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X-ray-based computed tomography is a well established technique for determining the three-dimensional structure of an object from its two-dimensional projections. In the past few decades, there have been significant advancements in the brightness and detector technology of tomography instruments at synchrotron sources. These advancements have led to the emergence of new observations and discoveries, with improved capabilities such as faster frame rates, larger fields of view, higher resolution and higher dimensionality. These advancements have enabled the material science community to expand the scope of tomographic measurements towards increasingly in situ and in operando measurements. In these new experiments, samples can be rapidly evolving, have complex geometries and restrictions on the field of view, limiting the number of projections that can be collected. In such cases, standard filtered back-projection often results in poor quality reconstructions. Iterative reconstruction algorithms, such as model-based iterative reconstructions (MBIR), have demonstrated considerable success in producing high-quality reconstructions under such restrictions, but typically require high-performance computing resources with hundreds of compute nodes to solve the problem in a reasonable time. Here, tomoCAM, is introduced, a new GPU-accelerated implementation of model-based iterative reconstruction that leverages non-uniform fast Fourier transforms to efficiently compute Radon and back-projection operators and asynchronous memory transfers to maximize the throughput to the GPU memory. The resulting code is significantly faster than traditional MBIR codes and delivers the reconstructive improvement offered by MBIR with affordable computing time and resources. tomoCAM has a Python front-end, allowing access from Jupyter-based frameworks, providing straightforward integration into existing workflows at synchrotron facilities.

Nanoscale structural and electronic heterogeneities are prevalent in condensed matter physics. Investigating these heterogeneities in 3D has become an important task for understanding material properties. To provide a tool to unravel the connection between nanoscale heterogeneity and macroscopic emergent properties in magnetic materials, scanning transmission X‐ray microscopy (STXM) is combined with X‐ray magnetic circular dichroism. A vector tomography algorithm has been developed to reconstruct the full 3D magnetic vector field without any prior noise assumptions or knowledge about the sample. Two tomographic scans around the vertical axis are acquired on single‐crystalline Nd2Fe14B pillars tilted at two different angles, with 2D STXM projections recorded using a focused 120 nm X‐ray beam with left and right circular polarization. Image alignment and iterative registration have been implemented based on the 2D STXM projections for the two tilts. Dichroic projections obtained from difference images are used for the tomographic reconstruction to obtain the 3D magnetization distribution at the nanoscale. [ABSTRACT FROM AUTHOR]

Nanoscale structural and electronic heterogeneities are prevalent in condensed matter physics. Investigating these heterogeneities in 3D has become an important task for understanding material properties. To provide a tool to unravel the connection between nanoscale heterogeneity and macroscopic emergent properties in magnetic materials, scanning transmission X-ray microscopy (STXM) is combined with X-ray magnetic circular dichroism. A vector tomography algorithm has been developed to reconstruct the full 3D magnetic vector field without any prior noise assumptions or knowledge about the sample. Two tomographic scans around the vertical axis are acquired on single-crystalline Nd2Fe14B pillars tilted at two different angles, with 2D STXM projections recorded using a focused 120 nm X-ray beam with left and right circular polarization. Image alignment and iterative registration have been implemented based on the 2D STXM projections for the two tilts. Dichroic projections obtained from difference images are used for the tomographic reconstruction to obtain the 3D magnetization distribution at the nanoscale.

X-ray-based computed tomography is a well established technique for determining the three-dimensional structure of an object from its two-dimensional projections. In the past few decades, there have been significant advancements in the brightness and detector technology of tomography instruments at synchrotron sources. These advancements have led to the emergence of new observations and discoveries, with improved capabilities such as faster frame rates, larger fields of view, higher resolution and higher dimensionality. These advancements have enabled the material science community to expand the scope of tomographic measurements towards increasingly in situ and in operando measurements. In these new experiments, samples can be rapidly evolving, have complex geometries and restrictions on the field of view, limiting the number of projections that can be collected. In such cases, standard filtered back-projection often results in poor quality reconstructions. Iterative reconstruction algorithms, such as model-based iterative reconstructions (MBIR), have demonstrated considerable success in producing high-quality reconstructions under such restrictions, but typically require high-performance computing resources with hundreds of compute nodes to solve the problem in a reasonable time. Here, tomoCAM, is introduced, a new GPU-accelerated implementation of model-based iterative reconstruction that leverages non-uniform fast Fourier transforms to efficiently compute Radon and back-projection operators and asynchronous memory transfers to maximize the throughput to the GPU memory. The resulting code is significantly faster than traditional MBIR codes and delivers the reconstructive improvement offered by MBIR with affordable computing time and resources. tomoCAM has a Python front-end, allowing access from Jupyter-based frameworks, providing straightforward integration into existing workflows at synchrotron facilities.

Synchrotron X-ray computed tomography is a non-destructive 3D imaging technique that offers the possibility to study the internal microstructure of samples with high spatial and temporal resolution. Given its unmatched image quality and acquisition speed, and the possibility to preserve the specimens, there is an increasing demand for this technique, from scientific users from innumerable disciplines. Computed tomography reconstruction is the computational process by which experimental radiographs are converted to a meaningful 3-dimensional image after the scan. The procedure involves pre-processing steps for image background and artifact correction on raw data, a reconstruction step approximating the inverse Radon-transform, and writing of the reconstructed volume image to disk. Several open-source Python packages exist to help scientists in the process of tomography reconstruction, by offering efficient implementations of reconstruction algorithms exploiting central or graphics processing unit (CPU and GPU, respectively), and by automating significant portions of the data processing pipeline. A further increase in productivity is attained by scheduling and parallelizing demanding reconstructions on high performance computing (HPC) clusters. Nevertheless, visual inspection and interactive selection of optimal reconstruction parameters remain crucial steps that are often performed in close interaction with the end-user of the data. As a result, the reconstruction task involves more than one software. Graphical user interfaces are provided to the user for fast inspection and optimization of reconstructions, while HPC resources are often accessed through scripts and command line interface. We propose Alrecon, a pure Python web application for tomographic reconstruction built using Solara. Alrecon offers users an intuitive and reactive environment for exploring data and customizing reconstruction pipelines. By leveraging upon popular 3D image visualization tools, and by providing a user-friendly interface for reconstruction scheduling on HPC resources, Alrecon guarantees productivity and efficient use of resources for any type of beamline user.

