- Chair of Biomedical Physics, Department of Physics and Munich School of BioEngineering, Technical University of Munich, 85748 Garching,
Germany
- Department of Diagnostic and Interventional Radiology, Klinikum Rechts der Isar, Technical University of Munich, 81675 Munich,
Germany
| | - Regine Gradl
- Chair of Biomedical Physics, Department of Physics and Munich School of BioEngineering, Technical University of Munich, 85748 Garching,
Germany
- Institute for Advanced Study, Technical University of Munich, 85748 Garching,
Germany
| | - Andrej Voss
- Bio-Inspired Information Processing, Munich School of BioEngineering, Munich School of Robotics and Machine Intelligence, Technical University of Munich, 85748 Garching,
Germany
| | - Benedikt Günther
- Chair of Biomedical Physics, Department of Physics and Munich School of BioEngineering, Technical University of Munich, 85748 Garching,
Germany
- Max-Planck-Institute of Quantum Optics, 85748 Garching,
Germany
| | - Martin Dierolf
- Chair of Biomedical Physics, Department of Physics and Munich School of BioEngineering, Technical University of Munich, 85748 Garching,
Germany
| | - Christoph Jud
- Chair of Biomedical Physics, Department of Physics and Munich School of BioEngineering, Technical University of Munich, 85748 Garching,
Germany
| | - Konstantin Willer
- Chair of Biomedical Physics, Department of Physics and Munich School of BioEngineering, Technical University of Munich, 85748 Garching,
Germany
- Department of Diagnostic and Interventional Radiology, Klinikum Rechts der Isar, Technical University of Munich, 81675 Munich,
Germany
| | - Sebastian Allner
- Chair of Biomedical Physics, Department of Physics and Munich School of BioEngineering, Technical University of Munich, 85748 Garching,
Germany
| | - Jörg U. Hammel
- Institute of Materials Research, Helmholtz-Zentrum Geesthacht, 21502 Geesthacht,
Germany
- Institut für Zoologie und Evolutionsforschung mit Phyletischem Museum, Ernst-Haeckel-Haus und Biologiedidaktik, Friedrich-Schiller-Universität Jena, 07743 Jena,
Germany
| | | | - Kaye S. Morgan
- Chair of Biomedical Physics, Department of Physics and Munich School of BioEngineering, Technical University of Munich, 85748 Garching,
Germany
- Institute for Advanced Study, Technical University of Munich, 85748 Garching,
Germany
- School of Physics and Astronomy, Monash University, Clayton VIC 3800,
Australia
| | - Julia Herzen
- Chair of Biomedical Physics, Department of Physics and Munich School of BioEngineering, Technical University of Munich, 85748 Garching,
Germany
| | - Werner Hemmert
- Bio-Inspired Information Processing, Munich School of BioEngineering, Munich School of Robotics and Machine Intelligence, Technical University of Munich, 85748 Garching,
Germany
| | - Franz Pfeiffer
- Chair of Biomedical Physics, Department of Physics and Munich School of BioEngineering, Technical University of Munich, 85748 Garching,
Germany
- Department of Diagnostic and Interventional Radiology, Klinikum Rechts der Isar, Technical University of Munich, 81675 Munich,
Germany
- Institute for Advanced Study, Technical University of Munich, 85748 Garching,
Germany
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38
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Tesařová M, Mancini L, Simon A, Adameyko I, Kaucká M, Elewa A, Lanzafame G, Zhang Y, Kalasová D, Szarowská B, Zikmund T, Novotná M, Kaiser J. A quantitative analysis of 3D-cell distribution in regenerating muscle-skeletal system with synchrotron X-ray computed microtomography. Sci Rep 2018; 8:14145. [PMID: 30237460 PMCID: PMC6148031 DOI: 10.1038/s41598-018-32459-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 09/10/2018] [Indexed: 02/07/2023] Open
Abstract
One of the greatest enigmas of modern biology is how the geometry of muscular and skeletal structures are created and how their development is controlled during growth and regeneration. Scaling and shaping of vertebrate muscles and skeletal elements has always been enigmatic and required an advanced technical level in order to analyse the cell distribution in 3D. In this work, synchrotron X-ray computed microtomography (µCT) and chemical contrasting has been exploited for a quantitative analysis of the 3D-cell distribution in tissues of a developing salamander (Pleurodeles waltl) limb – a key model organism for vertebrate regeneration studies. We mapped the limb muscles, their size and shape as well as the number and density of cells within the extracellular matrix of the developing cartilage. By using tomographic approach, we explored the polarity of the cells in 3D, in relation to the structure of developing joints. We found that the polarity of chondrocytes correlates with the planes in joint surfaces and also changes along the length of the cartilaginous elements. Our approach generates data for the precise computer simulations of muscle-skeletal regeneration using cell dynamics models, which is necessary for the understanding how anisotropic growth results in the precise shapes of skeletal structures.
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Affiliation(s)
- Markéta Tesařová
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Lucia Mancini
- Elettra-Sincrotrone Trieste S.C.p.A., Basovizza, Trieste, Italy
| | - Andras Simon
- Department of Cellular and Molecular Biology, Karolinska Institutet, Solna, 171777, Stockholm, Sweden
| | - Igor Adameyko
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, 171777, Stockholm, Sweden.,Department of Molecular Neurosciences, Medical University Vienna, Vienna, Austria
| | - Markéta Kaucká
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, 171777, Stockholm, Sweden.,Department of Molecular Neurosciences, Medical University Vienna, Vienna, Austria
| | - Ahmed Elewa
- Department of Cellular and Molecular Biology, Karolinska Institutet, Solna, 171777, Stockholm, Sweden
| | | | - Yi Zhang
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, 171777, Stockholm, Sweden.,Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Dominika Kalasová
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Bára Szarowská
- Department of Physiology and Pharmacology, Karolinska Institutet, Solna, 171777, Stockholm, Sweden
| | - Tomáš Zikmund
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Marie Novotná
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Jozef Kaiser
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic.
