A Backprojection Slice Theorem for Tomographic Reconstruction

Monte Carlo simulations of synchrotron X-ray dose affecting root growth during in vivo tomographic imaging

Synchrotron X-ray computed tomography (XCT) has been increasingly applied to study the in vivo dynamics of root growth and rhizosphere processes. However, minimizing radiation-induced damage to root growth warrants further investigation. Our objective was to develop a robust approach for modeling and evaluating ways to reduce synchrotron X-ray dose effects on root growth during in vivo imaging. Wheat roots growing in soil were exposed to X-rays during XCT experiments resolved in space (3D) plus time (4D). The dose rate and cumulative absorbed dose in roots were modelled using the Monte Carlo code FLUKA for different experimental conditions of polychromatic and quasi-monochromatic X-ray beam configurations. The most impactful factors affecting damage to roots were incident X-ray energy spectrum, stored current in the accelerator machine, position of the root in the soil, and possibly the number of exposures during the 4D XCT experiments. Our results imply that radiation dose during in vivo imaging of plant roots can be diminished by using monochromatic radiation at the highest energy suitable for a given sample thickness and field of view, and by controlling the rotation axis of off-centered roots to increase attenuation of radiation by the soil matrix.

The evaluation model of reconstruction effect of ancient villages under the influence of epidemic situation based on big data

In rural construction, affected by covid-19, it leads to the collection and demand survey of basic information data of relevant interest groups. The specific situation of the transformation of ancient villages is also gradually increasing. However, due to the complexity of rural space, the dispersion of settlement space and the diversity of information demand of rural planning work, the data coverage is large, information acquisition is difficult, the use effect of data collection is not ideal, and there is no planning feedback mechanism. However, during the epidemic period, the staff could not carry out a series of reconstruction of ancient villages. At present, the data of village planning and construction and architectural design are complex, the needs of relevant interest groups are diversified, and regional planning is difficult. In this paper, the big data function is applied to the reconstruction of ancient villages in the epidemic period of covid-19.

Fast reconstruction tools for ptychography at Sirius, the fourth-generation Brazilian synchrotron

Described here are image reconstruction optimizations for ptychographic coherent X-ray scattering data and X-ray fluorescence, which have been developed for the new fourth-generation synchrotron light source, Sirius, at the Brazilian Synchrotron Light Laboratory. The optimization strategy has been applied to the standard experimental strategy for ptychographic and fluorescence experiments on the Carnaúba beamline which involves the use of high-speed continuous scans (fly scans) for a fast acquisition time over large areas through the use of a newly proposed trajectory named the alternating linear trajectory. The scientific computing developments presented here target an efficient use of graphical processing units (GPUs) to the point where large fly-scan acquisitions can be processed in real time on a local high-performance computer. Some optimizations involving a custom fast Fourier transform implementation and use of mixed precision can be applied to other algorithms and phase-retrieval techniques, and therefore this work provides a general optimization scheme. Finally, the optimization strategy presented here has improved performance by a factor of ∼2.5 times faster when compared with non-optimized GPU implementations.

Computed tomography medical image reconstruction on affordable equipment by using Out-Of-Core techniques

BACKGROUND AND OBJECTIVE

As Computed Tomography scans are an essential medical test, many techniques have been proposed to reconstruct high-quality images using a smaller amount of radiation. One approach is to employ algebraic factorization methods to reconstruct the images, using fewer views than the traditional analytical methods. However, their main drawback is the high computational cost and hence the time needed to obtain the images, which is critical in the daily clinical practice. For this reason, faster methods for solving this problem are required.

METHODS

In this paper, we propose a new reconstruction method based on the QR factorization that is very efficient on affordable equipment (standard multicore processors and standard Solid-State Drives) by using Out-Of-Core techniques.

RESULTS

Combining both affordable hardware and the new software proposed in our work, the images can be reconstructed very quickly and with high quality. We analyze the reconstructions using real Computed Tomography images selected from a dataset, comparing the QR method to the LSQR and FBP. We measure the quality of the images using the metrics Peak Signal-To-Noise Ratio and Structural Similarity Index, obtaining very high values. We also compare the efficiency of using spinning disks versus Solid-State Drives, showing how the latter performs the Input/Output operations in a significantly lower amount of time.