We present in this work alternative analytic formulations for the fan-beam tomographic backprojection operation and its associated adjoint transform in standard (equiangular) and linear (equidistant) detector geometries. The proposed formulations are obtained from a recent backprojection theorem in parallel tomography. Such formulations are written as a Bessel–Neumann series in the frequency domain that can be implemented as an O ⁢ (N 2.3729) matrix multiplication. Proofs are provided together with numerical simulations compared with conventional fan-beam O ⁢ (N 3) backprojection representations showing more robustness when dealing with highly noisy data. [ABSTRACT FROM AUTHOR]

Laser absorption spectroscopy tomography is an effective combustion diagnostic method for obtaining simultaneous two-dimensional distribution measurements of temperature and gas molar concentrations. For the reconstruction process of complex combustion flames, a new algorithm named 'multi-iterative adaptive optimization regularization' (MIARO) is proposed. This algorithm is a further development of another algorithm known as the 'modified adaptive algebraic reconstruction technique' (MAART) with the improvement of the initial value and adaptive regularization parameter selections. In MIARO, the problem of the MAART's initial value sensitivity is compensated for, and in addition, reconstruction parameters are also introduced into the regularization so that both the quality of reconstruction and the convergence of regularization are guaranteed. In butane burner experiments, an average relative error of 1.82% was achieved with MIARO, compared to 2.44% with MAART, which is a significant reduction of 25.1%. The simulation and experimental results clearly demonstrate that the MIARO algorithm can be used to reconstruct dynamic combustion fields and eliminate boundary artifacts with improved measurement accuracy and robustness. [ABSTRACT FROM AUTHOR]

Computed tomography is a versatile imaging technique used to enable seeing internal structures of objects without opening or destroying them. This is possible through a process called tomographic reconstruction, which reconstructs images from projections of the object that are obtained by penetrating the object with beams of radiation, such as X-rays, from different angles. These projection data are often limited to low-resolution data in terms of projection angles. These limited or subsampled data make it difficult to obtain high-quality reconstruction results. Hence, upsampling projection data is necessary. In this paper, we propose a sinogram upsampling method via the sub-Riemannian diffusion process. We first lift the data into a feature space, and we fill in the missing angle parts by propagating information from the observed data to the missing parts. We observe that the sinogram with limited angle data has high directional dependency, and based on this observation, we suggest an adaptive weighting scheme to keep information propagating toward the missing regions. This adaptive weighting allows for diffusing toward the desired directions. The experimental results show the effectiveness of the proposed method in some scenarios regarding inpainting fine details, when compared to the existing model-based methods, such as Plug-and-Play and total generalized variation. [ABSTRACT FROM AUTHOR]

The detection of cancer lesions of a comparable size to that of the typical system resolution of modern scanners is a long-standing problem in Positron Emission Tomography. In this paper, the effect of composing an image-registering convolutional neural network with the modeling of the static data acquisition (i.e., the forward model) is investigated. Two algorithms for Positron Emission Tomography reconstruction with motion and attenuation correction are proposed and their performance is evaluated in the detectability of small pulmonary lesions. The evaluation is performed on synthetic data with respect to chosen figures of merit, visual inspection, and an ideal observer. The commonly used figures of merit—Peak Signal-to-Noise Ratio, Recovery Coefficient, and Signal Difference-to-Noise Ration—give inconclusive responses, whereas visual inspection and the Channelised Hotelling Observer suggest that the proposed algorithms outperform current clinical practice. [ABSTRACT FROM AUTHOR]

Synchrotron X-ray computed tomography is a non-destructive 3D imaging technique that offers the possibility to study the internal microstructure of samples with high spatial and temporal resolution. Given its unmatched image quality and acquisition speed, and the possibility to preserve the specimens, there is an increasing demand for this technique, from scientific users from innumerable disciplines. Computed tomography reconstruction is the computational process by which experimental radiographs are converted to a meaningful 3-dimensional image after the scan. The procedure involves pre-processing steps for image background and artifact correction on raw data, a reconstruction step approximating the inverse Radon-transform, and writing of the reconstructed volume image to disk. Several open-source Python packages exist to help scientists in the process of tomography reconstruction, by offering efficient implementations of reconstruction algorithms exploiting central or graphics processing unit (CPU and GPU, respectively), and by automating significant portions of the data processing pipeline. A further increase in productivity is attained by scheduling and parallelizing demanding reconstructions on high performance computing (HPC) clusters. Nevertheless, visual inspection and interactive selection of optimal reconstruction parameters remain crucial steps that are often performed in close interaction with the end-user of the data. As a result, the reconstruction task involves more than one software. Graphical user interfaces are provided to the user for fast inspection and optimization of reconstructions, while HPC resources are often accessed through scripts and command line interface. We propose Alrecon, a pure Python web application for tomographic reconstruction built using Solara. Alrecon offers users an intuitive and reactive environment for exploring data and customizing reconstruction pipelines. By leveraging upon popular 3D image visualization tools, and by providing a user-friendly interface for reconstruction scheduling on HPC resources, Alrecon guarantees productivity and efficient use of resources for any type of beamline user.