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39
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Croton LCP, Morgan KS, Paganin DM, Kerr LT, Wallace MJ, Crossley KJ, Miller SL, Yagi N, Uesugi K, Hooper SB, Kitchen MJ. In situ phase contrast X-ray brain CT. Sci Rep 2018; 8:11412. [PMID: 30061729 PMCID: PMC6065359 DOI: 10.1038/s41598-018-29841-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 07/17/2018] [Indexed: 11/09/2022] Open
Abstract
Phase contrast X-ray imaging (PCXI) is an emerging imaging modality that has the potential to greatly improve radiography for medical imaging and materials analysis. PCXI makes it possible to visualise soft-tissue structures that are otherwise unresolved with conventional CT by rendering phase gradients in the X-ray wavefield visible. This can improve the contrast resolution of soft tissues structures, like the lungs and brain, by orders of magnitude. Phase retrieval suppresses noise, revealing weakly-attenuating soft tissue structures, however it does not remove the artefacts from the highly attenuating bone of the skull and from imperfections in the imaging system that can obscure those structures. The primary causes of these artefacts are investigated and a simple method to visualise the features they obstruct is proposed, which can easily be implemented for preclinical animal studies. We show that phase contrast X-ray CT (PCXI-CT) can resolve the soft tissues of the brain in situ without a need for contrast agents at a dose ~400 times lower than would be required by standard absorption contrast CT. We generalise a well-known phase retrieval algorithm for multiple-material samples specifically for CT, validate its use for brain CT, and demonstrate its high stability in the presence of noise.
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Affiliation(s)
- Linda C P Croton
- School of Physics and Astronomy, Monash University, Clayton, Victoria, 3800, Australia.
| | - Kaye S Morgan
- School of Physics and Astronomy, Monash University, Clayton, Victoria, 3800, Australia.,Chair of Biomedical Physics, Department of Physics, Munich School of Bioengineering, and Institute of Advanced Study, Technische Universität München, 85748, Garching, Germany
| | - David M Paganin
- School of Physics and Astronomy, Monash University, Clayton, Victoria, 3800, Australia
| | - Lauren T Kerr
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, Victoria, 3800, Australia.,Cancer Research UK, Angel, London, United Kingdom
| | - Megan J Wallace
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, Victoria, 3800, Australia.,Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria, 3800, Australia
| | - Kelly J Crossley
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, Victoria, 3800, Australia.,Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria, 3800, Australia
| | - Suzanne L Miller
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, Victoria, 3800, Australia
| | - Naoto Yagi
- Japan Synchrotron Radiation Research Institute (JASRI/SPring-8), 1-1-1 Kouto, Sayo, Hyogo, 679-5198, Japan
| | - Kentaro Uesugi
- Japan Synchrotron Radiation Research Institute (JASRI/SPring-8), 1-1-1 Kouto, Sayo, Hyogo, 679-5198, Japan
| | - Stuart B Hooper
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, Victoria, 3800, Australia.,Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria, 3800, Australia
| | - Marcus J Kitchen
- School of Physics and Astronomy, Monash University, Clayton, Victoria, 3800, Australia
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40
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Vågberg W, Persson J, Szekely L, Hertz HM. Cellular-resolution 3D virtual histology of human coronary arteries using x-ray phase tomography. Sci Rep 2018; 8:11014. [PMID: 30030461 PMCID: PMC6054690 DOI: 10.1038/s41598-018-29344-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 07/11/2018] [Indexed: 11/27/2022] Open
Abstract
High-spatial-resolution histology of coronary artery autopsy samples play an important role for understanding heart disease such as myocardial infarction. Unfortunately, classical histology is often destructive, has thick slicing, requires extensive sample preparation, and is time-consuming. X-ray micro-CT provides fast nondestructive 3D imaging but absorption contrast is often insufficient, especially for observing soft-tissue features with high resolution. Here we show that propagation-based x-ray phase-contrast tomography has the resolution and contrast to image clinically relevant soft-tissue features in intact coronary artery autopsy samples with cellular resolution. We observe microscopic lipid-rich plaques, individual adipose cells, ensembles of few foam cells, and the thin fibrous cap. The method relies on a small-spot laboratory x-ray microfocus source, and provides high-spatial resolution in all three dimensions, fast data acquisition, minimum sample distortion and requires no sample preparation.
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Affiliation(s)
- William Vågberg
- Department of Applied Physics, KTH Royal Institute of Technology/Albanova, Stockholm, Sweden.
