arXiv subjects

Yoshio Suzuki

Publications and source records attributed to Yoshio Suzuki.

17 recordsLinked to original sources

arXiv2026

Development of an Extensible Unified Control System Using the STARS Framework and Common Commands for Detector Control

A zooming optical system comprising two Fresnel zone plates (FZPs) was developed and installed at the AR-NE1A beamline of the Photon Factory, High Energy Accelerator Research Organization (KEK), Japan. To ensure reliable and versatile operation, we implemented a dedicated control architecture based on the Simple Transmission and Retrieval System (STARS) framework and the newly proposed STARS Common Commands for Detector Control (CCDC)---a data-acquisition (DAQ) state model and command set designed specifically for detector control. The system serves both as a practical control system for the zooming optics and as a demonstration of modular extensibility using STARS and detector interoperability through CCDC. The system has been commissioned, and its performance has been verified at the AR-NE1A beamline. The architecture enables flexible configuration of optical components and provides a unified interface for both routine operation and advanced experimental protocols.

physics.ins-det↗

arXiv2026

Recent application studies of an INTPIX4NA SOIPIX detector-based X-ray camera using an SiTCP-XG 10GbE-based high-speed readout system at KEK facilities

The Silicon-On-Insulator PIXel (SOIPIX) detector is a unique monolithic structure imaging device currently being developed by the SOIPIX group, led by the High Energy Accelerator Research Organization (KEK). Our detector team at the KEK Photon Factory (PF) has developed an X-ray camera based on the INTPIX4NA SOIPIX detector. This detector provides a sensitive area of 14.1 $\times$ 8.7 $\mathrm{mm^2}$, with 425,984 pixels arranged in an 832-column $\times$ 512-row matrix and a pixel size of 17 $\times$ 17 $\mathrm{μm^{2}}$, and offers high spatial resolution and excellent sensitivity under low-intensity X-ray conditions. The readout system used in the X-ray camera is developed at the PF. It is equipped with SiTCP-XG, a 10 Gb Ethernet network controller implemented on a field-programmable gate array, enabling high-frame-rate imaging at several hundred hertz. We are currently investigating the applicability of this X-ray camera in several experiments at KEK. Herein, we report three recent application studies: (1) X-ray zooming microscope optics using two Fresnel zone plates at PF AR-NE1A; (2) phase-contrast X-ray imaging system using a two-crystal X-ray interferometer at PF BL-14C; and (3) nondestructive lithium detection in Li-ion battery electrode materials using muonic X-rays at J-PARC MLF Muon D2.

physics.ins-det↗

arXiv2025

Development of a new phase-retrieval algorithm from a single-shot image for X-ray schlieren microscopy

In this paper, a new phase-retrieval algorithm from an X-ray schlieren image is proposed. The schlieren method allows phase-contrast imaging with an objective lens and a knife-edge filter placed at the back focal plane of the objective. This method finds a wide range of applications in the visible-light region for transparent specimen visualization. The schlieren contrast does not directly correspond to the phase shift. However, the phase map can be reconstructed from a single-shot schlieren image of a transparent and weak-phase object using the filtered Fourier transform method. A proof-of-principle experiment was performed in the hard-X-ray region at the AR-NE1A beamline of the Photon Factory facility at the High Energy Accelerator Research Organization (KEK).

physics.ins-det↗

arXiv2024

Murine AI excels at cats and cheese: Structural differences between human and mouse neurons and their implementation in generative AIs

Mouse and human brains have different functions that depend on their neuronal networks. In this study, we analyzed nanometer-scale three-dimensional structures of brain tissues of the mouse medial prefrontal cortex and compared them with structures of the human anterior cingulate cortex. The obtained results indicated that mouse neuronal somata are smaller and neurites are thinner than those of human neurons. These structural features allow mouse neurons to be integrated in the limited space of the brain, though thin neurites should suppress distal connections according to cable theory. We implemented this mouse-mimetic constraint in convolutional layers of a generative adversarial network (GAN) and a denoising diffusion implicit model (DDIM), which were then subjected to image generation tasks using photo datasets of cat faces, cheese, human faces, and birds. The mouse-mimetic GAN outperformed a standard GAN in the image generation task using the cat faces and cheese photo datasets, but underperformed for human faces and birds. The mouse-mimetic DDIM gave similar results, suggesting that the nature of the datasets affected the results. Analyses of the four datasets indicated differences in their image entropy, which should influence the number of parameters required for image generation. The preferences of the mouse-mimetic AIs coincided with the impressions commonly associated with mice. The relationship between the neuronal network and brain function should be investigated by implementing other biological findings in artificial neural networks.

q-bio.NC↗

arXiv2024

X-ray imaging camera using INTPIX4NA SOIPIX detector with SiTCP-XG 10GbE based high-speed readout system