AreTomo, an abbreviation for Alignment and Reconstruction for Electron Tomography, is a GPU accelerated software package that fully automates motion-corrected marker-free tomographic alignment and reconstruction in a single package. By correcting in-plane rotation, translation, and importantly, the local motion resulting from beam-induced motion from tilt to tilt, AreTomo can produce tomograms with sufficient accuracy to be directly used for subtomogram averaging. Another major application is the on-the-fly reconstruction of tomograms in parallel with tilt series collection to provide users with real-time feedback of sample quality allowing users to make any necessary adjustments of collection parameters. Here, the multiple alignment algorithms implemented in AreTomo are described and the local motions measured on a typical tilt series are analyzed. The residual local motion after correction for global motion was found in the range of ± 80 Å, indicating that the accurate correction of local motion is critical for high-resolution cryo-electron tomography (cryoET).

In this work, a framework was developed to access and process raw data from a commercial X-ray Computed Tomography (CT) scanner for research purposes. Our method requires vendor-provided binaries to convert the data to a readable format and also to remove the effect of proprietary beam hardening preprocessing. As a result, custom reconstruction techniques, including beam-hardening corrections algorithms, can be applied. Small region-of-interest CT imaging techniques and different backprojection algorithms were investigated to improve image quality (spatial resolution, noise) with an in-house iterative reconstruction algorithm. For a reconstruction matrix of 512 pixels × 512 pixels, processing times of approximately 2.5 s per slice were obtained using a set of 8 x GPUs. With this framework, high-quality images of high density samples (e.g., minerals) can be obtained with reduced truncation-induced blurring, free of artifacts stemming from the reconstruction process and reduced beam-hardening artifacts.

The ITER bolometer diagnostic will provide measurements of the total radiation emitted from the plasma, a part of the overall energy balance. It will consist of some 550 lines of sight (LOS) of bolometer detector, bundled in multiple individual cameras, which will be located in the gaps between blanket modules on the vacuum vessel wall, in five divertor cassettes, in two upper port plugs and in one equatorial port plug (Meister et al., 2017). The LOS are optimised as much as possible with design constraints to capture the details of different plasma regions in which the intensity and local distribution of radiation will vary over a large range. This is especially true in the divertor, where up to 70 % of the total thermal exhaust power from the core will have to be radiated during burning plasma operation. This radiation will be tightly concentrated meaning that not only will tomographic reconstruction of the distribution be challenging, but the bolometer cameras themselves need to be properly designed to handle the resulting heat fluxes. This paper first presents an assessment of the photonic heat fluxes falling on bolometers in the divertor region during high performance operation (where the heat fluxes will be highest). These heat fluxes are computed using ray-tracing from radiation distributions obtained with the SOLPS (plasma boundary region) and JINTRAC (plasma core region) codes and will serve as essential input to the thermal design studies of bolometers. The same SOLPS and JINTRAC simulations are used as models for the second focus of the paper which examines how closely the radiation distribution obtained from tomographic inversion of synthetic signals from the bolometer LOS matches the model input. Some effort has also been devoted to a study of how the reconstructions are affected by loss of individual LOS.

3D printing is driving a shift in patient care away from a generalised model and towards personalised treatments. To complement fast-paced clinical environments, 3D printing technologies must provide sufficiently high throughputs for them to be feasibly implemented. Volumetric printing is an emerging 3D printing technology that affords such speeds, being capable of producing entire objects within seconds. In this study, for the first time, rotatory volumetric printing was used to simultaneously produce two torus- or cylinder-shaped paracetamol-loaded Printlets (3D printed tablets). Six resin formulations comprising paracetamol as the model drug, poly(ethylene glycol) diacrylate (PEGDA) 575 or 700 as photoreactive monomers, water and PEG 300 as non-reactive diluents, and lithium phenyl-2,4,6-trimethylbenzoylphosphinate (LAP) as the photoinitiator were investigated. Two printlets were successfully printed in 12 to 32 s and exhibited sustained drug release profiles. These results support the use of rotary volumetric printing for efficient and effective manufacturing of various personalised medicines at the same time. With the speed and precision it affords, rotatory volumetric printing has the potential to become one of the most promising alternative manufacturing technologies in the pharmaceutical industry.

Object-space model optimization (OSMO) has been proven to be a simple and high-accuracy approach for additive manufacturing of tomographic reconstructions compared with other approaches. In this paper, an improved OSMO algorithm is proposed in the context of OSMO. In addition to the two model optimization steps in each iteration of OSMO, another two steps are introduced: one step enhances the target regions' in-part edges of the intermediate model, and the other step weakens the target regions' out-of-part edges of the intermediate model to further improve the reconstruction accuracy of the target boundary. Accordingly, a new quality metric for volumetric printing, named 'Edge Error', is defined. Finally, reconstructions on diverse exemplary geometries show that all the quality metrics, such as VER, PW, IPDR, and Edge Error, of the new algorithm are significantly improved; thus, this improved OSMO approach achieves better performance in convergence and accuracy compared with OSMO. [ABSTRACT FROM AUTHOR]

We consider the problem of recovering the three-dimensional atomic structure of a flexible macromolecule from a heterogeneous cryogenic electron microscopy (cryo-EM) dataset. The dataset contains noisy tomographic projections of the electrostatic potential of the macromolecule, taken from different viewing directions, and in the heterogeneous case, each cryo-EM image corresponds to a different conformation of the macromolecule. Under the assumption that the macromolecule can be modelled as a chain, or discrete curve (as it is for instance the case for a protein backbone with a single chain of amino-acids), we introduce a method to estimate the deformation of the atomic model with respect to a given conformation, which is assumed to be known a priori. Our method consists on estimating the torsion and bond angles of the atomic model in each conformation as a linear combination of the eigenfunctions of the Laplace operator in the manifold of conformations. These eigenfunctions can be approximated by means of a well-known technique in manifold learning, based on the construction of a graph Laplacian using the cryo-EM dataset. Finally, we test our approach with synthetic datasets, for which we recover the atomic model of two-dimensional and three-dimensional flexible structures from simulated cryo-EM images. [ABSTRACT FROM AUTHOR]

