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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Pollock JA, Morgan KS, Croton LCP, Croughan MK, Ruben G, Yagi N, Sekiguchi H, Kitchen MJ. Precise phase retrieval for propagation-based images using discrete mathematics. Sci Rep 2022; 12:18469. [PMID: 36323686 DOI: 10.1038/s41598-022-19940-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [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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3
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Barbone GE, Bravin A, Mittone A, Pacureanu A, Mascio G, Di Pietro P, Kraiger MJ, Eckermann M, Romano M, Hrabě de Angelis M, Cloetens P, Bruno V, Battaglia G, Coan P. X-ray multiscale 3D neuroimaging to quantify cellular aging and neurodegeneration postmortem in a model of Alzheimer’s disease. Eur J Nucl Med Mol Imaging 2022; 49:4338-4357. [PMID: 35852558 PMCID: PMC9606093 DOI: 10.1007/s00259-022-05896-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 06/25/2022] [Indexed: 01/19/2023]
Abstract
Abstract
Purpose
Modern neuroimaging lacks the tools necessary for whole-brain, anatomically dense neuronal damage screening. An ideal approach would include unbiased histopathologic identification of aging and neurodegenerative disease.
Methods
We report the postmortem application of multiscale X-ray phase-contrast computed tomography (X-PCI-CT) for the label-free and dissection-free organ-level to intracellular-level 3D visualization of distinct single neurons and glia. In deep neuronal populations in the brain of aged wild-type and of 3xTgAD mice (a triply-transgenic model of Alzheimer’s disease), we quantified intracellular hyperdensity, a manifestation of aging or neurodegeneration.
Results
In 3xTgAD mice, the observed hyperdensity was identified as amyloid-β and hyper-phosphorylated tau protein deposits with calcium and iron involvement, by correlating the X-PCI-CT data to immunohistochemistry, X-ray fluorescence microscopy, high-field MRI, and TEM. As a proof-of-concept, X-PCI-CT was used to analyze hippocampal and cortical brain regions of 3xTgAD mice treated with LY379268, selective agonist of group II metabotropic glutamate receptors (mGlu2/3 receptors). Chronic pharmacologic activation of mGlu2/3 receptors significantly reduced the hyperdensity particle load in the ventral cortical regions of 3xTgAD mice, suggesting a neuroprotective effect with locoregional efficacy.
Conclusions
This multiscale micro-to-nano 3D imaging method based on X-PCI-CT enabled identification and quantification of cellular and sub-cellular aging and neurodegeneration in deep neuronal and glial cell populations in a transgenic model of Alzheimer’s disease. This approach quantified the localized and intracellular neuroprotective effects of pharmacological activation of mGlu2/3 receptors.
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Sena G, Fidalgo G, Paiva K, Barcelos R, Nogueira LP, Colaço MV, Gonzalez MS, Azambuja P, Colaço G, da Silva HR, de Moura Meneses AA, Barroso RC. Synchrotron X-ray biosample imaging: opportunities and challenges. Biophys Rev. [DOI: 10.1007/s12551-022-00964-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/25/2022] [Indexed: 12/17/2022] Open
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5
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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. Opt 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] [What about the content of this article? (0)] [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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Hofmann J, Zboray R. An In-House Cone-Beam Tomographic Reconstruction Package for Laboratory X-ray Phase-Contrast Imaging. Applied Sciences 2022; 12:1430. [DOI: 10.3390/app12031430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Phase-contrast, and in general, multi-modal, X-ray micro-tomography is proven to be very useful for low-density, low-attention samples enabling much better contrast than its attenuation-based pendant. Therefore, it is increasingly applied in bio- and life sciences primarily dealing with such samples. Although there is a plethora of literature regarding phase-retrieval algorithms, access to implementations of those algorithms is relatively limited and very few packages combining phase-retrieval methods with the full tomographic reconstruction pipeline are available. This is especially the case for laboratory-based phase-contrast imaging typically featuring cone-beam geometry. We present here an in-house cone-beam tomographic reconstruction package for laboratory X-ray phase-contrast imaging. It covers different phase-contrast techniques and phase retrieval methods. The paper explains their implementation and integration in the filtered back projection chain. Their functionality and efficiency will be demonstrated through applications on a few dedicated samples.
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Arhatari BD, Stevenson AW, Abbey B, Nesterets YI, Maksimenko A, Hall CJ, Thompson D, Mayo SC, Fiala T, Quiney HM, Taba ST, Lewis SJ, Brennan PC, Dimmock M, Häusermann D, Gureyev TE. X-ray Phase-Contrast Computed Tomography for Soft Tissue Imaging at the Imaging and Medical Beamline (IMBL) of the Australian Synchrotron. Applied Sciences 2021; 11:4120. [DOI: 10.3390/app11094120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Imaging and Medical Beamline (IMBL) is a superconducting multipole wiggler-based beamline at the 3 GeV Australian Synchrotron operated by the Australian Nuclear Science and Technology Organisation (ANSTO). The beamline delivers hard X-rays in the 25–120 keV energy range and offers the potential for a range of biomedical X-ray applications, including radiotherapy and medical imaging experiments. One of the imaging modalities available at IMBL is propagation-based X-ray phase-contrast computed tomography (PCT). PCT produces superior results when imaging low-density materials such as soft tissue (e.g., breast mastectomies) and has the potential to be developed into a valuable medical imaging tool. We anticipate that PCT will be utilized for medical breast imaging in the near future with the advantage that it could provide better contrast than conventional X-ray absorption imaging. The unique properties of synchrotron X-ray sources such as high coherence, energy tunability, and high brightness are particularly well-suited for generating PCT data using very short exposure times on the order of less than 1 min. The coherence of synchrotron radiation allows for phase-contrast imaging with superior sensitivity to small differences in soft-tissue density. Here we also compare the results of PCT using two different detectors, as these unique source characteristics need to be complemented with a highly efficient detector. Moreover, the application of phase retrieval for PCT image reconstruction enables the use of noisier images, potentially significantly reducing the total dose received by patients during acquisition. This work is part of ongoing research into innovative tomographic methods aimed at the introduction of 3D X-ray medical imaging at the IMBL to improve the detection and diagnosis of breast cancer. Major progress in this area at the IMBL includes the characterization of a large number of mastectomy samples, both normal and cancerous, which have been scanned at clinically acceptable radiation dose levels and evaluated by expert radiologists with respect to both image quality and cancer diagnosis.