The silicon-on-insulator pixel (SOIPIX) detector is a unique monolithic-structure imaging device currently being developed by the SOIPIX group led by the High Energy Accelerator Research Organization (KEK). The detector team at KEK Photon Factory (PF) is also developing an X-ray camera using INTPIX4NA with a 14.1 $\times$ 8.7 $\mathsf{mm^2}$ sensitive area and 425,984 (832 column $\times$ 512 row matrix) pixels, with a pixel size of 17 $\times$ 17 $\mathsf{μm^2}$. The detector has high resolution and sensitivity for low-intensity X-rays, making it suitable for imaging in optical systems with lower X-ray intensities, such as an X-ray zooming microscope using two Fresnel zone plates (FZPs), which is also under development at PF. To enable imaging under such conditions, we developed a detector cooling system using a Peltier element to support longer exposure time (~0.5 seconds per frame). Additionally, we developed a new readout system using DAQ boards developed by PF, equipped with SiTCP-XG (network controller implemented on field-programmable gate array) that supports 10 Gbps Ethernet for high-frame-rate imaging at several hundred hertz. The new X-ray camera was tested at the PF BL-14A, BL-14B, and AR-NE1A experimental stations, and the resolution and sensitivity characteristics were confirmed. Given these confirmed characteristics, this X-ray camera is suitable for X-ray imaging using 5--20 keV X-rays under low-intensity, low-contrast conditions. These conditions are ideal for capturing soft tissues with poor contrast, objects with fine structures, and specimens vulnerable to radiation damage.

physics.ins-det↗

arXiv2022

Structural aging of human neurons is the opposite of the changes in schizophrenia

Human mentality develops with age and is altered in psychiatric disorders, though their underlying mechanism is unknown. In this study, we analyzed nanometer-scale three-dimensional structures of brain tissues of the anterior cingulate cortex from eight schizophrenia and eight control cases. The distribution profiles of neurite curvature of the control cases showed a trend depending on their age, resulting in an age-correlated decrease in the standard deviation of neurite curvature (Pearson's r = -0.80, p = 0.018). In contrast to the control cases, the schizophrenia cases deviate upward from this correlation, exhibiting a 60% higher neurite curvature compared with the controls (p = 7.8 x 10^(-4)). The neurite curvature also showed a correlation with a hallucination score (Pearson's r = 0.80, p = 1.8 x 10^(-4)), indicating that neurite structure is relevant to brain function. We suggest that neurite curvature plays a pivotal role in brain aging and can be used as a hallmark to exploit a novel treatment of schizophrenia. This nano-CT paper is the result of our decade-long analysis and is unprecedented in terms of number of cases.

q-bio.NC↗

arXiv2020

Structural diverseness of neurons between brain areas and between cases

The cerebral cortex is composed of multiple cortical areas that exert a wide variety of brain functions. Although human brain neurons are genetically and areally mosaic, the three-dimensional structural differences between neurons in different brain areas or between the neurons of different individuals have not been delineated. Here, we report a nanometer-scale geometric analysis of brain tissues of the superior temporal gyrus of 4 schizophrenia and 4 control cases by using synchrotron radiation nanotomography. The results of the analysis and a comparison with results for the anterior cingulate cortex indicated that 1) neuron structures are dissimilar between brain areas and that 2) the dissimilarity varies from case to case. The structural diverseness was mainly observed in terms of the neurite curvature that inversely correlates with the diameters of the neurites and spines. The analysis also revealed the geometric differences between the neurons of the schizophrenia and control cases, suggesting that neuron structure is associated with brain function. The area dependency of the neuron structure and its diverseness between individuals should represent the individuality of brain functions.

q-bio.NC↗

arXiv2019

Three-dimensional alteration of neurites in schizophrenia

This paper reports nano-CT analysis of brain tissues of schizophrenia and control cases. The analysis revealed that: (1) neuronal structures vary between individuals, (2) the mean curvature of distal neurites of the schizophrenia cases was 1.5 times higher than that of the controls, and (3) dendritic spines were categorized into two geometrically distinctive groups, though no structural differences were observed between the disease and control cases. The differences in the neurite curvature result in differences in the spatial trajectory and hence alter neuronal circuits. We suggest that the structural alteration of neurons in the schizophrenia cases should reflect psychiatric symptoms of schizophrenia.

q-bio.NC↗

arXiv2017

Method for estimating modulation transfer function from sample images

The modulation transfer function (MTF) represents the frequency domain response of imaging modalities. Here, we report a method for estimating the MTF from sample images. Test images were generated from a number of images, including those taken with an electron microscope and with an observation satellite. These original images were convolved with point spread functions (PSFs) including those of circular apertures. The resultant test images were subjected to a Fourier transformation. The logarithm of the squared norm of the Fourier transform was plotted against the squared distance from the origin. Linear correlations were observed in the logarithmic plots, indicating that the PSF of the test images can be approximated with a Gaussian. The MTF was then calculated from the Gaussian-approximated PSF. The obtained MTF closely coincided with the MTF predicted from the original PSF. The MTF of an x-ray microtomographic section of a fly brain was also estimated with this method. The obtained MTF showed good agreement with the MTF determined from an edge profile of an aluminum test object. We suggest that this approach is an alternative way of estimating the MTF, independently of the image type.

eess.IV↗

arXiv2017

Estimating the resolution of real images

Image resolvability is the primary concern in imaging. This paper reports an estimation of the full width at half maximum of the point spread function from a Fourier domain plot of real sample images by neither using test objects, nor defining a threshold criterion. We suggest that this method can be applied to any type of image, independently of the imaging modality.