Shock waves and shock-shock interaction are typical phenomena in supersonic or hypersonic flows that have significant impacts on aerodynamic performance. To obtain a comprehensive understanding of the mechanism of shock wave interaction, shock wave detection (SWD) methods are required. However, it is often challenging for most current SWD methods to identify the relationship between shock waves (also known as shock topology). To address this issue, this paper proposes a novel three-dimensional shock topology detection method based on the tomographic reconstruction strategy. This method involves extracting parallel slices from the flow field, then utilizing a two-dimensional shock topology recognition algorithm to obtain shock lines. Shock bands are obtained by connecting shock lines for every two adjacent slices, and shock surfaces are generated by assembling shock bands. Interaction lines are also formed by connecting interaction points. The detected shock wave is a structure composed of "point-line-band-surface", and the topology relationship with other shock waves is obvious. Numerical results show that the shock waves detected by the proposed method can be categorized into families. Moreover, the shock surfaces generated by this method are free of gaps, holes, and un-physical fragments, which is an improvement over existing SWD methods. [ABSTRACT FROM AUTHOR]

Laser--plasma accelerated (LPA) proton bunches are now applied for research fields ranging from ultra-high-dose-rate radiobiology to material science. Yet, the capabilities to characterize the spectrally and angularly broad LPA bunches lag behind the rapidly evolving applications. The OCTOPOD translates the angularly resolved spectral characterization of LPA proton bunches into the spatially resolved detection of the volumetric dose distribution deposited in a liquid scintillator. Up to 24 multi-pinhole arrays record projections of the scintillation light distribution and allow for tomographic reconstruction of the volumetric dose deposition pattern, from which proton spectra may be retrieved. Applying the OCTOPOD at a cyclotron, we show the reliable retrieval of various spatial dose deposition patterns and detector sensitivity over a broad dose range. Moreover, the OCTOPOD was installed at an LPA proton source, providing real-time data on proton acceleration performance and attesting the system optimal performance in the harsh laser--plasma environment. [ABSTRACT FROM AUTHOR]

Laser absorption spectroscopy tomography is an effective combustion diagnostic method for obtaining simultaneous two-dimensional distribution measurements of temperature and gas molar concentrations. For the reconstruction process of complex combustion flames, a new algorithm named ‘multi-iterative adaptive optimization regularization’ (MIARO) is proposed. This algorithm is a further development of another algorithm known as the ‘modified adaptive algebraic reconstruction technique’ (MAART) with the improvement of the initial value and adaptive regularization parameter selections. In MIARO, the problem of the MAART’s initial value sensitivity is compensated for, and in addition, reconstruction parameters are also introduced into the regularization so that both the quality of reconstruction and the convergence of regularization are guaranteed. In butane burner experiments, an average relative error of 1.82% was achieved with MIARO, compared to 2.44% with MAART, which is a significant reduction of 25.1%. The simulation and experimental results clearly demonstrate that the MIARO algorithm can be used to reconstruct dynamic combustion fields and eliminate boundary artifacts with improved measurement accuracy and robustness.

The detection of cancer lesions of a comparable size to that of the typical system resolution of modern scanners is a long-standing problem in Positron Emission Tomography. In this paper, the effect of composing an image-registering convolutional neural network with the modeling of the static data acquisition (i.e., the forward model) is investigated. Two algorithms for Positron Emission Tomography reconstruction with motion and attenuation correction are proposed and their performance is evaluated in the detectability of small pulmonary lesions. The evaluation is performed on synthetic data with respect to chosen figures of merit, visual inspection, and an ideal observer. The commonly used figures of merit—Peak Signal-to-Noise Ratio, Recovery Coefficient, and Signal Difference-to-Noise Ration—give inconclusive responses, whereas visual inspection and the Channelised Hotelling Observer suggest that the proposed algorithms outperform current clinical practice.

Novel developments in X-ray sources, optics and detectors have significantly advanced the capability of X-ray microscopy at the nanoscale. Depending on the imaging modality and the photon energy, state-of-the-art X-ray microscopes are routinely operated at a spatial resolution of tens of nanometres for hard X-rays or ∼10 nm for soft X-rays. The improvement in spatial resolution, however, has led to challenges in the tomographic reconstruction due to the fact that the imperfections of the mechanical system become clearly detectable in the projection images. Without proper registration of the projection images, a severe point spread function will be introduced into the tomographic reconstructions, causing the reduction of the three-dimensional (3D) spatial resolution as well as the enhancement of image artifacts. Here the development of a method that iteratively performs registration of the experimentally measured projection images to those that are numerically calculated by reprojecting the 3D matrix in the corresponding viewing angles is shown. Multiple algorithms are implemented to conduct the registration, which corrects the translational and/or the rotational errors. A sequence that offers a superior performance is presented and discussed. Going beyond the visual assessment of the reconstruction results, the morphological quantification of a battery electrode particle that has gone through substantial cycling is investigated. The results show that the presented method has led to a better quality tomographic reconstruction, which, subsequently, promotes the fidelity in the quantification of the sample morphology.