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Kastner DB, Kharazia V, Nevers R, Smyth C, Astudillo-Maya DA, Williams GM, Yang Z, Holobetz CM, Santina LD, Parkinson DY, Frank LM. Scalable method for micro-CT analysis enables large scale quantitative characterization of brain lesions and implants. Sci Rep 2020; 10:20851. [PMID: 33257721 PMCID: PMC7705725 DOI: 10.1038/s41598-020-77796-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 11/17/2020] [Indexed: 12/18/2022] Open
Abstract
Anatomic evaluation is an important aspect of many studies in neuroscience; however, it often lacks information about the three-dimensional structure of the brain. Micro-CT imaging provides an excellent, nondestructive, method for the evaluation of brain structure, but current applications to neurophysiological or lesion studies require removal of the skull as well as hazardous chemicals, dehydration, or embedding, limiting their scalability and utility. Here we present a protocol using eosin in combination with bone decalcification to enhance contrast in the tissue and then employ monochromatic and propagation phase-contrast micro-CT imaging to enable the imaging of brain structure with the preservation of the surrounding skull. Instead of relying on descriptive, time-consuming, or subjective methods, we develop simple quantitative analyses to map the locations of recording electrodes and to characterize the presence and extent of hippocampal brain lesions.
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Affiliation(s)
- David B Kastner
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, 94143, USA. .,Kavli Institute for Fundamental Neuroscience and Department of Physiology, University of California, San Francisco, CA, 94158, USA.
| | - Viktor Kharazia
- Kavli Institute for Fundamental Neuroscience and Department of Physiology, University of California, San Francisco, CA, 94158, USA
| | - Rhino Nevers
- Kavli Institute for Fundamental Neuroscience and Department of Physiology, University of California, San Francisco, CA, 94158, USA
| | - Clay Smyth
- Kavli Institute for Fundamental Neuroscience and Department of Physiology, University of California, San Francisco, CA, 94158, USA
| | - Daniela A Astudillo-Maya
- Kavli Institute for Fundamental Neuroscience and Department of Physiology, University of California, San Francisco, CA, 94158, USA
| | - Greer M Williams
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, 94143, USA
| | - Zhounan Yang
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, 94143, USA
| | - Cristofer M Holobetz
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, 94143, USA
| | - Luca Della Santina
- Deparment of Ophthalmology, University of California, San Francisco, CA, 94143, USA.,Bakar Computational Health Science Unit, University of California, San Francisco, CA, 94158, USA
| | - Dilworth Y Parkinson
- Advanced Light Source, Lawrence Berkeley National Labs, Berkeley, CA, 94720, USA
| | - Loren M Frank
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, 94143, USA.,Kavli Institute for Fundamental Neuroscience and Department of Physiology, University of California, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Stroebel J, Horng A, Armbruster M, Mittone A, Reiser M, Bravin A, Coan P. Convolutional neuronal networks combined with X-ray phase-contrast imaging for a fast and observer-independent discrimination of cartilage and liver diseases stages. Sci Rep 2020; 10:20007. [PMID: 33203975 DOI: 10.1038/s41598-020-76937-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 10/27/2020] [Indexed: 12/19/2022] Open
Abstract
We applied transfer learning using Convolutional Neuronal Networks to high resolution X-ray phase contrast computed tomography datasets and tested the potential of the systems to accurately classify Computed Tomography images of different stages of two diseases, i.e. osteoarthritis and liver fibrosis. The purpose is to identify a time-effective and observer-independent methodology to identify pathological conditions. Propagation-based X-ray phase contrast imaging WAS used with polychromatic X-rays to obtain a 3D visualization of 4 human cartilage plugs and 6 rat liver samples with a voxel size of 0.7 × 0.7 × 0.7 µm3 and 2.2 × 2.2 × 2.2 µm3, respectively. Images with a size of 224 × 224 pixels are used to train three pre-trained convolutional neuronal networks for data classification, which are the VGG16, the Inception V3, and the Xception networks. We evaluated the performance of the three systems in terms of classification accuracy and studied the effect of the variation of the number of inputs, training images and of iterations. The VGG16 network provides the highest classification accuracy when the training and the validation-test of the network are performed using data from the same samples for both the cartilage (99.8%) and the liver (95.5%) datasets. The Inception V3 and Xception networks achieve an accuracy of 84.7% (43.1%) and of 72.6% (53.7%), respectively, for the cartilage (liver) images. By using data from different samples for the training and validation-test processes, the Xception network provided the highest test accuracy for the cartilage dataset (75.7%), while for the liver dataset the VGG16 network gave the best results (75.4%). By using convolutional neuronal networks we show that it is possible to classify large datasets of biomedical images in less than 25 min on a 8 CPU processor machine providing a precise, robust, fast and observer-independent method for the discrimination/classification of different stages of osteoarthritis and liver diseases.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Kitchen MJ, Buckley GA, Kerr LT, Lee KL, Uesugi K, Yagi N, Hooper SB. Emphysema quantified: mapping regional airway dimensions using 2D phase contrast X-ray imaging. Biomed Opt Express 2020; 11:4176-4190. [PMID: 32923035 PMCID: PMC7449757 DOI: 10.1364/boe.390587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
We have developed an analyser-based phase contrast X-ray imaging technique to measure the mean length scale of pores or particles that cannot be resolved directly by the system. By combining attenuation, phase and ultra-small angle X-ray scattering information, the technique was capable of measuring differences in airway dimension between lungs of healthy mice and those with mild and severe emphysema. Our measurements of airway dimensions from 2D images showed a 1:1 relationship to the actual airway dimensions measured using micro-CT. Using 80 images, the sensitivity and specificity were measured to be 0.80 and 0.89, respectively, with the area under the ROC curve close to ideal at 0.96. Reducing the number of images to 11 slightly decreased the sensitivity to 0.75 and the ROC curve area to 0.90, whilst the specificity remained high at 0.89.
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Affiliation(s)
- Marcus J. Kitchen
- School of Physics and Astronomy, Monash
University, Clayton, Victoria, 3800, Australia
| | - Genevieve A. Buckley
- School of Physics and Astronomy, Monash
University, Clayton, Victoria, 3800, Australia
| | | | - Katie L. Lee
- School of Physics and Astronomy, Monash
University, Clayton, Victoria, 3800, Australia
| | - Kentaro Uesugi
- The Ritchie Centre, MIMR-PHI Institute of
Medical Research and the Department of Obstetrics and Gynaecology,
Monash University, Clayton, Victoria, 3168, Australia
| | - Naoto Yagi
- The Ritchie Centre, MIMR-PHI Institute of
Medical Research and the Department of Obstetrics and Gynaecology,
Monash University, Clayton, Victoria, 3168, Australia
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Werdiger F, Donnelley M, Dubsky S, Murrie RP, Carnibella RP, Samarage CR, How YY, Zosky GR, Fouras A, Parsons DW, Morgan KS. Quantification of muco-obstructive lung disease variability in mice via laboratory X-ray velocimetry. Sci Rep 2020; 10:10859. [PMID: 32616726 DOI: 10.1038/s41598-020-67633-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 05/29/2020] [Indexed: 11/08/2022] Open
Abstract
To effectively diagnose, monitor and treat respiratory disease clinicians should be able to accurately assess the spatial distribution of airflow across the fine structure of lung. This capability would enable any decline or improvement in health to be located and measured, allowing improved treatment options to be designed. Current lung function assessment methods have many limitations, including the inability to accurately localise the origin of global changes within the lung. However, X-ray velocimetry (XV) has recently been demonstrated to be a sophisticated and non-invasive lung function measurement tool that is able to display the full dynamics of airflow throughout the lung over the natural breathing cycle. In this study we present two developments in XV analysis. Firstly, we show the ability of laboratory-based XV to detect the patchy nature of cystic fibrosis (CF)-like disease in β-ENaC mice. Secondly, we present a technique for numerical quantification of CF-like disease in mice that can delineate between two major modes of disease symptoms. We propose this analytical model as a simple, easy-to-interpret approach, and one capable of being readily applied to large quantities of data generated in XV imaging. Together these advances show the power of XV for assessing local airflow changes. We propose that XV should be considered as a novel lung function measurement tool for lung therapeutics development in small animal models, for CF and for other muco-obstructive diseases.