| | - Jonas Persson
- Karolinska Institutet, Division of Cardiovascular Medicine, Department of Clinical Sciences, Danderyd University Hospital, Stockholm, Sweden
| | - Laszlo Szekely
- Laboratory of Clinical Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden.,Department of Pathology, Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Hans M Hertz
- Department of Applied Physics, KTH Royal Institute of Technology/Albanova, Stockholm, Sweden
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41
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Zhou Z, Zhang L, Guo B, Ma W, Zhang L, Li J, Zhao H, Jiang J, Gao F. Improved phase-attenuation duality method with space-frequency joint domain iterative regularization. Med Phys 2018; 45:3681-3696. [PMID: 29957878 DOI: 10.1002/mp.13067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 06/17/2018] [Accepted: 06/19/2018] [Indexed: 12/25/2022] Open
Abstract
PURPOSE A common problem of in-line phase contrast imaging systems based on laboratory source and detector is the negative effects of finite source size, limited spatial resolution, and system noise. These negative effects swamp the fine phase contrast fringes and impede the precise retrieval of phase maps. This study aims to develop a novel phase retrieval method to restore phase information that is lost due to an imperfect system. METHODS An improved phase-attenuation duality (PAD) method based on space-frequency joint domain iterative regularization (JDIR) is proposed to overcome the problems of the analytical PAD method and the spatial-domain iterative regularization (SDIR) based PAD method. These problems include noise robustness and optical transfer function compensation. The proposed method was compared with the two former PAD methods through computer simulations and experiments for validation. RESULTS Results reveal that JDIR method outperforms the other two methods in terms of improving the visibility of structures in the retrieved phase maps. Among all the phase retrieval algorithms, the TV-norm-based JDIR method performed the best in considering the contrast and noise performance. CONCLUSIONS This paper provides a new method to investigate quantitative phase-contrast imaging when considering the negative effects of an imperfect system.
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Affiliation(s)
- Zhongxing Zhou
- School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, China
- Tianjin Key Laboratory of Biomedical Detecting Techniques and Instruments, Tianjin, 300072, China
| | - Lin Zhang
- School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, China
| | - Baikuan Guo
- School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, China
| | - Wenjuan Ma
- Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300072, China
| | - Limin Zhang
- School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, China
- Tianjin Key Laboratory of Biomedical Detecting Techniques and Instruments, Tianjin, 300072, China
| | - Jiao Li
- School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, China
- Tianjin Key Laboratory of Biomedical Detecting Techniques and Instruments, Tianjin, 300072, China
| | - Huijuan Zhao
- School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, China
- Tianjin Key Laboratory of Biomedical Detecting Techniques and Instruments, Tianjin, 300072, China
| | - Jingying Jiang
- Paul C Lauterbur Research Center for Biomedical Imaging, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, 518055, China
| | - Feng Gao
- School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, China
- Tianjin Key Laboratory of Biomedical Detecting Techniques and Instruments, Tianjin, 300072, China
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42
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Yu B, Weber L, Pacureanu A, Langer M, Olivier C, Cloetens P, Peyrin F. Evaluation of phase retrieval approaches in magnified X-ray phase nano computerized tomography applied to bone tissue. OPTICS EXPRESS 2018; 26:11110-11124. [PMID: 29716036 DOI: 10.1364/oe.26.011110] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 03/05/2018] [Indexed: 06/08/2023]
Abstract
X-ray phase contrast imaging offers higher sensitivity compared to conventional X-ray attenuation imaging and can be simply implemented by propagation when using a partially coherent synchrotron beam. We address the phase retrieval in in-line phase nano-CT using multiple propagation distances. We derive a method which extends Paganin's single distance method and compare it to the contrast transfer function (CTF) approach in the case of a homogeneous object. The methods are applied to phase nano-CT data acquired at the voxel size of 30 nm (ID16A, ESRF, Grenoble, France). Our results show a gain in image quality in terms of the signal-to-noise ratio and spatial resolution when using four distances instead of one. The extended Paganin's method followed by an iterative refinement step provides the best reconstructions while the homogeneous CTF method delivers quasi comparable results for our data, even without refinement step.
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43
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Quantitative Assessment of Degenerative Cartilage and Subchondral Bony Lesions in a Preserved Cadaveric Knee: Propagation-Based Phase-Contrast CT Versus Conventional MRI and CT. AJR Am J Roentgenol 2018; 210:1317-1322. [PMID: 29629804 DOI: 10.2214/ajr.17.18286] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
OBJECTIVE The aim of this study was to quantitatively assess hyaline cartilage and subchondral bone conditions in a fully preserved cadaveric human knee joint using high-resolution x-ray propagation-based phase-contrast imaging (PBI) CT and to compare the performance of the new technique with conventional CT and MRI. MATERIALS AND METHODS A cadaveric human knee was examined using an x-ray beam of 60 keV, a detector with a 90-mm2 FOV, and a pixel size of 46 × 46 μm2. PBI CT images were reconstructed with both the filtered back projection algorithm and the equally sloped tomography method. Conventional 3-T MRI and CT were also performed. Measurements of cartilage thickness, cartilage lesions, International Cartilage Repair Society scoring, and detection of subchondral bone changes were evaluated. Visual inspection of the specimen akin to arthroscopy was conducted and served as a standard of reference for lesion detection. RESULTS Loss of cartilage height was visible on PBI CT and MRI. Quantification of cartilage thickness showed a strong correlation between the two modalities. Cartilage lesions appeared darker than the adjacent cartilage on PBI CT. PBI CT showed similar agreement to MRI for depicting cartilage substance defects or lesions compared with the visual inspection. The assessment of subchondral bone cysts showed moderate to strong agreement between PBI CT and CT. CONCLUSION In contrast to the standard clinical methods of MRI and CT, PBI CT is able to simultaneously depict cartilage and bony changes at high resolution. Though still an experimental technique, PBI CT is a promising high-resolution imaging method to evaluate comprehensive changes of osteoarthritic disease in a clinical setting.