Laser–plasma accelerated (LPA) proton bunches are now applied for research fields ranging from ultra-high-dose-rate radiobiology to material science. Yet, the capabilities to characterize the spectrally and angularly broad LPA bunches lag behind the rapidly evolving applications. The OCTOPOD translates the angularly resolved spectral characterization of LPA proton bunches into the spatially resolved detection of the volumetric dose distribution deposited in a liquid scintillator. Up to 24 multi-pinhole arrays record projections of the scintillation light distribution and allow for tomographic reconstruction of the volumetric dose deposition pattern, from which proton spectra may be retrieved. Applying the OCTOPOD at a cyclotron, we show the reliable retrieval of various spatial dose deposition patterns and detector sensitivity over a broad dose range. Moreover, the OCTOPOD was installed at an LPA proton source, providing real-time data on proton acceleration performance and attesting the system optimal performance in the harsh laser–plasma environment.

The paper examines the features of segmentation of the upper respiratory tract to determine nasal air conduction. 2D and 3D illustrations of the segmentation process and the obtained results are given. When forming an analytical model of the aerodynamics of the nasal cavity, the main indicator that characterizes the configuration of the nasal canal is the equivalent diameter, which is determined at each intersection of the nasal cavity. It is calculated based on the area and perimeter of the corresponding section of the nasal canal. When segmenting the nasal cavity, it is first necessary to eliminate air structures that do not affect the aerodynamics of the upper respiratory tract - these are, first of all, intact spaces of the paranasal sinuses, in which diffuse air exchange prevails. In the automatic mode, this is possible by performing the elimination of unconnected isolated areas and finding the difference coefficients of the areas connected by confluences with the nasal canal in the next step. High coefficients of difference of sections between intersections will indicate the presence of separated areas and contribute to their elimination. The complex configuration and high individual variability of the structures of the nasal cavity does not allow segmentation to be fully automated, but this approach contributes to the absence of interactive correction in 80% of tomographic datasets. The proposed method, which takes into account the intensity of the image elements close to the contour ones, allows to reduce the averaging error from tomographic reconstruction up to 2 times due to artificial sub-resolution. The perspective of the work is the development of methods for fully automatic segmentation of the structures of the nasal cavity, taking into account the individual anatomical variability of the upper respiratory tract.

Nanoscale structural and electronic heterogeneities are prevalent in condensed matter physics. Investigating these heterogeneities in 3D has become an important task for understanding material properties. To provide a tool to unravel the connection between nanoscale heterogeneity and macroscopic emergent properties in magnetic materials, scanning transmission X-ray microscopy (STXM) is combined with X-ray magnetic circular dichroism. A vector tomography algorithm has been developed to reconstruct the full 3D magnetic vector field without any prior noise assumptions or knowledge about the sample. Two tomographic scans around the vertical axis are acquired on single-crystalline Nd 2 Fe 14 B pillars tilted at two different angles, with 2D STXM projections recorded using a focused 120 nm X-ray beam with left and right circular polarization. Image alignment and iterative registration have been implemented based on the 2D STXM projections for the two tilts. Dichroic projections obtained from difference images are used for the tomographic reconstruction to obtain the 3D magnetization distribution at the nanoscale., (open access.)

Object-space model optimization (OSMO) has been proven to be a simple and high-accuracy approach for additive manufacturing of tomographic reconstructions compared with other approaches. In this paper, an improved OSMO algorithm is proposed in the context of OSMO. In addition to the two model optimization steps in each iteration of OSMO, another two steps are introduced: one step enhances the target regions’ in-part edges of the intermediate model, and the other step weakens the target regions’ out-of-part edges of the intermediate model to further improve the reconstruction accuracy of the target boundary. Accordingly, a new quality metric for volumetric printing, named ‘Edge Error’, is defined. Finally, reconstructions on diverse exemplary geometries show that all the quality metrics, such as VER, PW, IPDR, and Edge Error, of the new algorithm are significantly improved; thus, this improved OSMO approach achieves better performance in convergence and accuracy compared with OSMO.

Purpose: Computed tomography (CT) is a technique of choice to image bone structure at different scales. Methods to enhance the quality of degraded reconstructions obtained from low‐dose CT data have shown impressive results recently, especially in the realm of supervised deep learning. As the choice of the loss function affects the reconstruction quality, it is necessary to focus on the way neural networks evaluate the correspondence between predicted and target images during the training stage. This is even more true in the case of bone microarchitecture imaging at high spatial resolution where both the quantitative analysis of bone mineral density (BMD) and bone microstructure is essential for assessing diseases such as osteoporosis. Our aim is thus to evaluate the quality of reconstruction on key metrics for diagnosis depending on the loss function that has been used for training the neural network. Methods: We compare and analyze volumes that are reconstructed with neural networks trained with pixelwise, structural, and adversarial loss functions or with a combination of them. We perform realistic simulations of various low‐dose acquisitions of bone microarchitecture. Our comparative study is performed with metrics that have an interest regarding the diagnosis of bone diseases. We therefore focus on bone‐specific metrics such as bone volume and the total volume (BV and TV), resolution, connectivity assessed with the Euler number, and quantitative analysis of BMD to evaluate the quality of reconstruction obtained with networks trained with the different loss functions. Results: We find that using L1$L_1$ norm as the pixelwise loss is the best choice compared to L2$L_2$ or no pixelwise loss since it improves resolution without deteriorating other metrics. Visual Geometry Group (VGG) perceptual loss, especially when combined with an adversarial loss, allows to better retrieve topological and morphological parameters of bone microarchitecture compared to Structural SIMilarity (SSIM) index. This however leads to a decreased resolution performance. The adversarial loss enhances the reconstruction performance in terms of BMD distribution accuracy. Conclusions: In order to retrieve the quantitative and structural characteristics of bone microarchitecture that are essential for postreconstruction diagnosis, our results suggest to use L1$L_1$ norm as part of the loss function. Then, trade‐offs should be made depending on the application: VGG perceptual loss improves accuracy in terms of connectivity at the cost of a deteriorated resolution, and adversarial losses help better retrieve BMD distribution while significantly increasing the training time. [ABSTRACT FROM AUTHOR]

