| 1. |
- Bellucci, Valerio, et al.
(författare)
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Hard X-ray stereographic microscopy for single-shot differential phase imaging
- 2023
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Ingår i: Optics Express. - 1094-4087. ; 31:11, s. 18399-18406
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Tidskriftsartikel (refereegranskat)abstract
- The characterisation of fast phenomena at the microscopic scale is required for the understanding of catastrophic responses of materials to loads and shocks, the processing of materials by optical or mechanical means, the processes involved in many key technologies such as additive manufacturing and microfluidics, and the mixing of fuels in combustion. Such processes are usually stochastic in nature and occur within the opaque interior volumes of materials or samples, with complex dynamics that evolve in all three dimensions at speeds exceeding many meters per second. There is therefore a need for the ability to record three-dimensional X-ray movies of irreversible processes with resolutions of micrometers and frame rates of microseconds. Here we demonstrate a method to achieve this by recording a stereo phase-contrast image pair in a single exposure. The two images are combined computationally to reconstruct a 3D model of the object. The method is extendable to more than two simultaneous views. When combined with megahertz pulse trains of X-ray free-electron lasers (XFELs) it will be possible to create movies able to resolve 3D trajectories with velocities of kilometers per second.
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| 2. |
- Carlsson, Marcus, et al.
(författare)
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Four-dimensional tomographic reconstruction by time domain decomposition
- 2019
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Ingår i: IEEE Transactions on Computational Imaging. - 2333-9403. ; 5:3, s. 409-419
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Tidskriftsartikel (refereegranskat)abstract
- For classical tomography, it is essential that the sample does not change during the acquisition of one tomographic rotation. We derived and successfully implemented a tomographic reconstruction method, which relaxes this requirement of quasistatic samples. In the present paper, dynamic tomographic data sets are decomposed in the temporal domain by projecting to a lower dimensional subspace of basis functions and deploying an additional L1 regularization technique where the penalty factor is taken for spatial and temporal derivatives. We adopted the primal-dual algorithm of Chambolle and Pock for solving the projected regularization problem and tested it on synthetic data containing different motion types. The proposed implementation on modern GPU systems demonstrates the applicability of the method for processing real data sets.
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| 3. |
- De Carlo, Francesco, et al.
(författare)
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TomoBank : A tomographic data repository for computational x-ray science
- 2018
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Ingår i: Measurement Science and Technology. - : IOP Publishing. - 0957-0233 .- 1361-6501. ; 29:3
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Tidskriftsartikel (refereegranskat)abstract
- There is a widening gap between the fast advancement of computational methods for tomographic reconstruction and their successful implementation in production software at various synchrotron facilities. This is due in part to the lack of readily available instrument datasets and phantoms representative of real materials for validation and comparison of new numerical methods. Recent advancements in detector technology have made sub-second and multi-energy tomographic data collection possible (Gibbs et al 2015 Sci. Rep. 5 11824), but have also increased the demand to develop new reconstruction methods able to handle in situ (Pelt and Batenburg 2013 IEEE Trans. Image Process. 22 5238-51) and dynamic systems (Mohan et al 2015 IEEE Trans. Comput. Imaging 1 96-111) that can be quickly incorporated in beamline production software (Gürsoy et al 2014 J. Synchrotron Radiat. 21 1188-93). The x-ray tomography data bank, tomoBank, provides a repository of experimental and simulated datasets with the aim to foster collaboration among computational scientists, beamline scientists, and experimentalists and to accelerate the development and implementation of tomographic reconstruction methods for synchrotron facility production software by providing easy access to challenging datasets and their descriptors.
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| 4. |
- García-Moreno, Francisco, et al.
(författare)
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Using X-ray tomoscopy to explore the dynamics of foaming metal
- 2019
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- The complex flow of liquid metal in evolving metallic foams is still poorly understood due to difficulties in studying hot and opaque systems. We apply X-ray tomoscopy –the continuous acquisition of tomographic (3D) images– to clarify key dynamic phenomena in liquid aluminium foam such as nucleation and growth, bubble rearrangements, liquid retraction, coalescence and the rupture of films. Each phenomenon takes place on a typical timescale which we cover by obtaining 208 full tomograms per second over a period of up to one minute. An additional data processing algorithm provides information on the 1 ms scale. Here we show that bubble coalescence is not only caused by gravity-induced drainage, as experiments under weightlessness show, and by stresses caused by foam growth, but also by local pressure peaks caused by the blowing agent. Moreover, details of foam expansion and phenomena such as rupture cascades and film thinning before rupture are quantified. These findings allow us to propose a way to obtain foams with smaller and more equally sized bubbles.