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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 Trans Med 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] [What about the content of this article? (0)] [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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15
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Barbone GE, Bravin A, Mittone A, Kraiger MJ, Hrabě de Angelis M, Bossi M, Ballarini E, Rodriguez-Menendez V, Ceresa C, Cavaletti G, Coan P. Establishing sample-preparation protocols for X-ray phase-contrast CT of rodent spinal cords: Aldehyde fixations and osmium impregnation. J Neurosci Methods 2020; 339:108744. [DOI: 10.1016/j.jneumeth.2020.108744] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 12/14/2022]
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Li K, Chen Y, Sun R, Yu B, Li G, Jiang X. Exploring potential of different X-ray imaging methods for early-stage lung cancer detection. Radiat Detect Technol Methods 2020; 4:213-221. [DOI: 10.1007/s41605-020-00173-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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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. Biomed Opt 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] [What about the content of this article? (0)] [Affiliation(s)] [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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18
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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. Opt 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] [What about the content of this article? (0)] [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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19
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Matsumoto T, Shimizu R, Uesugi K. 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] [What about the content of this article? (0)] [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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20
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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. Opt 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] [What about the content of this article? (0)] [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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21
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Donato S, Pacile’ S, Brombal L, Tromba G, Longo R. Phase-Contrast Breast-CT: Optimization of Experimental Parameters and Reconstruction Algorithms. IFMBE Proceedings 2019. [DOI: 10.1007/978-981-10-9035-6_20] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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22
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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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. Biomed Opt 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] [What about the content of this article? (0)] [Affiliation(s)] [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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24
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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25
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Brombal L, Donato S, Brun F, Delogu P, Fanti V, Oliva P, Rigon L, Di Trapani V, Longo R, Golosio B. Large-area single-photon-counting CdTe detector for synchrotron radiation computed tomography: a dedicated pre-processing procedure. J Synchrotron Radiat 2018; 25:1068-1077. [PMID: 29979168 DOI: 10.1107/s1600577518006197] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/23/2018] [Indexed: 06/08/2023]
Abstract
Large-area CdTe single-photon-counting detectors are becoming more and more attractive in view of low-dose imaging applications due to their high efficiency, low intrinsic noise and absence of a scintillating screen which affects spatial resolution. At present, however, since the dimensions of a single sensor are small (typically a few cm2), multi-module architectures are needed to obtain a large field of view. This requires coping with inter-module gaps and with close-to-edge pixels, which generally show a non-optimal behavior. Moreover, high-Z detectors often show gain variations in time due to charge trapping: this effect is detrimental especially in computed tomography (CT) applications where a single tomographic image requires hundreds of projections continuously acquired in several seconds. This work has been carried out at the SYRMEP beamline of the Elettra synchrotron radiation facility (Trieste, Italy), in the framework of the SYRMA-3D project, which aims to perform the world's first breast-CT clinical study with synchrotron radiation. An ad hoc data pre-processing procedure has been developed for the PIXIRAD-8 CdTe single-photon-counting detector, comprising an array of eight 30.7 mm × 24.8 mm modules tiling a 246 mm × 25 mm sensitive area, which covers the full synchrotron radiation beam. The procedure consists of five building blocks, namely dynamic flat-fielding, gap seaming, dynamic ring removal, projection despeckling and around-gap equalization. Each block is discussed and compared, when existing, with conventional approaches. The effectiveness of the pre-processing is demonstrated for phase-contrast CT images of a human breast specimen. The dynamic nature of the proposed procedure, which provides corrections dependent upon the projection index, allows the effective removal of time-dependent artifacts, preserving the main image features including phase effects.
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Affiliation(s)
- Luca Brombal
- Department of Physics, University of Trieste, 34127 Trieste, Italy
| | - Sandro Donato
- Department of Physics, University of Trieste, 34127 Trieste, Italy
| | | | - Pasquale Delogu
- Department of Physical Sciences, Earth and Environment, University of Siena, 53100 Siena, Italy
| | - Viviana Fanti
- Department of Physics, University of Cagliari, 09042 Monserrato (CA), Italy
| | | | - Luigi Rigon
- Department of Physics, University of Trieste, 34127 Trieste, Italy
| | - Vittorio Di Trapani
- Department of Physical Sciences, Earth and Environment, University of Siena, 53100 Siena, Italy
| | - Renata Longo
- Department of Physics, University of Trieste, 34127 Trieste, Italy
| | - Bruno Golosio
- Department of Physics, University of Cagliari, 09042 Monserrato (CA), Italy
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26
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Dyrby TB, Innocenti GM, Bech M, Lundell H. Validation strategies for the interpretation of microstructure imaging using diffusion MRI. Neuroimage 2018; 182:62-79. [PMID: 29920374 DOI: 10.1016/j.neuroimage.2018.06.049] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 06/08/2018] [Accepted: 06/15/2018] [Indexed: 12/19/2022] Open
Abstract
Extracting microanatomical information beyond the image resolution of MRI would provide valuable tools for diagnostics and neuroscientific research. A number of mathematical models already suggest microstructural interpretations of diffusion MRI (dMRI) data. Examples of such microstructural features could be cell bodies and neurites, e.g. the axon's diameter or their orientational distribution for global connectivity analysis using tractography, and have previously only been possible to access through conventional histology of post mortem tissue or invasive biopsies. The prospect of gaining the same knowledge non-invasively from the whole living human brain could push the frontiers for the diagnosis of neurological and psychiatric diseases. It could also provide a general understanding of the development and natural variability in the healthy brain across a population. However, due to a limited image resolution, most of the dMRI measures are indirect estimations and may depend on the whole chain from experimental parameter settings to model assumptions and implementation. Here, we review current literature in this field and highlight the integrative work across anatomical length scales that is needed to validate and trust a new dMRI method. We encourage interdisciplinary collaborations and data sharing in regards to applying and developing new validation techniques to improve the specificity of future dMRI methods.