This paper presents a method to invert the two-dimensional distribution of a temperature and volume concentration of soot particles from color images. By using numerical simulation, the temperature field and particle volume-concentration field of a non-uniform soot flame are simultaneously reconstructed using the wide-response spectrum of a color CCD camera without adding monochromatic filters. The influence of number of cameras, error of camera position angle, measurement noise and different reconstruction algorithms on measurement accuracy are analyzed. The numerical-simulation results demonstrate that camera-position angle errors play a crucial role in the reconstruction accuracy. In addition, increasing the number of cameras can improve the reconstruction result accuracy. Compared with the least squares algorithm, the Tikhonov-regularization algorithm has a stronger anti-noise ability and can resist 39 dB of noise. The conclusions obtained in this paper are helpful to guide following experimental studies. [ABSTRACT FROM AUTHOR]

The study aimed to create a pipeline from Monte Carlo simulated projections of a Gate PET system to reconstructed images. The PET system was modelled after the GE Discovery MI (DMI) PET/CT, and the simulated projections were reconstructed with the stand-alone reconstruction software CASToR. Attenuation correction, normalisation calibration, random estimation, and scatter estimation for the simulations were computed with in-house programs. The pipeline was compared in both projection and image space with data acquired on a clinical DMI and reconstructed with GE's off-line PET reconstruction software (PET Toolbox) and CASToR. The simulated and measured data were compared for the number of prompt coincidences, scatter fraction, contrast recovery coefficient (CRC), signal-to-noise ratio (SNR), background variability, residual lung error, and image profiles. A slight discrepancy was noted in the projection space, but good agreements were generally achieved in image space between simulated and measured data. The CRC was found to be 81 % for Gate – CASToR, 84 % for GE – CASToR, and 84 % for GE - PET Toolbox for the largest sphere of the NEMA image quality (IQ) phantom, and the SNR was found to be 98 for Gate – CASToR, 91 for GE – CASToR, and 93 for GE – PET Toolbox. Profiles drawn over the spheres for the NEMA IQ phantom and the Data Spectrum (DS) phantom show a good match between measurement and simulation. The results indicate feasibility to utilise the pipeline as a tool for off-line simulation-based studies. A complete pipeline introduces possibilities to study the impact of single parameters in the whole chain from simulation to reconstructed images.

Shock waves and shock-shock interaction are typical phenomena in supersonic or hypersonic flows that have significant impacts on aerodynamic performance. To obtain a comprehensive understanding of the mechanism of shock wave interaction, shock wave detection (SWD) methods are required. However, it is often challenging for most current SWD methods to identify the relationship between shock waves (also known as shock topology). To address this issue, this paper proposes a novel three-dimensional shock topology detection method based on the tomographic reconstruction strategy. This method involves extracting parallel slices from the flow field, then utilizing a two-dimensional shock topology recognition algorithm to obtain shock lines. Shock bands are obtained by connecting shock lines for every two adjacent slices, and shock surfaces are generated by assembling shock bands. Interaction lines are also formed by connecting interaction points. The detected shock wave is a structure composed of “point-line-band-surface”, and the topology relationship with other shock waves is obvious. Numerical results show that the shock waves detected by the proposed method can be categorized into families. Moreover, the shock surfaces generated by this method are free of gaps, holes, and un-physical fragments, which is an improvement over existing SWD methods.

Manipulation of heat distribution in the material is a long‐term goal that has been pursued in the field of thermal functional materials. Various thermal manipulation methods have been successfully developed, some of which have realized gorgeous thermal patterns. However, existing thermal functional materials are either difficult to avoid introducing massive external heaters and cables or it is hard to achieve dynamic thermal manipulation with a high thermal resolution and accuracy. In addition, the complicated manufacturing process also limits the wide application of thermal functional materials. Herein, a computed thermal patterning method is proposed, which can dynamically achieve a freewheeling thermal manipulation in the highly versatile and easily manufactured multi‐layered material. This method first introduces the principle of tomography into the thermal manipulation by treating heat beams as light energy via a multi‐angled rhythmical superposition, enabling the human characters to be written, paintings to be drawn, movies to be played, without embedding any external heaters or cables. A particular thermal diffusion problem in the tomographic process is solved by developing an inverse thermal diffusion optimization. Experimental cases demonstrate the great potential of this method in multi‐zoned thermal forming, encrypted messaging, 3D thermal printing, and morphing. [ABSTRACT FROM AUTHOR]

In this study, the temperature and volume fraction distributions of liquid silicon nanoparticles in the aerosol flow in gas-phase synthesis were retrieved using tomographic reconstruction of emission and extinction spectra in the 230–700 nm range. Measurements were done in an optically accessible microwave-plasma flow reactor fed with a SiH 4 /H 2 /Ar gas mixture. Optical emission and extinction spectra in the visible spectral range were captured along a line perpendicular to the flow direction covering the entire cross-section of the Si particle stream. Particle temperature and volume fraction distributions were determined and the preferred location of the silicon particles in a 1-mm thick zone at the circumference of the cylindric flow was revealed. The combined recording of line-resolved emission/extinction spectra is a promising method for spatially-resolved detection of nanoparticles in combustion or gas-phase synthesis. [Display omitted] • Silicon nanoparticles were generated in the aerosol flow in gas-phase synthesis. • Temperatures and volume fractions of particle-phase with 1-mm thickness were revealed. • Spatially and spectrally line-resolved emission and extinction spectra were combined. • Tomographic algorithm was used to reconstruct radial distributions. [ABSTRACT FROM AUTHOR]

AreTomo, an abbreviation for Alignment and Reconstruction for Electron Tomography, is a GPU accelerated software package that fully automates motion-corrected marker-free tomographic alignment and reconstruction in a single package. By correcting in-plane rotation, translation, and importantly, the local motion resulting from beam-induced motion from tilt to tilt, AreTomo can produce tomograms with sufficient accuracy to be directly used for subtomogram averaging. Another major application is the on-the-fly reconstruction of tomograms in parallel with tilt series collection to provide users with real-time feedback of sample quality allowing users to make any necessary adjustments of collection parameters. Here, the multiple alignment algorithms implemented in AreTomo are described and the local motions measured on a typical tilt series are analyzed. The residual local motion after correction for global motion was found in the range of ± 80 Å, indicating that the accurate correction of local motion is critical for high-resolution cryo-electron tomography (cryoET).