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| 5. |
- Kemppainen, Joni, et al.
(författare)
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Binocular mirror–symmetric microsaccadic sampling enables Drosophila hyperacute 3D vision
- 2022
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424. ; 119:12
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Tidskriftsartikel (refereegranskat)abstract
- Neural mechanisms behind stereopsis, which requires simultaneous disparity inputs from two eyes, have remained mysterious. Here we show how ultrafast mirror-symmetric photomechanical contractions in the frontal forward-facing left and right eye photoreceptors give Drosophila superresolution three-dimensional (3D) vision. By interlinking multiscale in vivo assays with multiscale simulations, we reveal how these photoreceptor microsaccades—by verging, diverging, and narrowing the eyes’ overlapping receptive fields—channel depth information, as phasic binocular image motion disparity signals in time. We further show how peripherally, outside stereopsis, microsaccadic sampling tracks a flying fly’s optic flow field to better resolve the world in motion. These results change our understanding of how insect compound eyes work and suggest a general dynamic stereo-information sampling strategy for animals, robots, and sensors.
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| 6. |
- Kördel, Mikael
(författare)
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Biological Laboratory X-Ray Microscopy
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Soft x-ray microscopy in the water window (? ≈ 2.3 − 4.3 nm) is a powerful technique for high-resolution biological imaging. The strong natural contrast between carbon-based structures and water allows visualization of hydrated and unstained samples, while providing enough transmission through up to ∼ 10 μm of organic matter. Furthermore, the full potential of this technique can be exploited by performing computed tomography, thus obtaining a complete 3D image of the object.Routine short-exposure water-window microscopy of whole cells and tissue is currently performed at synchrotron-radiation facilities around the world, but with a limited accessibility to the wider research community. For this reason, laboratory-based systems have been developed, which are now reaching maturity. The benefits compared to the synchrotron-based instruments include easier integration with complementary methods in the home laboratory, in addition to the increased access that allows for the often time-consuming optimization of experimental parameters as well as longitudinal studies.This Thesis presents recent developments of the Stockholm laboratory x-ray microscope as well as several biological applications. Work has been done on improving the mechanical and thermal stability of the microscope, resulting in a resolution of 25 nm (half period) in images of test targets. The biological applications were enabled by a significantly increased x-ray flux through the system as well as an improved operational stability. This work demonstrates 10-second exposure imaging of whole cryofixed cells, imaging of viral infections in cells, and 20 minutes total exposure cryotomography.
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| 7. |
- Langer, Max, et al.
(författare)
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PyPhase - A Python package for X-ray phase imaging
- 2021
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Ingår i: Journal of Synchrotron Radiation. - 0909-0495. ; 28, s. 1261-1266
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Tidskriftsartikel (refereegranskat)abstract
- X-ray propagation-based imaging techniques are well established at synchrotron radiation and laboratory sources. However, most reconstruction algorithms for such image modalities, also known as phase-retrieval algorithms, have been developed specifically for one instrument by and for experts, making the development and diffusion of such techniques difficult. Here, PyPhase, a free and open-source package for propagation-based near-field phase reconstructions, which is distributed under the CeCILL license, is presented. PyPhase implements some of the most popular phase-retrieval algorithms in a highly modular framework supporting its deployment on large-scale computing facilities. This makes the integration, the development of new phase-retrieval algorithms, and the deployment on different computing infrastructures straightforward. Its capabilities and simplicity are presented by application to data acquired at the synchrotron source MAX IV (Lund, Sweden).
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| 8. |
- Le Cann, Sophie, et al.
