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261 results on '"Brun, Emmanuel"'

1. Review of speckle-tracking algorithms for x-ray phase contrast imaging: low dose applications

Author

Celestre, Rafael, Quenot, Laurene, Ninham, Christopher, Brun, Emmanuel, and Fardin, Luca

Subjects
Physics - Medical Physics, Physics - Optics
Abstract

X-ray speckles have been used for a wide variety of experiments, ranging from imaging (and tomography), wavefront sensing, spatial coherence measurements all the way to x-ray photon correlation spectroscopy (XPCS) and ptychography. In the near-field regime, x-ray speckle-grains preserve shape and size under free-space propagation for a static random modulation of the illumination, which permits using them as wavefront markers. The introduction of an object in the modulated field will lead to a displacement of the speckles due to refraction. Retrieving the local displacements enables access to the gradient of the phase-shift induced by the sample. The numerical process to retrieve the phase information is not trivial and numerous algorithms have been developed in the past decade with various advantages and limitations. This review focuses on near-field x-ray speckle phase imaging in the differential mode as described previously, introducing the existing algorithms with their specifications and comparing their performances under various experimental conditions., Comment: 19 pages, 8 figures

Published
2024

2. Dark-field and directional dark-field on low coherence X-ray sources with random mask modulations: validation with SAXS anisotropy measurements

Author

Magnin, Clara, Quenot, Laurene, Bohic, Sylvain, Cenda, Dan Mihai, Martínez, Manuel Fernández, Lantz, Blandine, Faure, Bertrand, and Brun, Emmanuel

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Physics - Medical Physics, Physics - Optics
Abstract

Phase Contrast Imaging (PCI), Dark-Field (DF) and Directional Dark-Field (DDF) imaging are recent X-ray imaging modalities that have demonstrated their interest by providing access to information and contrasts different from those provided by conventional absorption X-ray imaging. However, access to these two types of images is currently limited because the acquisitions require the use of coherent sources such as synchrotron radiation or complicated optical setups to exploit the coherence requirements. This work demonstrates the possibility of efficiently performing phase contrast, dark-field and directional dark-field imaging on a low-coherence laboratory system equipped with a conventional X-ray tube, using a simple, fast and robust single-mask technique. The transfer to a low spatial coherence laboratory system was made possible by using random modulation based imaging (MoBI) and extending the low coherence system algorithm to retrieve dark-field and directional dark-field., Comment: 5 pages, 4 figures

Published
2023

3. Directional dark-field implicit x-ray speckle tracking using an anisotropic-diffusion Fokker-Planck equation

Author

Pavlov, Konstantin M., Paganin, David M., Morgan, Kaye S., Heyang, Li, Berujon, Sebastien, Quénot, Laurène, and Brun, Emmanuel

Subjects
Physics - Medical Physics, Physics - Applied Physics
Abstract

When a macroscopic-sized non-crystalline sample is illuminated using coherent x-ray radiation, a bifurcation of photon energy flow may occur. The coarse-grained complex refractive index of the sample may be considered to attenuate and refract the incident coherent beam, leading to a coherent component of the transmitted beam. Spatially-unresolved sample microstructure, associated with the fine-grained components of the complex refractive index, introduces a diffuse component to the transmitted beam. This diffuse photon-scattering channel may be viewed in terms of position-dependent fans of ultra-small-angle x-ray scatter. These position-dependent fans, at the exit surface of the object, may under certain circumstances be approximated as having a locally-elliptical shape. By using an anisotropic-diffusion Fokker-Planck approach to model this bifurcated x-ray energy flow, we show how all three components (attenuation, refraction and locally-elliptical diffuse scatter) may be recovered. This is done via x-ray speckle tracking, in which the sample is illuminated with spatially-random x-ray fields generated by coherent illumination of a spatially-random membrane. The theory is developed, and then successfully applied to experimental x-ray data., Comment: To be published in Physical Review A; accepted version with minor revisions compared to the previous version

Published
2021
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5. X-ray Multimodal Intrinsic-Speckle-Tracking

Author

Pavlov, Konstantin M., Paganin, David M., Li, Heyang, Berujon, Sebastien, Rougé-Labriet, Hélène, and Brun, Emmanuel

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Physics - Applied Physics, Physics - Optics
Abstract