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Affiliation(s)
- Tim B Dyrby
- Danish Research Centre for Magnetic Resonance, Center for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark; Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Giorgio M Innocenti
- Karolinska Institutet, Department of Neuroscience, Stockholm, Sweden; Brain and Mind Institute, Swiss Federal Institute of Technology in Lausanne, Lausanne, Switzerland
| | - Martin Bech
- Medical Radiation Physics, Lund University, Lund, Sweden
| | - Henrik Lundell
- Danish Research Centre for Magnetic Resonance, Center for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
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27
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Barbone GE, Bravin A, Romanelli P, Mittone A, Bucci D, Gaaβ T, Le Duc G, Auweter S, Reiser MF, Kraiger MJ, Hrabě de Angelis M, Battaglia G, Coan P. Micro-imaging of Brain Cancer Radiation Therapy Using Phase-contrast Computed Tomography. Int J Radiat Oncol Biol Phys 2018; 101:965-984. [PMID: 29976510 DOI: 10.1016/j.ijrobp.2018.03.063] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 03/23/2018] [Accepted: 03/29/2018] [Indexed: 01/20/2023]
Abstract
PURPOSE Experimental neuroimaging provides a wide range of methods for the visualization of brain anatomic morphology down to subcellular detail. Still, each technique-specific detection mechanism presents compromises among the achievable field-of-view size, spatial resolution, and nervous tissue sensitivity, leading to partial sample coverage, unresolved morphologic structures, or sparse labeling of neuronal populations and often also to obligatory sample dissection or other sample invasive manipulations. X-ray phase-contrast imaging computed tomography (PCI-CT) is an experimental imaging method that simultaneously provides micrometric spatial resolution, high soft-tissue sensitivity, and ex vivo full organ rodent brain coverage without any need for sample dissection, staining or labeling, or contrast agent injection. In the present study, we explored the benefits and limitations of PCI-CT use for in vitro imaging of normal and cancerous brain neuromorphology after in vivo treatment with synchrotron-generated x-ray microbeam radiation therapy (MRT), a spatially fractionated experimental high-dose radiosurgery. The goals were visualization of the MRT effects on nervous tissue and a qualitative comparison of the results to the histologic and high-field magnetic resonance imaging findings. METHODS AND MATERIALS MRT was administered in vivo to the brain of both healthy and cancer-bearing rats. At 45 days after treatment, the brain was dissected out and imaged ex vivo using propagation-based PCI-CT. RESULTS PCI-CT visualizes the brain anatomy and microvasculature in 3 dimensions and distinguishes cancerous tissue morphology, necrosis, and intratumor accumulation of iron and calcium deposits. Moreover, PCI-CT detects the effects of MRT throughout the treatment target areas (eg, the formation of micrometer-thick radiation-induced tissue ablation). The observed neurostructures were confirmed by histologic and immunohistochemistry examination and related to the micro-magnetic resonance imaging data. CONCLUSIONS PCI-CT enabled a unique 3D neuroimaging approach for ex vivo studies on small animal models in that it concurrently delivers high-resolution insight of local brain tissue morphology in both normal and cancerous micro-milieu, localizes radiosurgical damage, and highlights the deep microvasculature. This method could assist experimental small animal neurology studies in the postmortem evaluation of neuropathology or treatment effects.
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Affiliation(s)
- Giacomo E Barbone
- Department of Physics, Ludwig Maximilians University, Garching, Germany
| | - Alberto Bravin
- European Synchrotron Radiation Facility, Grenoble, France
| | | | | | - Domenico Bucci
- Department of Molecular Pathology, Neuropharmacology Section, I.R.C.C.S. Neuromed, Pozzilli, Italy
| | - Thomas Gaaβ
- Department of Clinical Radiology, Ludwig Maximilians University, Munich, Germany
| | | | - Sigrid Auweter
- Department of Clinical Radiology, Ludwig Maximilians University, Munich, Germany
| | - Maximilian F Reiser
- Department of Clinical Radiology, Ludwig Maximilians University, Munich, Germany
| | - Markus J Kraiger
- Institute of Experimental Genetics and German Mouse Clinic, German Research Center for Environmental Health, Neuherberg, Germany
| | - Martin Hrabě de Angelis
- Institute of Experimental Genetics and German Mouse Clinic, German Research Center for Environmental Health, Neuherberg, Germany; Department of Experimental Genetics, School of Life Science Weihenstephan, Technical University of Munich, Freising, Germany; German Center for Diabetes Research, Neuherberg, Germany
| | - Giuseppe Battaglia
- Department of Molecular Pathology, Neuropharmacology Section, I.R.C.C.S. Neuromed, Pozzilli, Italy
| | - Paola Coan
- Department of Physics, Ludwig Maximilians University, Garching, Germany; Department of Clinical Radiology, Ludwig Maximilians University, Munich, Germany.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Abstract
Detection and visualization of lung tissue structures is impaired by predominance of air. However, by using synchrotron x-rays, refraction of x-rays at the interface of tissue and air can be utilized to generate contrast which may in turn enable quantification of lung optical properties. We utilized multiple image radiography, a variant of diffraction enhanced imaging, at the Canadian light source to quantify changes in unique x-ray optical properties of lungs, namely attenuation, refraction and ultra small-angle scatter (USAXS or width) contrast ratios as a function of lung orientation in free-breathing or respiratory-gated mice before and after intra-nasal bacterial endotoxin (lipopolysaccharide) instillation. The lung ultra small-angle scatter and attenuation contrast ratios were significantly higher 9 h post lipopolysaccharide instillation compared to saline treatment whereas the refraction contrast decreased in magnitude. In ventilated mice, end-expiratory pressures result in an increase in ultra small-angle scatter contrast ratio when compared to end-inspiratory pressures. There were no detectable changes in lung attenuation or refraction contrast ratio with change in lung pressure alone. In effect, multiple image radiography can be applied towards following optical properties of lung air-tissue barrier over time during pathologies such as acute lung injury.
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Affiliation(s)
- G K Aulakh
- Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
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30
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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31
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Liao S, Ni S, Cao Y, Yin X, Wu T, Lu H, Hu J, Wu H, Lang Y. The 3D characteristics of post-traumatic syringomyelia in a rat model: a propagation-based synchrotron radiation microtomography study. J Synchrotron Radiat 2017; 24:1218-1225. [PMID: 29091065 DOI: 10.1107/s1600577517011201] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 07/30/2017] [Indexed: 06/07/2023]
Abstract
Many published literature sources have described the histopathological characteristics of post-traumatic syringomyelia (PTS). However, three-dimensional (3D) visualization studies of PTS have been limited due to the lack of reliable 3D imaging techniques. In this study, the imaging efficiency of propagation-based synchrotron radiation microtomography (PB-SRµCT) was determined to detect the 3D morphology of the cavity and surrounding microvasculature network in a rat model of PTS. The rat model of PTS was established using the infinite horizon impactor to produce spinal cord injury (SCI), followed by a subarachnoid injection of kaolin to produce arachnoiditis. PB-SRµCT imaging and histological examination, as well as fluorescence staining, were conducted on the animals at the tenth week after SCI. The 3D morphology of the cystic cavity was vividly visualized using PB-SRµCT imaging. The quantitative parameters analyzed by PB-SRµCT, including the lesion and spared spinal cord tissue area, the minimum and maximum diameters in the cystic cavity, and cavity volume, were largely consistent with the results of the histological assessment. Moreover, the 3D morphology of the cavity and surrounding angioarchitecture could be simultaneously detected on the PB-SRµCT images. This study demonstrated that high-resolution PB-SRµCT could be used for the 3D visualization of trauma-induced spinal cord cavities and provides valuable quantitative data for cavity characterization. PB-SRµCT could be used as a reliable imaging technique and offers a novel platform for tracking cavity formation and morphological changes in an experimental animal model of PTS.