The rapid and accurate measurement of the flame temperature distribution is of great significance to the structural design and health diagnosis of the engine. Aiming at the low reconstruction efficiency of traditional flame temperature distribution reconstruction algorithms, a Direct Solution algorithm for flame temperature distribution reconstruction is proposed in this paper based on the structural characteristics of the reconstruction equations. By setting several numerical cases, the performance of the Direct Solution algorithm and some commonly used traditional algorithms, such as Simultaneous Algebraic Reconstruction Technique (SART), Least Squares QR-factorization (LSQR) algorithm, Non-Negative Least Squares QR-factorization (NNLS) algorithm, is compared in the reconstruction of the flame temperature distribution. The results show that the efficiency of the Direct Solution method is 169.4, 7.4, and 3483.3 times higher than that of the SART, LSQR, and NNLS algorithms under the condition of 40 × 40 grids. In addition, with the increase of the number of grids, the growth rate of the reconstruction time of the Direct Solution algorithm is much lower than that of other algorithms. The overall reconstruction accuracy of the Direct Solution algorithm is better than that of SART and LSQR algorithms. This shows that it has an excellent comprehensive performance and has a great application prospect in the rapid reconstruction of the temperature distribution.

Synchrotron X-ray computed tomography is a non-destructive 3D imaging technique that offers the possibility to study the internal microstructure of samples with high spatial and temporal resolution. Given its unmatched image quality and acquisition speed, and the possibility to preserve the specimens, there is an increasing demand for this technique, from scientific users from innumerable disciplines. Computed tomography reconstruction is the computational process by which experimental radiographs are converted to a meaningful 3-dimensional image after the scan. The procedure involves pre-processing steps for image background and artifact correction on raw data, a reconstruction step approximating the inverse Radon-transform, and writing of the reconstructed volume image to disk. Several open-source Python packages exist to help scientists in the process of tomography reconstruction, by offering efficient implementations of reconstruction algorithms exploiting central or graphics processing unit (CPU and GPU, respectively), and by automating significant portions of the data processing pipeline. A further increase in productivity is attained by scheduling and parallelizing demanding reconstructions on high performance computing (HPC) clusters. Nevertheless, visual inspection and interactive selection of optimal reconstruction parameters remain crucial steps that are often performed in close interaction with the end-user of the data. As a result, the reconstruction task involves more than one software. Graphical user interfaces are provided to the user for fast inspection and optimization of reconstructions, while HPC resources are often accessed through scripts and command line interface. We propose Alrecon, a pure Python web application for tomographic reconstruction built using Solara. Alrecon offers users an intuitive and reactive environment for exploring data and customizing reconstruction pipelines. By leveraging upon popular 3D image visualization tools, and by providing a user-friendly interface for reconstruction scheduling on HPC resources, Alrecon guarantees productivity and efficient use of resources for any type of beamline user., Competing Interests: No competing interests were disclosed., (Copyright: © 2024 Iori G et al.)

Cerenkov luminescence tomography (CLT) has attracted much attention because of the wide clinically-used probes and three-dimensional (3D) quantification ability. However, due to the serious morbidity of 3D optical imaging, the reconstructed images of CLT are not appreciable, especially when single-view measurements are used. Single-view CLT improves the efficiency of data acquisition. It is much consistent with the actual imaging environment of using commercial imaging system, but bringing the problem that the reconstructed results will be closer to the animal surface on the side where the single-view image is collected. To avoid this problem to the greatest extent possible, we proposed a prior compensation algorithm for CLT reconstruction based on depth calibration strategy. This method takes full account of the fact that the attenuation of light in the tissue will depend heavily on the depth of the light source as well as the distance between the light source and the detection plane. Based on this consideration, a depth calibration matrix was designed to calibrate the attenuation between the surface light flux and the density of the internal light source. The feature of the algorithm was that the depth calibration matrix directly acts on the system matrix of CLT reconstruction, rather than modifying the regularization penalty items. The validity and effectiveness of the proposed algorithm were evaluated with a numerical simulation and a mouse-based experiment, whose results illustrated that it located the radiation sources accurately by using single-view measurements. [ABSTRACT FROM AUTHOR]

For reconstructing large tomographic datasets fast, filtered backprojection‐type or Fourier‐based algorithms are still the method of choice, as they have been for decades. These robust and computationally efficient algorithms have been integrated in a broad range of software packages. The continuous mathematical formulas used for image reconstruction in such algorithms are unambiguous. However, variations in discretization and interpolation result in quantitative differences between reconstructed images, and corresponding segmentations, obtained from different software. This hinders reproducibility of experimental results, making it difficult to ensure that results and conclusions from experiments can be reproduced at different facilities or using different software. In this paper, a way to reduce such differences by optimizing the filter used in analytical algorithms is proposed. These filters can be computed using a wrapper routine around a black‐box implementation of a reconstruction algorithm, and lead to quantitatively similar reconstructions. Use cases for this approach are demonstrated by computing implementation‐adapted filters for several open‐source implementations and applying them to simulated phantoms and real‐world data acquired at the synchrotron. Our contribution to a reproducible reconstruction step forms a building block towards a fully reproducible synchrotron tomography data processing pipeline. [ABSTRACT FROM AUTHOR]