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44
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Hehn L, Morgan K, Bidola P, Noichl W, Gradl R, Dierolf M, Noël PB, Pfeiffer F. Nonlinear statistical iterative reconstruction for propagation-based phase-contrast tomography. APL Bioeng 2018; 2:016105. [PMID: 31069290 PMCID: PMC6481703 DOI: 10.1063/1.4990387] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 12/26/2017] [Indexed: 11/25/2022] Open
Abstract
Propagation-based phase-contrast tomography has become a valuable tool for visualization of three-dimensional biological samples, due to its high sensitivity and its potential in providing increased contrast between materials with similar absorption properties. We present a statistical iterative reconstruction algorithm for this imaging technique in the near-field regime. Under the assumption of a single material, the propagation of the x-ray wavefield-relying on the transport-of-intensity equation-is made an integral part of the tomographic reconstruction problem. With a statistical approach acting directly on the measured intensities, we find an unconstrained nonlinear optimization formulation whose solution yields the three-dimensional distribution of the sample. This formulation not only omits the intermediate step of retrieving the projected thicknesses but also takes the statistical properties of the measurements into account and incorporates prior knowledge about the sample in the form of regularization techniques. We show some advantages of this integrated approach compared to two-step approaches on data obtained using a commercially available x-ray micro-tomography system. In particular, we address one of the most considerable challenges of the imaging technique, namely, the artifacts arising from samples containing highly absorbing features. With the use of statistical weights in our noise model, we can account for these materials and recover features in the vicinity of the highly absorbing features that are lost in the conventional two-step approaches. In addition, the statistical modeling of our reconstruction approach will prove particularly beneficial in the ongoing transition of this imaging technique from synchrotron facilities to laboratory setups.
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Affiliation(s)
| | | | - Pidassa Bidola
- Chair of Biomedical Physics, Department of Physics and Munich School of Bioengineering, Technical University of Munich, 85748 Garching, Germany
| | - Wolfgang Noichl
- Chair of Biomedical Physics, Department of Physics and Munich School of Bioengineering, Technical University of Munich, 85748 Garching, Germany
| | | | - Martin Dierolf
- Chair of Biomedical Physics, Department of Physics and Munich School of Bioengineering, Technical University of Munich, 85748 Garching, Germany
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45
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Kitchen MJ, Buckley GA, Gureyev TE, Wallace MJ, Andres-Thio N, Uesugi K, Yagi N, Hooper SB. CT dose reduction factors in the thousands using X-ray phase contrast. Sci Rep 2017; 7:15953. [PMID: 29162913 PMCID: PMC5698457 DOI: 10.1038/s41598-017-16264-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/09/2017] [Indexed: 11/24/2022] Open
Abstract
Phase-contrast X-ray imaging can improve the visibility of weakly absorbing objects (e.g. soft tissues) by an order of magnitude or more compared to conventional radiographs. Combining phase retrieval with computed tomography (CT) can increase the signal-to-noise ratio (SNR) by up to two orders of magnitude over conventional CT at the same radiation dose, without loss of image quality. Our experiments reveal that as the radiation dose decreases, the relative improvement in SNR increases. We show that this enhancement can be traded for a reduction in dose greater than the square of the gain in SNR. Upon reducing the dose 300 fold, the phase-retrieved SNR was still up to 9.6 ± 0.2 times larger than the absorption contrast data with spatial resolution in the tens of microns. We show that this theoretically reveals the potential for dose reduction factors in the tens of thousands without loss in image quality, which would have a profound impact on medical and industrial imaging applications.
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Affiliation(s)
- Marcus J Kitchen
- School of Physics and Astronomy, Monash University, Melbourne, 3800, Australia.
| | - Genevieve A Buckley
- School of Physics and Astronomy, Monash University, Melbourne, 3800, Australia
| | - Timur E Gureyev
- School of Physics and Astronomy, Monash University, Melbourne, 3800, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, 3052, Australia.,School of Science and Technology, University of New England, Armidale, 2351, Australia
| | - Megan J Wallace
- The Ritchie Centre, Hudson Institute for Medical Research, Melbourne, 3168, Australia.,Department of Obstetrics and Gynaecology, Monash University, Melbourne, 3800, Australia
| | - Nico Andres-Thio
- School of Engineering, University of Melbourne, Parkville, 3052, Australia.,School of Mathematics and Statistics, University of Melbourne, Parkville, 3052, Australia
| | - Kentaro Uesugi
- Japan Synchrotron Radiation Research Institute (JASRI/SPring-8), 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Naoto Yagi
- Japan Synchrotron Radiation Research Institute (JASRI/SPring-8), 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Stuart B Hooper
- The Ritchie Centre, Hudson Institute for Medical Research, Melbourne, 3168, Australia.,Department of Obstetrics and Gynaecology, Monash University, Melbourne, 3800, Australia
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46
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Carrel M, Beltran MA, Morales VL, Derlon N, Morgenroth E, Kaufmann R, Holzner M. Biofilm imaging in porous media by laboratory X-Ray tomography: Combining a non-destructive contrast agent with propagation-based phase-contrast imaging tools. PLoS One 2017; 12:e0180374. [PMID: 28732010 PMCID: PMC5521744 DOI: 10.1371/journal.pone.0180374] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 06/14/2017] [Indexed: 11/21/2022] Open
Abstract
X-ray tomography is a powerful tool giving access to the morphology of biofilms, in 3D porous media, at the mesoscale. Due to the high water content of biofilms, the attenuation coefficient of biofilms and water are very close, hindering the distinction between biofilms and water without the use of contrast agents. Until now, the use of contrast agents such as barium sulfate, silver-coated micro-particles or 1-chloronaphtalene added to the liquid phase allowed imaging the biofilm 3D morphology. However, these contrast agents are not passive and potentially interact with the biofilm when injected into the sample. Here, we use a natural inorganic compound, namely iron sulfate, as a contrast agent progressively bounded in dilute or colloidal form into the EPS matrix during biofilm growth. By combining a very long source-to-detector distance on a X-ray laboratory source with a Lorentzian filter implemented prior to tomographic reconstruction, we substantially increase the contrast between the biofilm and the surrounding liquid, which allows revealing the 3D biofilm morphology. A comparison of this new method with the method proposed by Davit et al (Davit et al., 2011), which uses barium sulfate as a contrast agent to mark the liquid phase was performed. Quantitative evaluations between the methods revealed substantial differences for the volumetric fractions obtained from both methods. Namely, contrast agent—biofilm interactions (e.g. biofilm detachment) occurring during barium sulfate injection caused a reduction of the biofilm volumetric fraction of more than 50% and displacement of biofilm patches elsewhere in the column. Two key advantages of the newly proposed method are that passive addition of iron sulfate maintains the integrity of the biofilm prior to imaging, and that the biofilm itself is marked by the contrast agent, rather than the liquid phase as in other available methods. The iron sulfate method presented can be applied to understand biofilm development and bioclogging mechanisms in porous materials and the obtained biofilm morphology could be an ideal basis for 3D numerical calculations of hydrodynamic conditions to investigate biofilm-flow coupling.