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Affiliation(s)
- Shenghui Liao
- School of Information Science and Engineering, Central South University, Changsha 410008, People's Republic of China
| | - Shuangfei Ni
- Department of Spine Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Yong Cao
- Department of Spine Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Xianzhen Yin
- Center for Drug Delivery System, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Tianding Wu
- Department of Spine Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Hongbin Lu
- Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Changsha 410008, People's Republic of China
| | - Jianzhong Hu
- Department of Spine Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Hao Wu
- Department of Spine Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Ye Lang
- Department of Spine Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
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32
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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33
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34
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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. Opt 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] [What about the content of this article? (0)] [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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35
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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36
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Ruiz-Yaniz M, Zanette I, Sarapata A, Birnbacher L, Marschner M, Chabior M, Olbinado M, Pfeiffer F, Rack A. Hard X-ray phase-contrast tomography of non-homogeneous specimens: grating interferometry versus propagation-based imaging. J Synchrotron Radiat 2016; 23:1202-9. [PMID: 27577776 DOI: 10.1107/s1600577516009164] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 06/07/2016] [Indexed: 05/15/2023]
Abstract
X-ray phase-contrast imaging is an effective approach to drastically increase the contrast and sensitivity of microtomographic techniques. Numerous approaches to depict the real part of the complex-valued refractive index of a specimen are nowadays available. A comparative study using experimental data from grating-based interferometry and propagation-based phase contrast combined with single-distance phase retrieval applied to a non-homogeneous sample is presented (acquired at beamline ID19-ESRF). It is shown that grating-based interferometry can handle density gradients in a superior manner. The study underlines the complementarity of the two techniques for practical applications.
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Affiliation(s)
- Maite Ruiz-Yaniz
- European Synchrotron Radiation Facility, 71 Rue des Martyrs, 38000 Grenoble, France
| | - Irene Zanette
- Lehrstuhl für Biomedizinische Physik, Physik-Department and Institut für Medizintechnik, Technische Universität München, James-Franck-Strasse 1, 85748 Garching, Germany
| | - Adrian Sarapata
- Lehrstuhl für Biomedizinische Physik, Physik-Department and Institut für Medizintechnik, Technische Universität München, James-Franck-Strasse 1, 85748 Garching, Germany
| | - Lorenz Birnbacher
- Lehrstuhl für Biomedizinische Physik, Physik-Department and Institut für Medizintechnik, Technische Universität München, James-Franck-Strasse 1, 85748 Garching, Germany
| | - Mathias Marschner
- Lehrstuhl für Biomedizinische Physik, Physik-Department and Institut für Medizintechnik, Technische Universität München, James-Franck-Strasse 1, 85748 Garching, Germany
| | - Michael Chabior
- Lehrstuhl für Biomedizinische Physik, Physik-Department and Institut für Medizintechnik, Technische Universität München, James-Franck-Strasse 1, 85748 Garching, Germany
| | - Margie Olbinado
- European Synchrotron Radiation Facility, 71 Rue des Martyrs, 38000 Grenoble, France
| | - Franz Pfeiffer
- Lehrstuhl für Biomedizinische Physik, Physik-Department and Institut für Medizintechnik, Technische Universität München, James-Franck-Strasse 1, 85748 Garching, Germany
| | - Alexander Rack
- European Synchrotron Radiation Facility, 71 Rue des Martyrs, 38000 Grenoble, France
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37
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Miao P, Wu Z, Li M, Ji Y, Xie B, Lin X, Yang GY. Synchrotron Radiation X-Ray Phase-Contrast Tomography Visualizes Microvasculature Changes in Mice Brains after Ischemic Injury. Neural Plast 2016; 2016:3258494. [PMID: 27563468 DOI: 10.1155/2016/3258494] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 06/02/2016] [Accepted: 06/23/2016] [Indexed: 12/15/2022] Open
Abstract
Imaging brain microvasculature is important in plasticity studies of cerebrovascular diseases. Applying contrast agents, traditional μCT and μMRI methods gain imaging contrast for vasculature. The aim of this study is to develop a synchrotron radiation X-ray inline phase-contrast tomography (SRXPCT) method for imaging the intact mouse brain (micro)vasculature in high resolution (~3.7 μm) without contrast agent. A specific preparation protocol was proposed to enhance the phase contrast of brain vasculature by using density difference over gas-tissue interface. The CT imaging system was developed and optimized to obtain 3D brain vasculature of adult male C57BL/6 mice. The SRXPCT method was further applied to investigate the microvasculature changes in mouse brains (n = 14) after 14-day reperfusion from transient middle cerebral artery occlusion (tMCAO). 3D reconstructions of brain microvasculature demonstrated that the branching radius ratio (post- to preinjury) of small vessels (radius < 7.4 μm) in the injury group was significantly smaller than that in the sham group (p < 0.05). This result revealed the active angiogenesis in the recovery brain after stroke. As a high-resolution and contrast-agent-free method, the SRXPCT method demonstrates higher potential in investigations of functional plasticity in cerebrovascular diseases.
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Astolfo A, Lathuilière A, Laversenne V, Schneider B, Stampanoni M. Amyloid-β plaque deposition measured using propagation-based X-ray phase contrast CT imaging. J Synchrotron Radiat 2016; 23:813-9. [PMID: 27140162 PMCID: PMC5315008 DOI: 10.1107/s1600577516004045] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/10/2016] [Indexed: 05/28/2023]
Abstract
Amyloid beta accumulation into insoluble plaques (Aβp) is known to play a significant role in the pathological process in Alzheimer's disease (AD). The presence of Aβp is also one of the neuropathological hallmarks for the disease. AD final diagnosis is generally acknowledged after the evaluation of Aβp deposition in the brain. Insoluble Aβp accumulation may also concur to cause AD as postulated in the so-called amyloid hypothesis. Therefore, the visualization, evaluation and quantification of Aβp are nowadays the keys for a better understanding of the disease, which may point to a possible cure for AD in the near future. Synchrotron-based X-ray phase contrast (XPC) has been demonstrated as the only imaging method that can retrieve the Aβp signal with high spatial resolution (up to 10 µm), high sensitivity and three-dimensional information at the same time. Although at the moment XPC is suitable for ex vivo samples only, it may develop into an alternative to positron emission tomography and magnetic resonance imaging in Aβp imaging. In this contribution the possibility of using synchrotron-based X-ray phase propagation computed tomography to visualize and measure Aβp on mouse brains is presented. A careful setup optimization for this application leads to a significant improvement of spatial resolution (∼1 µm), data acquisition speed (five times faster), X-ray dose (five times lower) and setup complexity, without a substantial loss in sensitivity when compared with the classic implementation of grating-based X-ray interferometry.