CONCLUSIONS

The results indicate that our proposed me thod and software are valid to efficiently solve large-scale systems and can be applied to the Computed Tomography reconstruction problem to obtain high-quality images.

Decreased nuclear distribution nudE-like 1 enzyme activity in an animal model with dysfunctional disrupted-in-schizophrenia 1 signaling featuring aberrant neurodevelopment and amphetamine-supersensitivity

BACKGROUND

Interaction of nuclear-distribution element-like 1 with disrupted-in-schizophrenia 1 protein is crucial for neurite outgrowth/neuronal migration, and this interaction competitively inhibits nuclear-distribution element-like 1 peptidase activity. Nuclear-distribution element-like 1 activity is reduced in antipsychotic-naïve first-episode psychosis and in medicated chronic schizophrenia, with even lower activity in treatment-resistant schizophrenia.

AIMS

The purpose of this study was to investigate in a rat model overexpressing human non-mutant disrupted-in-schizophrenia 1, with consequent dysfunctional disrupted-in-schizophrenia 1 signaling, the relation of nuclear-distribution element-like 1 activity with neurodevelopment and dopamine-related phenotypes.

METHODS

We measured cell distribution in striatum and cortex by histology and microtomography, and quantified the basal and amphetamine-stimulated locomotion and nuclear-distribution element-like 1 activity (in blood and brain) of transgenic disrupted-in-schizophrenia 1 rat vs wild-type littermate controls.

RESULTS

3D assessment of neuronal cell body number and spatial organization of mercury-impregnated neurons showed defective neuronal positioning, characteristic of impaired cell migration, in striatum/nucleus accumbens, and prefrontal cortex of transgenic disrupted-in-schizophrenia 1 compared to wild-type brains. Basal nuclear-distribution element-like 1 activity was lower in the blood and also in several brain regions of transgenic disrupted-in-schizophrenia 1 compared to wild-type. Locomotion and nuclear-distribution element-like 1 activity were both significantly increased by amphetamine in transgenic disrupted-in-schizophrenia 1, but not in wild-type.

CONCLUSIONS

Our findings in the transgenic disrupted-in-schizophrenia 1 rat allow us to state that decreased nuclear-distribution element-like 1 activity reflects both a trait (neurodevelopmental phenotype) and a state (amphetamine-induced dopamine release). We thus define here a role for decreased nuclear-distribution element-like 1 peptidase activity both for the developing brain (the neurodevelopmental phenotype) and for the adult (interaction with dopaminergic responses), and present nuclear-distribution element-like 1 activity in a novel way, as unifying neurodevelopmental with dysfunctional dopamine response phenotypes.

Comparative analysis of sample preparation protocols of soft biological tissues for morphometric studies using synchrotron-based X-ray microtomography

The spread of microtomography as a tool for visualization of soft tissues has had a significant impact on a better understanding of complex biological systems. This technique allows a detailed three-dimensional quantitative view of the specimen to be obtained, correlating its morphological organization with its function, providing valuable insights on the functionality of the tissue. Regularly overlooked, but of great importance, proper sample mounting and preparation are fundamental for achieving the highest possible image quality even for the high-resolution imaging systems currently under development. Here, a quantitative analysis compares some of the most common sample-mounting strategies used for synchrotron-based X-ray microtomography of soft tissues: alcoholic-immersion, paraffin-embedding and critical-point drying. These three distinct sample-mounting strategies were performed on the same specimen in order to investigate their impact on sample morphology regardless of individual sample variation. In that sense, the alcoholic-immersion strategy, although causing less shrinkage to the tissue, proved to be the most unsuitable approach for a high-throughput high-resolution imaging experiment due to sample drifting. Also, critical-point drying may present some interesting advantages regarding image quality but is also incompatible with a high-throughput experiment. Lastly, paraffin-embedding is shown to be the most suitable strategy for current soft tissue microtomography experiments. Such detailed analysis of biological sample-mounting strategies for synchrotron-based X-ray microtomography are expected to offer valuable insights on the best approach for using this technique for 3D imaging of soft tissues and following morphometric analysis.