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Affiliation(s)
- Maxence Carrel
- Institute of Environmental Engineering, ETH Zürich, Stefano Franscini-Platz 5, 8093 Zurich, Switzerland
| | - Mario A. Beltran
- Swiss Federal Laboratories for Materials Science and Technology (EMPA), Dübendorf, Switzerland
| | - Verónica L. Morales
- Institute of Environmental Engineering, ETH Zürich, Stefano Franscini-Platz 5, 8093 Zurich, Switzerland
- Department of Civil and Environmental Engineering, University of California Davis, Davis, California, United States of America
| | - Nicolas Derlon
- Institute of Environmental Engineering, ETH Zürich, Stefano Franscini-Platz 5, 8093 Zurich, Switzerland
- Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Dübendorf, Switzerland
| | - Eberhard Morgenroth
- Institute of Environmental Engineering, ETH Zürich, Stefano Franscini-Platz 5, 8093 Zurich, Switzerland
- Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Dübendorf, Switzerland
| | - Rolf Kaufmann
- Swiss Federal Laboratories for Materials Science and Technology (EMPA), Dübendorf, Switzerland
| | - Markus Holzner
- Institute of Environmental Engineering, ETH Zürich, Stefano Franscini-Platz 5, 8093 Zurich, Switzerland
- * E-mail:
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47
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Zamir A, Diemoz PC, Vittoria FA, Hagen CK, Endrizzi M, Olivo A. Edge illumination X-ray phase tomography of multi-material samples using a single-image phase retrieval algorithm. OPTICS EXPRESS 2017; 25:11984-11996. [PMID: 28788753 DOI: 10.1364/oe.25.011984] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In this paper we present a single-image phase retrieval algorithm for multi-material samples, developed for the edge illumination (EI) X-ray phase contrast imaging method. The theoretical derivation is provided, along with any assumptions made. The algorithm is evaluated quantitatively using both simulated and experimental results from a computed tomography (CT) scan using the EI laboratory implementation. Qualitative CT results are provided for a biological sample containing both bone and soft-tissue. Using a single EI image per projection and knowledge of the complex refractive index, the algorithm can accurately retrieve the interface between a given pair of materials. A composite CT slice can be created by splicing together multiple CT reconstructions, each retrieved for a different pair of materials.
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48
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Pelaz B, Alexiou C, Alvarez-Puebla RA, Alves F, Andrews AM, Ashraf S, Balogh LP, Ballerini L, Bestetti A, Brendel C, Bosi S, Carril M, Chan WCW, Chen C, Chen X, Chen X, Cheng Z, Cui D, Du J, Dullin C, Escudero A, Feliu N, Gao M, George M, Gogotsi Y, Grünweller A, Gu Z, Halas NJ, Hampp N, Hartmann RK, Hersam MC, Hunziker P, Jian J, Jiang X, Jungebluth P, Kadhiresan P, Kataoka K, Khademhosseini A, Kopeček J, Kotov NA, Krug HF, Lee DS, Lehr CM, Leong KW, Liang XJ, Ling Lim M, Liz-Marzán LM, Ma X, Macchiarini P, Meng H, Möhwald H, Mulvaney P, Nel AE, Nie S, Nordlander P, Okano T, Oliveira J, Park TH, Penner RM, Prato M, Puntes V, Rotello VM, Samarakoon A, Schaak RE, Shen Y, Sjöqvist S, Skirtach AG, Soliman MG, Stevens MM, Sung HW, Tang BZ, Tietze R, Udugama BN, VanEpps JS, Weil T, Weiss PS, Willner I, Wu Y, Yang L, Yue Z, Zhang Q, Zhang Q, Zhang XE, Zhao Y, Zhou X, Parak WJ. Diverse Applications of Nanomedicine. ACS NANO 2017; 11:2313-2381. [PMID: 28290206 PMCID: PMC5371978 DOI: 10.1021/acsnano.6b06040] [Citation(s) in RCA: 765] [Impact Index Per Article: 109.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Indexed: 04/14/2023]
Abstract
The design and use of materials in the nanoscale size range for addressing medical and health-related issues continues to receive increasing interest. Research in nanomedicine spans a multitude of areas, including drug delivery, vaccine development, antibacterial, diagnosis and imaging tools, wearable devices, implants, high-throughput screening platforms, etc. using biological, nonbiological, biomimetic, or hybrid materials. Many of these developments are starting to be translated into viable clinical products. Here, we provide an overview of recent developments in nanomedicine and highlight the current challenges and upcoming opportunities for the field and translation to the clinic.