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Affiliation(s)
- Alberto Astolfo
- TOMCAT Beamline, Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Aurélien Lathuilière
- Neurodegenerative Studies Laboratory, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Vanessa Laversenne
- Neurodegenerative Studies Laboratory, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Bernard Schneider
- Neurodegenerative Studies Laboratory, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Marco Stampanoni
- TOMCAT Beamline, Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
- Institute for Biomedical Engineering, University and ETH Zurich, Zurich, Switzerland
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Longo R, Arfelli F, Bellazzini R, Bottigli U, Brez A, Brun F, Brunetti A, Delogu P, Di Lillo F, Dreossi D, Fanti V, Fedon C, Golosio B, Lanconelli N, Mettivier G, Minuti M, Oliva P, Pinchera M, Rigon L, Russo P, Sarno A, Spandre G, Tromba G, Zanconati F. Towards breast tomography with synchrotron radiation at Elettra: first images. Phys Med Biol 2016; 61:1634-49. [PMID: 26836274 DOI: 10.1088/0031-9155/61/4/1634] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The aim of the SYRMA-CT collaboration is to set-up the first clinical trial of phase-contrast breast CT with synchrotron radiation (SR). In order to combine high image quality and low delivered dose a number of innovative elements are merged: a CdTe single photon counting detector, state-of-the-art CT reconstruction and phase retrieval algorithms. To facilitate an accurate exam optimization, a Monte Carlo model was developed for dose calculation using GEANT4. In this study, high isotropic spatial resolution (120 μm)(3) CT scans of objects with dimensions and attenuation similar to a human breast were acquired, delivering mean glandular doses in the range of those delivered in clinical breast CT (5-25 mGy). Due to the spatial coherence of the SR beam and the long distance between sample and detector, the images contain, not only absorption, but also phase information from the samples. The application of a phase-retrieval procedure increases the contrast-to-noise ratio of the tomographic images, while the contrast remains almost constant. After applying the simultaneous algebraic reconstruction technique to low-dose phase-retrieved data sets (about 5 mGy) with a reduced number of projections, the spatial resolution was found to be equal to filtered back projection utilizing a four fold higher dose, while the contrast-to-noise ratio was reduced by 30%. These first results indicate the feasibility of clinical breast CT with SR.
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40
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Rositi H, Frindel C, Wiart M, Langer M, Olivier C, Peyrin F, Rousseau D. Computer vision tools to optimize reconstruction parameters in x-ray in-line phase tomography. Phys Med Biol 2016; 59:7767-75. [PMID: 25419867 DOI: 10.1088/0031-9155/59/24/7767] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In this article, a set of three computer vision tools, including scale invariant feature transform (SIFT), a measure of focus, and a measure based on tractography are demonstrated to be useful in replacing the eye of the expert in the optimization of the reconstruction parameters in x-ray in-line phase tomography. We demonstrate how these computer vision tools can be used to inject priors on the shape and scale of the object to be reconstructed. This is illustrated with the Paganin single intensity image phase retrieval algorithm in heterogeneous soft tissues of biomedical interest, where the selection of the reconstruction parameters was previously made from visual inspection or physical assumptions on the composition of the sample.
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Affiliation(s)
- H Rositi
- Université de Lyon, Laboratoire CREATIS, CNRS UMR5220, INSERM U1044, Université Lyon 1, INSA-Lyon, 69621 Villeurbanne, France
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41
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Ren Y, Wang Y, Zhou G, He Y, Xie H, Du G, Deng B, Lin X, Yang GY, Xiao T. X-ray propagation-based equally sloped tomography for mouse brain. J Xray Sci Technol 2016; 24:79-86. [PMID: 26890902 DOI: 10.3233/xst-160533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
BACKGROUND The outstanding functional importance of the brain implies a strong need for brain imaging modalities. However, the current imaging approaches that target the brain in rodents remain suboptimal. OBJECTIVE AND METHODS In this paper, X-ray propagation-based phase contrast imaging combined with equally sloped tomography (PPCI-EST) was employed to nondestructively investigate the mouse brain. RESULTS The grey and white matters, which have extremely small differences in electron density, were clearly discriminated. The fine structures, including the corpus callosum (cc), the optic chiasma (ox) and the caudate putamen (CPu), were revealed. Compared to the filtered back projection reconstruction, the PPCI-EST significantly reduce projection number while maintaining sufficient image quality. CONCLUSIONS It could be a potential tool for fast and low-dose phase-contrast imaging to biomedical specimens.
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Affiliation(s)
- Yuqi Ren
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
| | - Yudan Wang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
| | - Guangzhao Zhou
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
| | - You He
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
| | - Honglan Xie
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guohao Du
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
| | - Biao Deng
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaojie Lin
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Guo-Yuan Yang
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Tiqiao Xiao
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
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42
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Ullherr M, Zabler S. Correcting multi material artifacts from single material phase retrieved holo-tomograms with a simple 3D Fourier method. Opt Express 2015; 23:32718-27. [PMID: 26699061 DOI: 10.1364/oe.23.032718] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Here we present a method for the removal of multi-material artifacts which occur during the application of a single material phase retrieval procedure to X-ray tomographic data sets. For the phase retrieval we chose the most common method which is the single material filter. The correction method which we describe in the following has been designed for samples consisting of three distinct materials, hence effectively two different material interfaces. Furthermore the material phase with the strongest X-ray interaction needs to show sufficient absorption in order to allow for segmenting this phase through application of a grey value threshold. If these conditions are fulfilled the method is easy to apply through post processing as is shown for the volume images of two sample types.
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43
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Zamir A, Arthurs OJ, Hagen CK, Diemoz PC, Brochard T, Bravin A, Sebire NJ, Olivo A. X-ray phase contrast tomography; proof of principle for post-mortem imaging. Br J Radiol 2015; 89:20150565. [PMID: 26612467 DOI: 10.1259/bjr.20150565] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
OBJECTIVE To demonstrate the feasibility of using X-ray phase-contrast tomography to assess internal organs in a post-mortem piglet model, as a possible non-invasive imaging autopsy technique. METHODS Tomographic images of a new-born piglet were obtained using a free-space propagation X-ray phase-contrast imaging setup at a synchrotron (European Synchrotron Radiation Facility, Grenoble, France). A monochromatic X-ray beam (52 keV) was used in combination with a detector pixel size of 46 × 46 µm(2). A phase-retrieval algorithm was applied to all projections, which were then reconstructed into tomograms using the filtered-back projection algorithm. Images were assessed for diagnostic quality. RESULTS Images obtained with the free-space propagation setup presented high soft-tissue contrast and sufficient resolution for resolving organ structure. All of the main body organs (heart, lungs, kidneys, liver and intestines) were easily identified and adequately visualized. In addition, grey/white matter differentiation in the cerebellum while still contained within the skull was shown. CONCLUSION The feasibility of using X-ray phase-contrast tomography as a post-mortem imaging technique in an animal model has been demonstrated. Future studies will focus on translating this experiment to a laboratory-based setup. ADVANCES IN KNOWLEDGE Appropriate image processing and analysis enable the simultaneous visualization of both soft- and hard-tissue structures in X-ray phase-contrast images of a complex, thick sample.