We develop X-ray Multi-modal Intrinsic-Speckle-Tracking (MIST), a form of X-ray speckle-tracking that is able to recover both the position-dependent phase shift and the position-dependent small-angle X-ray scattering (SAXS) signal of a phase object. MIST is based on combining a Fokker-Planck description of paraxial X-ray optics, with an optical-flow formalism for X-ray speckle-tracking. Only two images need to be taken in the presence of the sample, corresponding to two different transverse positions of the speckle-generating membrane, in order to recover both the refractive and local-SAXS properties of the sample. Like the optical-flow X-ray phase-retrieval method which it generalises, the MIST method implicitly rather than explicitly tracks both the transverse motion and the diffusion of speckles that is induced by the presence of a sample. Application to X-ray synchrotron data shows the method to be efficient, rapid and stable.

Published
2019
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6. Single-shot x-ray speckle-based imaging of a single-material object

Author

Pavlov, Konstantin M., Heyang, Li, Paganin, David M., Berujon, Sebastien, Rougé-Labriet, Hélène, and Brun, Emmanuel

Subjects
Physics - Medical Physics, Physics - Applied Physics
Abstract

We develop a means for speckle-based phase imaging of the projected thickness of a single-material object, under the assumption of illumination by spatially random time-independent x-ray speckles. These speckles are generated by passing x rays through a suitable spatially random mask. The method makes use of a single image obtained in the presence of the object, which serves to deform the illuminating speckle field relative to a reference speckle field (which only needs to be measured once) obtained in the presence of the mask and the absence of the object. The method implicitly rather than explicitly tracks speckles, and utilizes the transport-of-intensity equation to give a closed-form solution to the inverse problem of determining the complex transmission function of the object. Implementation using x-ray synchrotron data shows the method to be robust and efficient with respect to noise. Applications include x-ray phase--amplitude radiography and tomography, as well as time-dependent imaging of dynamic and radiation-sensitive samples using low-flux sources.

Published
2019
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7. 4D nanoimaging of early age cement hydration

Author

Shirani, Shiva, Cuesta, Ana, Morales-Cantero, Alejandro, Santacruz, Isabel, Diaz, Ana, Trtik, Pavel, Holler, Mirko, Rack, Alexander, Lukic, Bratislav, Brun, Emmanuel, Salcedo, Inés R., and Aranda, Miguel A. G.

Published
2023
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9. Single-Image Geometric-Flow X-Ray Speckle Tracking

Author

Paganin, David M., Labriet, Helene, Brun, Emmanuel, and Berujon, Sebastien

Subjects
Physics - Medical Physics
Abstract

We develop a speckle-tracking method for x-ray phase-contrast imaging, based on the concept of geometric flow. This flow is a conserved current associated with deformation of illuminating x-ray speckles induced by passage through a sample. The method provides a rapid, efficient, and accurate algorithm for quantitative phase imaging. It is highly photon efficient and able to image dynamic objects, since a single radiograph of the sample is sufficient for the phase recovery. We experimentally quantify the resolution and contrast of the approach with both two-dimensional and three-dimensional phase-imaging applications using x-ray synchrotron radiation. Finally, we discuss adaptations of the method to imaging with compact x-ray sources that have a large source size and significant spectral bandwidth., Comment: 3 figures

Published
2018
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12. PyHST2: an hybrid distributed code for high speed tomographic reconstruction with iterative reconstruction and a priori knowledge capabilities

Author

Mirone, Alessandro, Gouillart, Emmanuelle, Brun, Emmanuel, Tafforeau, Paul, and Kieffer, Jerome

Subjects
Mathematics - Numerical Analysis, Computer Science - Computer Vision and Pattern Recognition
Abstract

We present the PyHST2 code which is in service at ESRF for phase-contrast and absorption tomography. This code has been engineered to sustain the high data flow typical of the third generation synchrotron facilities (10 terabytes per experiment) by adopting a distributed and pipelined architecture. The code implements, beside a default filtered backprojection reconstruction, iterative reconstruction techniques with a-priori knowledge. These latter are used to improve the reconstruction quality or in order to reduce the required data volume and reach a given quality goal. The implemented a-priori knowledge techniques are based on the total variation penalisation and a new recently found convex functional which is based on overlapping patches. We give details of the different methods and their implementations while the code is distributed under free license. We provide methods for estimating, in the absence of ground-truth data, the optimal parameters values for a-priori techniques.