(författare)
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Investigating the mechanical characteristics of bone-metal implant interface using in situ synchrotron tomographic imaging
- 2019
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Ingår i: Frontiers in Bioengineering and Biotechnology. - : Frontiers Media SA. - 2296-4185. ; 6:JAN
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Tidskriftsartikel (refereegranskat)abstract
- Long-term stability of endosseous implants depends on successful bone formation, ingrowth and adaptation to the implant. Specifically, it will define the mechanical properties of the newly formed bone-implant interface. 3D imaging during mechanical loading tests (in situ loading) can improve the understanding of the local processes leading to bone damage and failure. In this study, titanium screws were implanted into rat tibiae and were allowed to integrate for 4 weeks with or without the addition of the growth factor Bone Morphogenetic Protein and the bisphosphonate Zoledronic Acid. Samples were subjected to in situ pullout using high-resolution synchrotron x-ray tomography at the Tomcat beamline (SLS, PSI, Switzerland) at 30 keV with 25 ms exposure time, resulting in a total acquisition time of 45 s per scan, with a 3.6 μm isotropic voxel size. Using a custom-made loading device positioned inside the beamline, screws were pulled out with 0.05 mm increment, acquiring multiple scans until rupture of the sample. The in situ loading protocol was adapted to ensure short imaging time, which enabled multiple samples to be tested with short loading steps, while keeping the total testing time low and reducing dose deposition. Higher trabecular bone content was quantified in the surrounding of the screw in the treated groups, which correlated with increased mechanical strength and stiffness. Differences in screw implantation, such as contact between threads and cortex as well as minor tilt of the screw were also correlated to the mechanical parameters. In situ loading enabled the investigation of crack propagation during the pullout, highlighting the mechanical behavior of the interface. Three typical crack types were observed: (1) rupture at the interface of trabecular and cortical bone tissues, close to the screw, (2) large crack inside the cortex connected to the implant, and (3) first failure away from the screw with cracks propagating toward the screw-bone interface. Mechanical properties of in vivo integrated bone-metal screws rely on a combination of multiple parameters that are difficult to identify and separate one from the other.
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| 9. |
- Lovric, Goran, et al.
(författare)
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A multi-purpose imaging endstation for high-resolution micrometer-scaled sub-second tomography
- 2016
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Ingår i: Physica Medica. - : Elsevier BV. - 1120-1797. ; 32:12, s. 1771-1778
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Tidskriftsartikel (refereegranskat)abstract
- Time-resolved imaging of dynamic processes, ranging from biological in vivo studies to materials under in situ and in operando conditions, requires a flexible endstation capable of controlling complex components that interact in different configurations and at high speeds. At the X02DA TOMCAT beamline we have recently achieved in situ tomographic measurements at a rate of 20 Hz. Independently, we have shown the feasibility of in vivo lung imaging down to the micrometer scale. In the present paper, we discuss the latest developments in view of instrumentation and the accompanying components for achieving these two types of measurements. As the prime example, we focus on the technical requirements for in vivo tomographic microscopy of the lung at the micrometer scale in terms of acquisition schemes, triggering and radiation dose. We identify ultra-short single-projection exposures combined with accurate triggering capabilities as the main prerequisites to obtain high-quality reconstructions while limiting the X-ray dose imparted on the living sample. The presented endstation offers generic high-speed imaging capabilities, as it is compatible with a variety of experimental setups and suitable for a wide range of time-resolved studies.
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| 10. |
- Lovric, Goran, et al.
(författare)
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Automated computer-assisted quantitative analysis of intact murine lungs at the alveolar scale
- 2017
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 12:9
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Tidskriftsartikel (refereegranskat)abstract
- Using state-of-the-art X-ray tomographic microscopy we can image lung tissue in three dimensions in intact animals down to a micrometer precision. The structural complexity and hierarchical branching scheme of the lung at this level of details, however, renders the extraction of biologically relevant quantities particularly challenging. We have developed a methodology for a detailed description of lung inflation patterns by measuring the size and the local curvature of the parenchymal airspaces. These quantitative tools for morphological and topological analyses were applied to high-resolution murine 3D lung image data, inflated at different pressure levels under immediate post mortem conditions. We show for the first time direct indications of heterogeneous intra-lobar and inter-lobar distension patterns at the alveolar level. Furthermore, we did not find any indication that a cyclic opening- and-collapse (recruitment) of a large number of alveoli takes place.
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