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Affiliation(s)
- Anna Zamir
- 1 Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - Owen J Arthurs
- 2 Great Ormond Street Hospital for Children NHS Foundation Trust, London UK.,3 Institute of Child Health, University College London, London, UK
| | - Charlotte K Hagen
- 1 Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - Paul C Diemoz
- 1 Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | | | - Alberto Bravin
- 4 European Synchrotron Radiation Facility, Grenoble, France
| | - Neil J Sebire
- 2 Great Ormond Street Hospital for Children NHS Foundation Trust, London UK.,3 Institute of Child Health, University College London, London, UK
| | - Alessandro Olivo
- 1 Department of Medical Physics and Biomedical Engineering, University College London, London, UK
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44
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Nesterets YI, Gureyev TE, Mayo SC, Stevenson AW, Thompson D, Brown JMC, Kitchen MJ, Pavlov KM, Lockie D, Brun F, Tromba G. A feasibility study of X-ray phase-contrast mammographic tomography at the Imaging and Medical beamline of the Australian Synchrotron. J Synchrotron Radiat 2015; 22:1509-1523. [PMID: 26524316 DOI: 10.1107/s160057751501766x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 09/21/2015] [Indexed: 06/05/2023]
Abstract
Results are presented of a recent experiment at the Imaging and Medical beamline of the Australian Synchrotron intended to contribute to the implementation of low-dose high-sensitivity three-dimensional mammographic phase-contrast imaging, initially at synchrotrons and subsequently in hospitals and medical imaging clinics. The effect of such imaging parameters as X-ray energy, source size, detector resolution, sample-to-detector distance, scanning and data processing strategies in the case of propagation-based phase-contrast computed tomography (CT) have been tested, quantified, evaluated and optimized using a plastic phantom simulating relevant breast-tissue characteristics. Analysis of the data collected using a Hamamatsu CMOS Flat Panel Sensor, with a pixel size of 100 µm, revealed the presence of propagation-based phase contrast and demonstrated significant improvement of the quality of phase-contrast CT imaging compared with conventional (absorption-based) CT, at medically acceptable radiation doses.
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Affiliation(s)
- Yakov I Nesterets
- Commonwealth Scientific and Industrial Research Organisation, Melbourne, Australia
| | - Timur E Gureyev
- Commonwealth Scientific and Industrial Research Organisation, Melbourne, Australia
| | - Sheridan C Mayo
- Commonwealth Scientific and Industrial Research Organisation, Melbourne, Australia
| | - Andrew W Stevenson
- Commonwealth Scientific and Industrial Research Organisation, Melbourne, Australia
| | - Darren Thompson
- Commonwealth Scientific and Industrial Research Organisation, Melbourne, Australia
| | - Jeremy M C Brown
- School of Physics and Astronomy, Monash University, Melbourne, Australia
| | - Marcus J Kitchen
- School of Physics and Astronomy, Monash University, Melbourne, Australia
| | - Konstantin M Pavlov
- School of Science and Technology, University of New England, Armidale, Australia
| | | | - Francesco Brun
- Department of Engineering and Architecture, University of Trieste, Trieste, Italy
| | - Giuliana Tromba
- Elettra - Sincrotrone Trieste SCpA, Basovizza (Trieste), Italy
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45
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Kitchen MJ, Buckley GA, Leong AFT, Carnibella RP, Fouras A, Wallace MJ, Hooper SB. X-ray specks: low dose in vivo imaging of lung structure and function. Phys Med Biol 2015; 60:7259-76. [PMID: 26348552 DOI: 10.1088/0031-9155/60/18/7259] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Respiratory health is directly linked to the structural and mechanical properties of the airways of the lungs. For studying respiratory development and pathology, the ability to quantitatively measure airway dimensions and changes in their size during respiration is highly desirable. Real-time imaging of the terminal airways with sufficient contrast and resolution during respiration is currently not possible. Herein we reveal a simple method for measuring lung airway dimensions in small animals during respiration from a single propagation-based phase contrast x-ray image, thereby requiring minimal radiation. This modality renders the lungs visible as a speckled intensity pattern. In the near-field regime, the size of the speckles is directly correlated with that of the dominant length scale of the airways. We demonstrate that Fourier space quantification of the speckle texture can be used to statistically measure regional airway dimensions at the alveolar scale, with measurement precision finer than the spatial resolution of the imaging system. Using this technique we discovered striking differences in developmental maturity in the lungs of rabbit kittens at birth.
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Affiliation(s)
- Marcus J Kitchen
- School of Physics and Astronomy, Monash University, Clayton, Victoria, Australia
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46
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Dullin C, Larsson E, Tromba G, Markus AM, Alves F. Phase-contrast computed tomography for quantification of structural changes in lungs of asthma mouse models of different severity. J Synchrotron Radiat 2015; 22:1106-11. [PMID: 26134818 PMCID: PMC4489538 DOI: 10.1107/s1600577515006177] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 03/26/2015] [Indexed: 05/03/2023]
Abstract
Lung imaging in mouse disease models is crucial for the assessment of the severity of airway disease but remains challenging due to the small size and the high porosity of the organ. Synchrotron inline free-propagation phase-contrast computed tomography (CT) with its intrinsic high soft-tissue contrast provides the necessary sensitivity and spatial resolution to analyse the mouse lung structure in great detail. Here, this technique has been applied in combination with single-distance phase retrieval to quantify alterations of the lung structure in experimental asthma mouse models of different severity. In order to mimic an in vivo situation as close as possible, the lungs were inflated with air at a constant physiological pressure. Entire mice were embedded in agarose gel and imaged using inline free-propagation phase-contrast CT at the SYRMEP beamline (Synchrotron Light Source, `Elettra', Trieste, Italy). The quantification of the obtained phase-contrast CT data sets revealed an increasing lung soft-tissue content in mice correlating with the degree of the severity of experimental allergic airways disease. In this way, it was possible to successfully discriminate between healthy controls and mice with either mild or severe allergic airway disease. It is believed that this approach may have the potential to evaluate the efficacy of novel therapeutic strategies that target airway remodelling processes in asthma.