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Affiliation(s)
- Beatriz Pelaz
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Christoph Alexiou
- ENT-Department, Section of Experimental Oncology & Nanomedicine
(SEON), Else Kröner-Fresenius-Stiftung-Professorship for Nanomedicine, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Ramon A. Alvarez-Puebla
- Department of Physical Chemistry, Universitat Rovira I Virgili, 43007 Tarragona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Frauke Alves
- Department of Haematology and Medical Oncology, Department of Diagnostic
and Interventional Radiology, University
Medical Center Göttingen, 37075 Göttingen Germany
- Department of Molecular Biology of Neuronal Signals, Max-Planck-Institute for Experimental Medicine, 37075 Göttingen, Germany
| | - Anne M. Andrews
- California NanoSystems Institute, Department of Chemistry
and Biochemistry and Department of Psychiatry and Semel Institute
for Neuroscience and Human Behavior, Division of NanoMedicine and Center
for the Environmental Impact of Nanotechnology, and Department of Materials Science
and Engineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Sumaira Ashraf
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Lajos P. Balogh
- AA Nanomedicine & Nanotechnology Consultants, North Andover, Massachusetts 01845, United States
| | - Laura Ballerini
- International School for Advanced Studies (SISSA/ISAS), 34136 Trieste, Italy
| | - Alessandra Bestetti
- School of Chemistry & Bio21 Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Cornelia Brendel
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Susanna Bosi
- Department of Chemical
and Pharmaceutical Sciences, University
of Trieste, 34127 Trieste, Italy
| | - Monica Carril
- CIC biomaGUNE, Paseo de Miramón 182, 20014, Donostia - San Sebastián, Spain
- Ikerbasque, Basque Foundation
for Science, 48013 Bilbao, Spain
| | - Warren C. W. Chan
- Institute of Biomaterials
and Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Chunying Chen
- CAS Center for Excellence in Nanoscience and CAS Key
Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of
China, Beijing 100190, China
| | - Xiaodong Chen
- School of Materials
Science and Engineering, Nanyang Technological
University, Singapore 639798
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine,
National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Zhen Cheng
- Molecular
Imaging Program at Stanford and Bio-X Program, Canary Center at Stanford
for Cancer Early Detection, Stanford University, Stanford, California 94305, United States
| | - Daxiang Cui
- Institute of Nano Biomedicine and Engineering, Department of Instrument
Science and Engineering, School of Electronic Information and Electronical
Engineering, National Center for Translational Medicine, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Jianzhong Du
- Department of Polymeric Materials, School of Materials
Science and Engineering, Tongji University, Shanghai, China
| | - Christian Dullin
- Department of Haematology and Medical Oncology, Department of Diagnostic
and Interventional Radiology, University
Medical Center Göttingen, 37075 Göttingen Germany
| | - Alberto Escudero
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
- Instituto
de Ciencia de Materiales de Sevilla. CSIC, Universidad de Sevilla, 41092 Seville, Spain
| | - Neus Feliu
- Department of Clinical Science, Intervention, and Technology (CLINTEC), Karolinska Institutet, 141 86 Stockholm, Sweden
| | - Mingyuan Gao
- Institute of Chemistry, Chinese
Academy of Sciences, 100190 Beijing, China
| | | | - Yury Gogotsi
- Department of Materials Science and Engineering and A.J. Drexel Nanomaterials
Institute, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Arnold Grünweller
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Zhongwei Gu
- College of Polymer Science and Engineering, Sichuan University, 610000 Chengdu, China
| | - Naomi J. Halas
- Departments of Physics and Astronomy, Rice
University, Houston, Texas 77005, United
States
| | - Norbert Hampp
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Roland K. Hartmann
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Mark C. Hersam
- Departments of Materials Science and Engineering, Chemistry,
and Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Patrick Hunziker
- University Hospital, 4056 Basel, Switzerland
- CLINAM,
European Foundation for Clinical Nanomedicine, 4058 Basel, Switzerland
| | - Ji Jian
- Department of Polymer Science and Engineering and Center for
Bionanoengineering and Department of Chemical and Biological Engineering, Zhejiang University, 310027 Hangzhou, China
| | - Xingyu Jiang
- CAS Center for Excellence in Nanoscience and CAS Key
Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of
China, Beijing 100190, China
| | - Philipp Jungebluth
- Thoraxklinik Heidelberg, Universitätsklinikum
Heidelberg, 69120 Heidelberg, Germany
| | - Pranav Kadhiresan
- Institute of Biomaterials
and Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada
| | | | | | - Jindřich Kopeček
- Biomedical Polymers Laboratory, University of Utah, Salt Lake City, Utah 84112, United States
| | - Nicholas A. Kotov
- Emergency Medicine, University of Michigan, Ann Arbor, Michigan 48019, United States
| | - Harald F. Krug
- EMPA, Federal Institute for Materials
Science and Technology, CH-9014 St. Gallen, Switzerland
| | - Dong Soo Lee
- Department of Molecular Medicine and Biopharmaceutical
Sciences and School of Chemical and Biological Engineering, Seoul National University, Seoul, South Korea
| | - Claus-Michael Lehr
- Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
- HIPS - Helmhotz Institute for Pharmaceutical Research Saarland, Helmholtz-Center for Infection Research, 66123 Saarbrücken, Germany
| | - Kam W. Leong
- Department of Biomedical Engineering, Columbia University, New York City, New York 10027, United States
| | - Xing-Jie Liang