Published
2013
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13. A Convex Functional for Image Denoising based on Patches with Constrained Overlaps and its vectorial application to Low Dose Differential Phase Tomography

Author

Mirone, Alessandro, Brun, Emmanuel, and Coan, Paola

Subjects
Mathematics - Numerical Analysis, Computer Science - Computer Vision and Pattern Recognition
Abstract

We solve the image denoising problem with a dictionary learning technique by writing a convex functional of a new form. This functional contains beside the usual sparsity inducing term and fidelity term, a new term which induces similarity between overlapping patches in the overlap regions. The functional depends on two free regularization parameters: a coefficient multiplying the sparsity-inducing $L_{1}$ norm of the patch basis functions coefficients, and a coefficient multiplying the $L_{2}$ norm of the differences between patches in the overlapping regions. The solution is found by applying the iterative proximal gradient descent method with FISTA acceleration. In the case of tomography reconstruction we calculate the gradient by applying projection of the solution and its error backprojection at each iterative step. We study the quality of the solution, as a function of the regularization parameters and noise, on synthetic datas for which the solution is a-priori known. We apply the method on experimental data in the case of Differential Phase Tomography. For this case we use an original approach which consists in using vectorial patches, each patch having two components: one per each gradient component. The resulting algorithm, implemented in the ESRF tomography reconstruction code PyHST, results to be robust, efficient, and well adapted to strongly reduce the required dose and the number of projections in medical tomography.

Published
2013
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17. Virtual histology of Alzheimer’s disease: Biometal entrapment within amyloid-β plaques allows for detection via X-ray phase-contrast imaging

Author

Chourrout, Matthieu, primary, Sandt, Christophe, additional, Weitkamp, Timm, additional, Dučić, Tanja, additional, Meyronet, David, additional, Baron, Thierry, additional, Klohs, Jan, additional, Rama, Nicolas, additional, Boutin, Hervé, additional, Singh, Shifali, additional, Olivier, Cécile, additional, Wiart, Marlène, additional, Brun, Emmanuel, additional, Bohic, Sylvain, additional, and Chauveau, Fabien, additional

Published
2023
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22. A novel injectable radiopaque hydrogel with potent properties for multicolor CT imaging in the context of brain and cartilage regenerative therapy

Author

Said, Moustoifa, primary, Tavakoli, Clément, additional, Dumot, Chloé, additional, Toupet, Karine, additional, Dong, Yuxi Clara, additional, Collomb, Nora, additional, Auxenfans, Céline, additional, Moisan, Anaïck, additional, Favier, Bertrand, additional, Chovelon, Benoit, additional, Barbier, Emmanuel Luc, additional, Jorgensen, Christian, additional, Cormode, David Peter, additional, Noël, Danièle, additional, Brun, Emmanuel, additional, Elleaume, Hélène, additional, Wiart, Marlène, additional, Detante, Olivier, additional, Rome, Claire, additional, and Auzély-Velty, Rachel, additional

Published
2023
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23. Human fetal virtual histology with X-ray phase contrast imaging

Author

Vérot, Pierre-Louis, primary, Charnay, Laura, additional, Tavakoli, Clément, additional, Singh, Shifali, additional, Quénot, Laurène, additional, Cruz, Eva Solé, additional, Barnat, Monia, additional, Humbert, Sandrine, additional, Dommergues, Marc, additional, Durr, Alexandra, additional, Piolat, Christian, additional, Rabattu, Pierre-Yves, additional, and Brun, Emmanuel, additional

Published
2023
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25. High-resolution synchrotron K-edge subtraction CT allows tracking and quantifying therapeutic cells and their scaffold in a rat model of focal cerebral injury and can serve as a reference for spectral photon counting CT

Author

Tavakoli, Clément, primary, Cuccione, Elisa, additional, Dumot, Chloé, additional, Balegamire, Joëlle, additional, Si-Mohamed, Salim Aymeric, additional, Kim, Johoon, additional, Crola-da-Silva, Claire, additional, Chevalier, Yves, additional, Boussel, Loïc, additional, Douek, Philippe, additional, Cormode, David, additional, Elleaume, Hélène, additional, Brun, Emmanuel, additional, and Wiart, Marlène, additional

Published
2023
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33. Why are amyloid-β plaques detected by X-ray phase-contrast imaging? Role of metals revealed through combined synchrotron infrared and X-ray fluorescence microscopies