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Affiliation(s)
- Christian Dullin
- Institute of Diagnostic and Interventional Radiology, University Medical Center Goettingen, Robert Koch Strasse 40, Goettingen, Lower Saxony 37075, Germany
| | - Emanuel Larsson
- Elettra-Sincrotrone Trieste, Strada Statale 14, km 163,5 in AREA Science Park, Basovizza (Trieste) 34149, Italy
- Department of Architecture and Engineering, University of Trieste, Trieste, Italy
- Department of Physics, Chemistry and Biology, Linkoeping University, SE-581 83 Linkoeping, Sweden
| | - Giuliana Tromba
- Elettra-Sincrotrone Trieste, Strada Statale 14, km 163,5 in AREA Science Park, Basovizza (Trieste) 34149, Italy
| | - Andrea M. Markus
- Department of Haematology and Medical Oncology, University Medical Center Goettingen, Robert Koch Strasse 40, Goettingen, Lower Saxony 37075, Germany
| | - Frauke Alves
- Institute of Diagnostic and Interventional Radiology, University Medical Center Goettingen, Robert Koch Strasse 40, Goettingen, Lower Saxony 37075, Germany
- Department of Haematology and Medical Oncology, University Medical Center Goettingen, Robert Koch Strasse 40, Goettingen, Lower Saxony 37075, Germany
- Department of Molecular Biology of Neuronal Signals, Max Planck Institut for Experimental Medicine, Hermann-Rein-Strasse 3, Goettingen, Lower Saxony 37075, Germany
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47
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Pratt IV, Belev G, Zhu N, Chapman LD, Cooper DML. In vivoimaging of rat cortical bone porosity by synchrotron phase contrast micro computed tomography. Phys Med Biol 2014; 60:211-32. [DOI: 10.1088/0031-9155/60/1/211] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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48
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Zhang M, Peng G, Sun D, Xie Y, Xia J, Long H, Hu K, Xiao B. Synchrotron radiation imaging is a powerful tool to image brain microvasculature. Med Phys 2014; 41:031907. [PMID: 24593725 DOI: 10.1118/1.4865784] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Synchrotron radiation (SR) imaging is a powerful experimental tool for micrometer-scale imaging of microcirculation in vivo. This review discusses recent methodological advances and findings from morphological investigations of cerebral vascular networks during several neurovascular pathologies. In particular, it describes recent developments in SR microangiography for real-time assessment of the brain microvasculature under various pathological conditions in small animal models. It also covers studies that employed SR-based phase-contrast imaging to acquire 3D brain images and provide detailed maps of brain vasculature. In addition, a brief introduction of SR technology and current limitations of SR sources are described in this review. In the near future, SR imaging could transform into a common and informative imaging modality to resolve subtle details of cerebrovascular function.
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Affiliation(s)
- Mengqi Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, People's Republic of China
| | - Guanyun Peng
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People's Republic of China
| | - Danni Sun
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, People's Republic of China
| | - Yuanyuan Xie
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, People's Republic of China
| | - Jian Xia
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, People's Republic of China
| | - Hongyu Long
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, People's Republic of China
| | - Kai Hu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, People's Republic of China
| | - Bo Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, People's Republic of China
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49
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Irvine S, Mokso R, Modregger P, Wang Z, Marone F, Stampanoni M. Simple merging technique for improving resolution in qualitative single image phase contrast tomography. Opt Express 2014; 22:27257-27269. [PMID: 25401876 DOI: 10.1364/oe.22.027257] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
For dynamic samples and/or for simple ease-of-use experiments, single-image phase contrast tomography is a very effective method for the 3D visualization of materials which would otherwise be indiscernible in attenuation based x-ray imaging. With binary samples (e.g. air-material) and monochromatic wavefields a transport-of-intensity (TIE)-based phase retrieval algorithm is known to retrieve accurate quantitative maps of the phase distribution. For mixed material samples and/or white beam radiation the algorithm can still produce useful qualitative tomographic reconstructions with significantly improved area contrast. The stability of the algorithm comes with a recognized associated loss of spatial resolution due to its essential behaviour as a low-pass filter. One possible answer to this is an image fusion technique that merges the slices reconstructed from raw phase contrast images and those after phase retrieval, where the improved contrast may be acquired without the associated loss of high-frequency information. We present this technique as a simple few-parameter Fourier method, which is easily tunable and highly compatible with current reconstruction steps.
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50
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Mohammadi S, Larsson E, Alves F, Dal Monego S, Biffi S, Garrovo C, Lorenzon A, Tromba G, Dullin C. Quantitative evaluation of a single-distance phase-retrieval method applied on in-line phase-contrast images of a mouse lung. J Synchrotron Radiat 2014; 21:784-9. [PMID: 24971975 PMCID: PMC4073959 DOI: 10.1107/s1600577514009333] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 04/25/2014] [Indexed: 05/19/2023]
Abstract
Propagation-based X-ray phase-contrast computed tomography (PBI) has already proven its potential in a great variety of soft-tissue-related applications including lung imaging. However, the strong edge enhancement, caused by the phase effects, often hampers image segmentation and therefore the quantitative analysis of data sets. Here, the benefits of applying single-distance phase retrieval prior to the three-dimensional reconstruction (PhR) are discussed and quantified compared with three-dimensional reconstructions of conventional PBI data sets in terms of contrast-to-noise ratio (CNR) and preservation of image features. The PhR data sets show more than a tenfold higher CNR and only minor blurring of the edges when compared with PBI in a predominately absorption-based set-up. Accordingly, phase retrieval increases the sensitivity and provides more functionality in computed tomography imaging.
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Affiliation(s)
- Sara Mohammadi
- The Abdus Salam International Centre for Theoretical Physics, Trieste, Italy
- Synchrotron Light Source ‘Elettra’ Trieste, Strada Statale 14, km 163.5 in AREA Science Park, Basovizza 34149, Italy
- Correspondence e-mail: ,
| | - Emanuel Larsson
- Synchrotron Light Source ‘Elettra’ Trieste, Strada Statale 14, km 163.5 in AREA Science Park, Basovizza 34149, Italy
- Department of Physics, Chemistry and Biology, Linköping University, SE-581 83, Sweden
- Department of Architecture and Engineering, University of Trieste, Trieste, Italy
| | - Frauke Alves
- Department of Hematology/Oncology, University Hospital Goettingen, Robert Koch Strasse 40, Goettingen, Lower Saxony 37075, Germany
| | - Simeone Dal Monego
- Cluster in Biomedicine s.c.r.l., AREA Science Park, Strada Statale 14, km 163.5, Basovizza, 34149 Trieste, Italy
| | - Stefania Biffi
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, via dell’Istria 65/1, 34137 Trieste, Italy
| | - Chiara Garrovo
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, via dell’Istria 65/1, 34137 Trieste, Italy
| | - Andrea Lorenzon
- Cluster in Biomedicine s.c.r.l., AREA Science Park, Strada Statale 14, km 163.5, Basovizza, 34149 Trieste, Italy
| | - Giuliana Tromba
- Synchrotron Light Source ‘Elettra’ Trieste, Strada Statale 14, km 163.5 in AREA Science Park, Basovizza 34149, Italy
| | - Christian Dullin
- Department of Diagnostic and Interventional Radiology, University Hospital Goettingen, Robert Koch Strasse 40, Goettingen, Lower Saxony 37075, Germany
- Correspondence e-mail: ,
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