Efficient Bandwidth Estimation in 2D Filtered Backprojection Reconstruction

A generalized cross-validation approach to estimate the reconstruction filter bandwidth in 2D filtered backprojection is presented. The method writes the reconstruction equation in equivalent backprojected filtering form, derives results on eigendecomposition of symmetric 2D circulant matrices, and applies them to make bandwidth estimation a computationally efficient operation within the context of standard backprojected filtering reconstruction. Performance evaluations on a range of simulated emission tomography experiments give promising results. The superior performance holds at both low and high total expected counts, pointing to the method's applicability even in weak signal-to-noise-ratio situations. The approach also applies to the more general class of elliptically symmetric filters, with the reconstructed estimate's performance often better than even that obtained with the true optimal radially symmetric filter.

Evaluation of a novel tomographic ultrasound device for abdominal examinations

Conventional ultrasound (US) is the first-line imaging method for abdominal pathologies, but its diagnostic accuracy is operator-dependent, and data storage is usually limited to two-dimensional images. A novel tomographic US system (Curefab CS, Munich, Germany) processes imaging data combined with three-dimensional spatial information using a magnetic field tracking. This enables standardized image presentation in axial planes and a review of the entire examination. The applicability and diagnostic performance of this tomographic US approach was analyzed in an abdominal setting using conventional US as reference. Tomographic US data were successfully compiled in all subjects of a training cohort (20 healthy volunteers) and in 50 patients with abdominal lesions. Image quality (35% and 79% for training and patient cohort respectively) and completeness of organ visualization (45% and 44%) were frequently impaired in tomographic US compared to conventional US. Conventional and tomographic US showed good agreement for measurement of organ sizes in the training cohort (right liver lobe and both kidneys with a median deviation of 5%). In the patient cohort, tomographic US identified 57 of 74 hepatic or renal lesions detected by conventional ultrasound (sensitivity 77%). In conclusion, this study illustrates the diagnostic potential of abdominal tomographic US, but current significant limitations of the tomographic ultrasound device demand further technical improvements before this and comparable approaches can be implemented in clinical practice.

Location of water in fresh sugarcane bagasse observed by synchrotron X-ray microtomography

Sugarcane bagasse is a vast lignocellulosic byproduct generated in the industry with ~50% humidity (1 kg dry matter associated with 1 kg water). Although the presence of water brings deleterious consequences for combustion, storage and sugar extraction, the location of water in fresh bagasse remains unknown. In this work, we use synchrotron X-ray microtomography for non-invasive 3D imaging of fresh bagasse particles, which allows the visualization of intraparticle water. The sclerified fiber cells in the sheaths surrounding xylem vessels are often found full of water. We suggest this can be juice preserved from the native stalks as many sclerified fibers seem to keep their structural integrity despite the mechanical action during sugarcane crushing. The microtomograms of fresh bagasse also shows mineral particles adhered to biomass surfaces, with adhesion presumably favored by the presence of water. In summary, this work unveils the location of water in fresh bagasse, solving an old mystery of sugarcane technology.

Responsive alignment for X-ray tomography beamlines

X-ray computed tomography (CT) is an imaging technique intended to obtain the internal structure and three-dimensional representation of a sample. In general, parallel-beam CT reconstruction algorithms require a precise angular alignment and knowledge of the exact axis of rotation position. Highly brilliant X-ray sources with ever-increasing data-acquisition rates demand optimized alignment techniques to avoid compromising in situ data analysis. This paper presents a method to automatically align the angular orientation and linear position of the rotation axis in a tomography setup, correlating image features from different X-ray projections.

High-resolution synchrotron-based X-ray microtomography as a tool to unveil the three-dimensional neuronal architecture of the brain

The assessment of neuronal number, spatial organization and connectivity is fundamental for a complete understanding of brain function. However, the evaluation of the three-dimensional (3D) brain cytoarchitecture at cellular resolution persists as a great challenge in the field of neuroscience. In this context, X-ray microtomography has shown to be a valuable non-destructive tool for imaging a broad range of samples, from dense materials to soft biological specimens, arisen as a new method for deciphering the cytoarchitecture and connectivity of the brain. In this work we present a method for imaging whole neurons in the brain, combining synchrotron-based X-ray microtomography with the Golgi-Cox mercury-based impregnation protocol. In contrast to optical 3D techniques, the approach shown here does neither require tissue slicing or clearing, and allows the investigation of several cells within a 3D region of the brain.