Author

Chourrout, Matthieu, primary, Sandt, Christophe, additional, Weitkamp, Timm, additional, Dučić, Tanja, additional, Meyronet, David, additional, Baron, Thierry, additional, Klohs, Jan, additional, Rama, Nicolas, additional, Boutin, Hervé, additional, Singh, Shifali, additional, Olivier, Cécile, additional, Wiart, Marlène, additional, Brun, Emmanuel, additional, Bohic, Sylvain, additional, and Chauveau, Fabien, additional

Published
2022
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35. Brain virtual histology with X-ray phase-contrast tomography Part II: 3D morphologies of amyloid-β plaques in Alzheimer’s disease models

Author

Chourrout, Matthieu, primary, Roux, Margaux, additional, Boisvert, Carlie, additional, Gislard, Coralie, additional, Legland, David, additional, Arganda-Carreras, Ignacio, additional, Olivier, Cécile, additional, Peyrin, Françoise, additional, Boutin, Hervé, additional, Rama, Nicolas, additional, Baron, Thierry, additional, Meyronet, David, additional, Brun, Emmanuel, additional, Rositi, Hugo, additional, Wiart, Marlène, additional, and Chauveau, Fabien, additional

Published
2022
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36. Brain virtual histology with X-ray phase-contrast tomography Part I: whole-brain myelin mapping in white-matter injury models

Author

Chourrout, Matthieu, primary, Rositi, Hugo, additional, Ong, Elodie, additional, Hubert, Violaine, additional, Paccalet, Alexandre, additional, Foucault, Louis, additional, Autret, Awen, additional, Fayard, Barbara, additional, Olivier, Cécile, additional, Bolbos, Radu, additional, Peyrin, Françoise, additional, Crola-da-Silva, Claire, additional, Meyronet, David, additional, Raineteau, Olivier, additional, Elleaume, Héléne, additional, Brun, Emmanuel, additional, Chauveau, Fabien, additional, and Wiart, Marlene, additional

Published
2022
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39. Multimodal Imaging with NanoGd Reveals Spatiotemporal Features of Neuroinflammation after Experimental Stroke

Author

Hubert, Violaine, Hristovska, Ines, Karpati, Szilvia, Benkeder, Sarah, Dey, Arindam, Dumot, Chloé, Amaz, Camille, Chounlamountri, Naura, Watrin, Chantal, Comte, Jean‐Christophe, Chauveau, Fabien, Brun, Emmanuel, Marche, Patrice, Lerouge, Fréderic, Parola, Stéphane, Berthezène, Yves, Vorup‐Jensen, Thomas, Pascual, Olivier, Wiart, Marlène, Cardiovasculaire, métabolisme, diabétologie et nutrition (CarMeN), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut NeuroMyoGène (INMG), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Chimie - UMR5182 (LC), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon)-Institut de Chimie du CNRS (INC), Institute for Advanced Biosciences / Institut pour l'Avancée des Biosciences (Grenoble) (IAB), Centre Hospitalier Universitaire [Grenoble] (CHU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement français du sang - Auvergne-Rhône-Alpes (EFS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Hospices Civils de Lyon (HCL), Hôpital Louis Pradel [CHU - HCL], Centre de recherche en neurosciences de Lyon (CRNL), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier le Vinatier [Bron], Synchrotron Radiation for Biomedicine = Rayonnement SynchroTROn pour la Recherche BiomédicalE (STROBE), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Centre de Recherche en Acquisition et Traitement de l'Image pour la Santé (CREATIS), Université Jean Monnet [Saint-Étienne] (UJM)-Hospices Civils de Lyon (HCL)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Aarhus University [Aarhus], Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA), European Synchroton Radiation Facility [Grenoble] (ESRF), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Modeling & analysis for medical imaging and Diagnosis (MYRIAD), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), ANR-15-CE18-0026,NanoBrain,Imagerie de l'inflammation cérébrale dans l'AVC ischémique : développement d'une sonde nanoparticulaire multimodale & méthodes d'imagerie cérébrale(2015), ANR-16-RHUS-0009,MARVELOUS,MARVELOUS(2016), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Wiart, Marlene, Imagerie de l'inflammation cérébrale dans l'AVC ischémique : développement d'une sonde nanoparticulaire multimodale & méthodes d'imagerie cérébrale - - NanoBrain2015 - ANR-15-CE18-0026 - AAPG2015 - VALID, and MARVELOUS - - MARVELOUS2016 - ANR-16-RHUS-0009 - RHUS - VALID