Background: Time-of-Flight (TOF) is a leading technological development of Positron Emission Tomography (PET) scanners. It reduces noise at the Maximum-Likelihood solution, depending on the coincidence–timing–resolution (CTR). However, in clinical applications, it is still not clear how to best exploit TOF information, as early stopped reconstructions are generally used. Methods: A contrast-recovery (CR) matching rule for systems with different CTRs and non-TOF systems is theoretically derived and validated using (1) digital simulations of objects with different contrasts and background diameters, (2) realistic phantoms of different sizes acquired on two scanners with different CTRs. Results: With TOF, the CR matching rule prescribes modifying the iterations number by the CTRs ratio. Without TOF, the number of iterations depends on the background dimension. CR matching was confirmed by simulated and experimental data. With TOF, image noise followed the square root of the CTR when the rule was applied on simulated data, while a significant reduction was obtained on phantom data. Without TOF, preserving the CR on larger objects significantly increased the noise. Conclusions: TOF makes PET reconstructions less dependent on background dimensions, thus, improving the quantification robustness. Better CTRs allows performing fewer updates, thus, maintaining accuracy while minimizing noise. [ABSTRACT FROM AUTHOR]

Deep Learning is developing interesting tools that are of great interest for inverse imaging applications. In this work, we consider a medical imaging reconstruction task from subsampled measurements, which is an active research field where Convolutional Neural Networks have already revealed their great potential. However, the commonly used architectures are very deep and, hence, prone to overfitting and unfeasible for clinical usages. Inspired by the ideas of the green AI literature, we propose a shallow neural network to perform efficient Learned Post-Processing on images roughly reconstructed by the filtered backprojection algorithm. The results show that the proposed inexpensive network computes images of comparable (or even higher) quality in about one-fourth of time and is more robust than the widely used and very deep ResUNet for tomographic reconstructions from sparse-view protocols. [ABSTRACT FROM AUTHOR]

Limited view tomographic reconstruction aims to reconstruct a tomographic image from a limited number of projection views arising from sparse view or limited angle acquisitions that reduce radiation dose or shorten scanning time. However, such a reconstruction suffers from severe artifacts due to the incompleteness of sinogram. To derive quality reconstruction, previous methods use UNet-like neural architectures to directly predict the full view reconstruction from limited view data; but these methods leave the deep network architecture issue largely intact and cannot guarantee the consistency between the sinogram of the reconstructed image and the acquired sinogram, leading to a non-ideal reconstruction. In this work, we propose a cascaded residual dense spatial-channel attention network consisting of residual dense spatial-channel attention networks and projection data fidelity layers. We evaluate our methods on two datasets. Our experimental results on AAPM Low Dose CT Grand Challenge datasets demonstrate that our algorithm achieves a consistent and substantial improvement over the existing neural network methods on both limited angle reconstruction and sparse view reconstruction. In addition, our experimental results on Deep Lesion datasets demonstrate that our method is able to generate high-quality reconstruction for 8 major lesion types. [ABSTRACT FROM AUTHOR]

Cerenkov luminescence tomography (CLT) has attracted much attention because of the wide clinically-used probes and three-dimensional (3D) quantification ability. However, due to the serious morbidity of 3D optical imaging, the reconstructed images of CLT are not appreciable, especially when single-view measurements are used. Single-view CLT improves the efficiency of data acquisition. It is much consistent with the actual imaging environment of using commercial imaging system, but bringing the problem that the reconstructed results will be closer to the animal surface on the side where the single-view image is collected. To avoid this problem to the greatest extent possible, we proposed a prior compensation algorithm for CLT reconstruction based on depth calibration strategy. This method takes full account of the fact that the attenuation of light in the tissue will depend heavily on the depth of the light source as well as the distance between the light source and the detection plane. Based on this consideration, a depth calibration matrix was designed to calibrate the attenuation between the surface light flux and the density of the internal light source. The feature of the algorithm was that the depth calibration matrix directly acts on the system matrix of CLT reconstruction, rather than modifying the regularization penalty items. The validity and effectiveness of the proposed algorithm were evaluated with a numerical simulation and a mouse-based experiment, whose results illustrated that it located the radiation sources accurately by using single-view measurements.

The method of tomographic reconstruction of inhomogeneities in case of an arbitrary directional diagram and scanning along one coordinate is described. It is shown that in this case registered data (projections) are represented as the sum of the line-by-line convolutions of the lines of the directional diagram and the corresponding line of the reconstructed distribution. The features of projection data, backprojections are analyzed. It is proposed to construct a cumulative image as an additive or conjunctive combination of the backprojection results for different orientation diagrams. An iterative procedure for constructing sequential approximations to the desired solution is proposed. [ABSTRACT FROM AUTHOR]

This paper presents a method to invert the two-dimensional distribution of a temperature and volume concentration of soot particles from color images. By using numerical simulation, the temperature field and particle volume-concentration field of a non-uniform soot flame are simultaneously reconstructed using the wide-response spectrum of a color CCD camera without adding monochromatic filters. The influence of number of cameras, error of camera position angle, measurement noise and different reconstruction algorithms on measurement accuracy are analyzed. The numerical-simulation results demonstrate that camera-position angle errors play a crucial role in the reconstruction accuracy. In addition, increasing the number of cameras can improve the reconstruction result accuracy. Compared with the least squares algorithm, the Tikhonov-regularization algorithm has a stronger anti-noise ability and can resist 39 dB of noise. The conclusions obtained in this paper are helpful to guide following experimental studies.