- CAS Center for Excellence in Nanoscience and CAS Key
Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of
China, Beijing 100190, China
- Laboratory of Controllable Nanopharmaceuticals, Chinese Academy of Sciences (CAS), 100190 Beijing, China
| | - Mei Ling Lim
- Department of Clinical Science, Intervention, and Technology (CLINTEC), Karolinska Institutet, 141 86 Stockholm, Sweden
| | - Luis M. Liz-Marzán
- CIC biomaGUNE, Paseo de Miramón 182, 20014, Donostia - San Sebastián, Spain
- Ikerbasque, Basque Foundation
for Science, 48013 Bilbao, Spain
- Biomedical Research Networking Center in Bioengineering Biomaterials and Nanomedicine, Ciber-BBN, 20014 Donostia - San Sebastián, Spain
| | - Xiaowei Ma
- Laboratory of Controllable Nanopharmaceuticals, Chinese Academy of Sciences (CAS), 100190 Beijing, China
| | - Paolo Macchiarini
- Laboratory of Bioengineering Regenerative Medicine (BioReM), Kazan Federal University, 420008 Kazan, Russia
| | - Huan Meng
- California NanoSystems Institute, Department of Chemistry
and Biochemistry and Department of Psychiatry and Semel Institute
for Neuroscience and Human Behavior, Division of NanoMedicine and Center
for the Environmental Impact of Nanotechnology, and Department of Materials Science
and Engineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Helmuth Möhwald
- Department of Interfaces, Max-Planck
Institute of Colloids and Interfaces, 14476 Potsdam, Germany
| | - Paul Mulvaney
- School of Chemistry & Bio21 Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andre E. Nel
- California NanoSystems Institute, Department of Chemistry
and Biochemistry and Department of Psychiatry and Semel Institute
for Neuroscience and Human Behavior, Division of NanoMedicine and Center
for the Environmental Impact of Nanotechnology, and Department of Materials Science
and Engineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Shuming Nie
- Emory University, Atlanta, Georgia 30322, United States
| | - Peter Nordlander
- Departments of Physics and Astronomy, Rice
University, Houston, Texas 77005, United
States
| | - Teruo Okano
- Tokyo Women’s Medical University, Tokyo 162-8666, Japan
| | | | - Tai Hyun Park
- Department of Molecular Medicine and Biopharmaceutical
Sciences and School of Chemical and Biological Engineering, Seoul National University, Seoul, South Korea
- Advanced Institutes of Convergence Technology, Suwon, South Korea
| | - Reginald M. Penner
- Department of Chemistry, University of
California, Irvine, California 92697, United States
| | - Maurizio Prato
- Department of Chemical
and Pharmaceutical Sciences, University
of Trieste, 34127 Trieste, Italy
- CIC biomaGUNE, Paseo de Miramón 182, 20014, Donostia - San Sebastián, Spain
- Ikerbasque, Basque Foundation
for Science, 48013 Bilbao, Spain
| | - Victor Puntes
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
- Institut Català de Nanotecnologia, UAB, 08193 Barcelona, Spain
- Vall d’Hebron University Hospital
Institute of Research, 08035 Barcelona, Spain
| | - Vincent M. Rotello
- Department
of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Amila Samarakoon
- Institute of Biomaterials
and Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Raymond E. Schaak
- Department of Chemistry, The
Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Youqing Shen
- Department of Polymer Science and Engineering and Center for
Bionanoengineering and Department of Chemical and Biological Engineering, Zhejiang University, 310027 Hangzhou, China
| | - Sebastian Sjöqvist
- Department of Clinical Science, Intervention, and Technology (CLINTEC), Karolinska Institutet, 141 86 Stockholm, Sweden
| | - Andre G. Skirtach
- Department of Interfaces, Max-Planck
Institute of Colloids and Interfaces, 14476 Potsdam, Germany
- Department of Molecular Biotechnology, University of Ghent, B-9000 Ghent, Belgium
| | - Mahmoud G. Soliman
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Molly M. Stevens
- Department of Materials,
Department of Bioengineering, Institute for Biomedical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Hsing-Wen Sung
- Department of Chemical Engineering and Institute of Biomedical
Engineering, National Tsing Hua University, Hsinchu City, Taiwan,
ROC 300
| | - Ben Zhong Tang
- Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Hong Kong, China
| | - Rainer Tietze
- ENT-Department, Section of Experimental Oncology & Nanomedicine
(SEON), Else Kröner-Fresenius-Stiftung-Professorship for Nanomedicine, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Buddhisha N. Udugama
- Institute of Biomaterials
and Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada
| | - J. Scott VanEpps
- Emergency Medicine, University of Michigan, Ann Arbor, Michigan 48019, United States
| | - Tanja Weil
- Institut für
Organische Chemie, Universität Ulm, 89081 Ulm, Germany
- Max-Planck-Institute for Polymer Research, 55128 Mainz, Germany
| | - Paul S. Weiss
- California NanoSystems Institute, Department of Chemistry
and Biochemistry and Department of Psychiatry and Semel Institute
for Neuroscience and Human Behavior, Division of NanoMedicine and Center
for the Environmental Impact of Nanotechnology, and Department of Materials Science
and Engineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Itamar Willner
- Institute of Chemistry, The Center for
Nanoscience and Nanotechnology, The Hebrew
University of Jerusalem, Jerusalem 91904, Israel
| | - Yuzhou Wu
- Max-Planck-Institute for Polymer Research, 55128 Mainz, Germany
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, 430074 Wuhan, China
| | | | - Zhao Yue
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Qian Zhang
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Qiang Zhang
- School of Pharmaceutical Science, Peking University, 100191 Beijing, China
| | - Xian-En Zhang
- National Laboratory of Biomacromolecules,
CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Yuliang Zhao
- CAS Center for Excellence in Nanoscience and CAS Key
Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of
China, Beijing 100190, China
| | - Xin Zhou
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Wolfgang J. Parak
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
- CIC biomaGUNE, Paseo de Miramón 182, 20014, Donostia - San Sebastián, Spain
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49
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Dullin C, Ufartes R, Larsson E, Martin S, Lazzarini M, Tromba G, Missbach-Guentner J, Pinkert-Leetsch D, Katschinski DM, Alves F. μCT of ex-vivo stained mouse hearts and embryos enables a precise match between 3D virtual histology, classical histology and immunochemistry. PLoS One 2017; 12:e0170597. [PMID: 28178293 PMCID: PMC5298245 DOI: 10.1371/journal.pone.0170597] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 01/06/2017] [Indexed: 12/13/2022] Open
Abstract
The small size of the adult and developing mouse heart poses a great challenge for imaging in preclinical research. The aim of the study was to establish a phosphotungstic acid (PTA) ex-vivo staining approach that efficiently enhances the x-ray attenuation of soft-tissue to allow high resolution 3D visualization of mouse hearts by synchrotron radiation based μCT (SRμCT) and classical μCT. We demonstrate that SRμCT of PTA stained mouse hearts ex-vivo allows imaging of the cardiac atrium, ventricles, myocardium especially its fibre structure and vessel walls in great detail and furthermore enables the depiction of growth and anatomical changes during distinct developmental stages of hearts in mouse embryos. Our x-ray based virtual histology approach is not limited to SRμCT as it does not require monochromatic and/or coherent x-ray sources and even more importantly can be combined with conventional histological procedures. Furthermore, it permits volumetric measurements as we show for the assessment of the plaque volumes in the aortic valve region of mice from an ApoE-/- mouse model. Subsequent, Masson-Goldner trichrome staining of paraffin sections of PTA stained samples revealed intact collagen and muscle fibres and positive staining of CD31 on endothelial cells by immunohistochemistry illustrates that our approach does not prevent immunochemistry analysis. The feasibility to scan hearts already embedded in paraffin ensured a 100% correlation between virtual cut sections of the CT data sets and histological heart sections of the same sample and may allow in future guiding the cutting process to specific regions of interest. In summary, since our CT based virtual histology approach is a powerful tool for the 3D depiction of morphological alterations in hearts and embryos in high resolution and can be combined with classical histological analysis it may be used in preclinical research to unravel structural alterations of various heart diseases.
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Affiliation(s)
- Christian Dullin
- Institute for Diagnostic and Interventional Radiology, University Medical Center, Goettingen, Germany
- Synchrotron Light Source ‘Elettra,’ Trieste, Italy
- * E-mail:
| | - Roser Ufartes
- Department of Molecular Biology of Neuronal Signals, Max Planck Institute of Experimental Medicine, Goettingen, Germany
| | | | - Sabine Martin
- Department of Molecular Biology of Neuronal Signals, Max Planck Institute of Experimental Medicine, Goettingen, Germany
- Center Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Goettingen, Germany
| | - Marcio Lazzarini
- Department of Molecular Biology of Neuronal Signals, Max Planck Institute of Experimental Medicine, Goettingen, Germany
| | | | - Jeannine Missbach-Guentner
- Institute for Diagnostic and Interventional Radiology, University Medical Center, Goettingen, Germany
- Clinic for Haematology and Medical Oncology, University Medical Center, Goettingen, Germany
| | - Diana Pinkert-Leetsch
- Clinic for Haematology and Medical Oncology, University Medical Center, Goettingen, Germany
| | - Dörthe M. Katschinski
- Institute of Cardiovascular Physiology, University Medical Center, Goettingen, Germany
| | - Frauke Alves
- Institute for Diagnostic and Interventional Radiology, University Medical Center, Goettingen, Germany
- Department of Molecular Biology of Neuronal Signals, Max Planck Institute of Experimental Medicine, Goettingen, Germany
- Clinic for Haematology and Medical Oncology, University Medical Center, Goettingen, Germany
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50
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Guo E, Zeng G, Kazantsev D, Rockett P, Bent J, Kirkland M, Van Dalen G, Eastwood DS, StJohn D, Lee PD. Synchrotron X-ray tomographic quantification of microstructural evolution in ice cream – a multi-phase soft solid. RSC Adv 2017. [DOI: 10.1039/c7ra00642j] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Synchrotron X-ray tomography reveals the evolving internal morphology of a multi-phase soft solid, ice cream, enabling time dependent quantitation.
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Affiliation(s)
- Enyu Guo
- School of Materials
- The University of Manchester
- Manchester
- UK
- Research Complex at Harwell
| | - Guang Zeng
- School of Materials
- The University of Manchester
- Manchester
- UK
- Research Complex at Harwell
| | - Daniil Kazantsev
- School of Materials
- The University of Manchester
- Manchester
- UK
- Research Complex at Harwell
| | - Peter Rockett
- School of Materials
- The University of Manchester
- Manchester
- UK
| | | | | | | | - David S. Eastwood
- School of Materials
- The University of Manchester
- Manchester
- UK
- Research Complex at Harwell
| | - David StJohn
- School of Mechanical and Mining Engineering
- The University of Queensland
- St Lucia
- Australia
| | - Peter D. Lee
- School of Materials
- The University of Manchester
- Manchester
- UK
- Research Complex at Harwell
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