Subjects
[SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, Science, Gadolinium, Multimodal Imaging, neuroinflammation, intravital two‐photon microscopy, MICROGLIA, intravital two-photon microscopy, Mice, multimodal nanoprobe, Animals, Nanotechnology, magnetic resonance imaging, Research Articles, neurology, Brain, nanoscience, stroke, Disease Models, Animal, Microscopy, Electron, [SDV.IB.IMA] Life Sciences [q-bio]/Bioengineering/Imaging, inflammation, Neuroinflammatory Diseases, microglia/macrophage, Research Article
Abstract

The purpose of this study is to propose and validate a preclinical in vivo magnetic resonance imaging (MRI) tool to monitor neuroinflammation following ischemic stroke, based on injection of a novel multimodal nanoprobe, NanoGd, specifically designed for internalization by phagocytic cells. First, it is verified that NanoGd is efficiently internalized by microglia in vitro. In vivo MRI coupled with intravenous injection of NanoGd in a permanent middle cerebral artery occlusion mouse model results in hypointense signals in the ischemic lesion. In these mice, longitudinal two‐photon intravital microscopy shows NanoGd internalization by activated CX3CR1‐GFP/+ cells. Ex vivo analysis, including phase contrast imaging with synchrotron X‐ray, histochemistry, and transmission electron microscopy corroborate NanoGd accumulation within the ischemic lesion and uptake by immune phagocytic cells. Taken together, these results confirm the potential of NanoGd‐enhanced MRI as an imaging biomarker of neuroinflammation at the subacute stage of ischemic stroke. As far as it is known, this work is the first to decipher the working mechanism of MR signals induced by a nanoparticle passively targeted at phagocytic cells by performing intravital microscopy back‐to‐back with MRI. Furthermore, using a gadolinium‐based rather than an iron‐based contrast agent raises future perspectives for the development of molecular imaging with emerging computed tomography technologies., Neuroinflammation at the subacute stage of stroke is challenging to monitor in vivo. Here, a novel gadolinium‐based fluorophore‐grafted nanoprobe named NanoGd, specifically designed for internalization by phagocytic cells, is worked with. An in vivo magnetic resonance imaging (MRI) tool is proposed to monitor neuroinflammation following ischemic stroke in mice, which is validated using two‐photon intravital imaging back‐to‐back with MRI for the first time.

Published
2021
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42. Brain virtual histology with X-ray phase-contrast tomography Part I: whole-brain myelin mapping in white-matter injury models

Author

Chourrout, Matthieu, Rositi, Hugo, Ong, Elodie, Hubert, Violaine, Paccalet, Alexandre, Foucault, Louis, Autret, Awen, Fayard, Barbara, Olivier, Cécile, Bolbos, Radu, Peyrin, Françoise, Crola-Da-Silva, Claire, Meyronet, David, Raineteau, Olivier, Elleaume, Hélène, Brun, Emmanuel, Chauveau, Fabien, Wiart, Marlène, Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Pascal (IP), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA)-Institut national polytechnique Clermont Auvergne (INP Clermont Auvergne), Université Clermont Auvergne (UCA)-Université Clermont Auvergne (UCA), Cardiovasculaire, métabolisme, diabétologie et nutrition (CarMeN), Université de Lyon-Université de Lyon-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut cellule souche et cerveau / Stem Cell and Brain Research Institute (U1208 Inserm - UCBL1 / SBRI - USC 1361 INRAE), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Novitom [Grenoble], Centre de Recherche en Acquisition et Traitement de l'Image pour la Santé (CREATIS), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre d'Etude et de Recherche Multimodal Et Pluridisciplinaire en imagerie du vivant (CERMEP - imagerie du vivant), Université de Lyon-Université de Lyon-CHU Grenoble-Hospices Civils de Lyon (HCL)-CHU Saint-Etienne-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Hospices Civils de Lyon (HCL), Université de Lyon, Synchrotron Radiation for Biomedicine = Rayonnement SynchroTROn pour la Recherche BiomédicalE (STROBE), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut cellule souche et cerveau / Stem Cell and Brain Research Institute (SBRI), Imagerie Tomographique et Radiothérapie, Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-CHU Grenoble-Hospices Civils de Lyon (HCL)-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA), ANR-15-CE18-0026,NanoBrain,Imagerie de l'inflammation cérébrale dans l'AVC ischémique : développement d'une sonde nanoparticulaire multimodale & méthodes d'imagerie cérébrale(2015), Centre de recherche en neurosciences de Lyon (CRNL), Université Jean Monnet [Saint-Étienne] (UJM)-Hospices Civils de Lyon (HCL)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL)

Subjects
0303 health sciences, Pathology, medicine.medical_specialty, [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, business.industry, Multiple sclerosis, White Matter Injury, Tissue Processing, Histology, Human brain, medicine.disease, Article, 03 medical and health sciences, Myelin, 0302 clinical medicine, medicine.anatomical_structure, medicine, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Tomography, business, 030217 neurology & neurosurgery, 030304 developmental biology, Diffusion MRI
Abstract

White-matter injury leads to severe functional loss in many neurological diseases. Myelin staining on histological samples is the most common technique to investigate white-matter fibers. However, tissue processing and sectioning may affect the reliability of 3D volumetric assessments. The purpose of this study was to propose an approach that enables myelin fibers to be mapped in the whole rodent brain with microscopic resolution and without the need for strenuous staining. With this aim, we coupled inline (propagation-based) X-ray phase-contrast tomography (XPCT) to ethanol-induced brain sample dehydration. We here provide the proof-of-concept that this approach enhances myelinated axons in rodent and human brain tissue. In addition, we demonstrated that white-matter injuries could be detected and quantified with this approach, using three animal models: ischemic stroke, premature birth and multiple sclerosis. Furthermore, in analogy to diffusion tensor imaging (DTI), we retrieved fiber directions and DTI-like diffusion metrics from our XPCT data to quantitatively characterize white-matter microstructure. Finally, we showed that this non-destructive approach was compatible with subsequent complementary brain sample analysis by conventional histology. In-line XPCT might thus become a novel gold-standard for investigating white-matter injury in the intact brain. This is Part I of a series of two articles reporting the value of in-line XPCT for virtual histology of the brain; Part II shows how in-line XPCT enables the whole-brain 3D morphometric analysis of amyloid-β (Aβ) plaques.HighlightsX-ray phase-contrast tomography (XPCT) enables myelin mapping of the whole brainXPCT detects and quantifies white-matter injuries in a range of diseasesFiber directions and anisotropy metrics can be retrieved from XPCT dataXPCT is compatible with subsequent conventional histology of brain samplesXPCT is a powerful virtual histology tool that requires minimal sample preparationGraphical Abstract

Published
2021
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43. Supplementary document for Implicit tracking approach for X-Ray Phase-Contrast Imaging with a random mask and a conventional system - 5433154.pdf

Author

Quenot, laurene, Helene, Rouge-Labriet, Bohic, Sylvain, Berujon, Sebastien, and brun, emmanuel

Subjects
Physics::Instrumentation and Detectors, Physics::Medical Physics
Abstract

Results of a numerical simulation on a biological phantom using a clinical compatible experimental set-up with a large spot (70��m) X-ray source, a pixel size of 70��m and a source to detector distance of 1m

Published
2021
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46. Brain virtual histology with X-ray phase-contrast tomography Part II: 3D morphologies of amyloid-β plaques in Alzheimer’s disease models

Author

Chourrout, Matthieu, primary, Roux, Margaux, additional, Boisvert, Carlie, additional, Gislard, Coralie, additional, Legland, David, additional, Arganda-Carreras, Ignacio, additional, Olivier, Cécile, additional, Peyrin, Françoise, additional, Boutin, Hervé, additional, Rama, Nicolas, additional, Baron, Thierry, additional, Meyronet, David, additional, Brun, Emmanuel, additional, Rositi, Hugo, additional, Wiart, Marlène, additional, and Chauveau, Fabien, additional

Published
2021
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47. Brain virtual histology with X-ray phase-contrast tomography Part I: whole-brain myelin mapping in white-matter injury models

Author

Chourrout, Matthieu, primary, Rositi, Hugo, additional, Ong, Elodie, additional, Hubert, Violaine, additional, Paccalet, Alexandre, additional, Foucault, Louis, additional, Autret, Awen, additional, Fayard, Barbara, additional, Olivier, Cécile, additional, Bolbos, Radu, additional, Peyrin, Françoise, additional, Crola-da-Silva, Claire, additional, Meyronet, David, additional, Raineteau, Olivier, additional, Elleaume, Hélène, additional, Brun, Emmanuel, additional, Chauveau, Fabien, additional, and Wiart, Marlène, additional

Published
2021
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