physics.data-an↗

arXiv2016

Three-dimensional microtomographic imaging of human brain cortex

This paper describes an x-ray microtomographic technique for imaging the three-dimensional structure of the human cerebral cortex. Neurons in the brain constitute a neural circuit as a three-dimensional network. The brain tissue is composed of light elements that give little contrast in a hard x-ray transmission image. The contrast was enhanced by staining neural cells with metal compounds. The obtained structure revealed the microarchitecture of the gray and white matter regions of the frontal cortex, which is responsible for the higher brain functions.

physics.bio-ph↗

arXiv2016

X-ray microtomographic visualization of Escherichia coli by metalloprotein overexpression

This paper reports X-ray microtomographic visualization of the microorganism Escherichia coli overexpressing a metalloprotein ferritin. The three-dimensional distribution of linear absorption coefficients determined using a synchrotron radiation microtomograph with a simple projection geometry revealed that the X-ray absorption was homogeneously distributed, suggesting that every E. coli cell was labeled with the ferritin. The ferritin-expressing E. coli exhibited linear absorption coefficients comparable to those of phosphotungstic-acid stained cells. The submicrometer structure of the ferritin-expressing E. coli cells was visualized by Zernike phase contrast using an imaging microtomograph equipped with a Fresnel zone plate. The obtained images revealed curved columnar or bunching oval structures corresponding to the E. coli cells. These results indicate that the metalloprotein overexpression facilitates X-ray visualization of three-dimensional cellular structures of biological objects.

physics.bio-ph↗

arXiv2016

Three-dimensional network of Drosophila brain hemisphere

The first step to understanding brain function is to determine the brain's network structure. We report a three-dimensional analysis of the brain network of the fruit fly Drosophila melanogaster by synchrotron-radiation tomographic microscopy. A skeletonized wire model of the left half of the brain network was built by tracing the three-dimensional distribution of X-ray absorption coefficients. The obtained models of neuronal processes were classified into groups on the basis of their three-dimensional structures. These classified groups correspond to neuronal tracts that send long-range projections or repeated structures of the optic lobe. The skeletonized model is also composed of neuronal processes that could not be classified into the groups. The distribution of these unclassified structures correlates with the distribution of contacts between neuronal processes. This suggests that neurons that cannot be classified into typical structures should play important roles in brain functions. The quantitative description of the brain network provides a basis for structural and statistical analyses of the Drosophila brain. The challenge is to establish a methodology for reconstructing the brain network in a higher-resolution image, leading to a comprehensive understanding of the brain structure.

q-bio.NC↗

arXiv2016

Submicrometer tomographic resolution examined using a micro-fabricated test object

To estimate the spatial resolution of microtomographs, a test object on the submicrometer scale was prepared by focused ion beam milling and subjected to microtomographic analysis. Since human tissues are composed of cells and extracellular matrices with micrometer and submicrometer structures, it is important to investigate the three-dimensional spatial resolution of microtomographs used to visualize microstructures of human tissues. The resolutions along the direction within the tomographic slice plane (in-plane resolution) and perpendicular to it (through-plane resolution) were determined from the modulation transfer function of square-wave patterns. The in-plane resolution was estimated to be 1.2 um from the modulation transfer function of the non-zoom image. In contrast, the zoom image gave the in-plane resolution of 0.8 um. This in-plane resolution is comparable to the through-plane resolution, which was estimated to be 0.8 um. Although the two-dimensional radiographs were taken with the pixel width of half the x-ray optics resolution, these three-dimensional resolution analyses indicated that the zoom reconstruction should be performed to achieve the in-plane resolution comparable to the x-ray optics resolution. The submicrometer three-dimensional analysis was applied in the structural study of human cerebral tissue stained with high-Z elements and the obtained tomograms revealed that the microtomographic analysis allows visualization of the subcellular structures of the cerebral tissue.

physics.ins-det↗

arXiv2016

X-ray microtomography in biology

Progress in high-resolution x-ray microtomography has provided us with a practical approach to determining three-dimensional (3D) structures of opaque samples at micrometer to submicrometer resolution. In this review, we give an introduction to hard x-ray microtomography and its application to the visualization of 3D structures of biological soft tissues. Practical aspects of sample preparation, handling, data collection, 3D reconstruction, and structure analysis are described. Furthermore, different sample contrasting methods are approached in detail. Examples of microtomographic studies are overviewed to present an outline of biological applications of x-ray microtomography. We also provide perspectives of biological microtomography as the convergence of sciences in x-ray optics, biology, and structural analysis.

physics.bio-ph↗

arXiv2016

Estimation of presampling modulation transfer function in synchrotron radiation microtomography

The spatial resolution achieved by recent synchrotron radiation microtomographs should be estimated from the modulation transfer function (MTF) on the micrometer scale. Step response functions of a synchrotron radiation microtomograph were determined by the slanted edge method by using high-precision surfaces of diamond crystal and ion-milled aluminum wire. Tilted reconstruction was introduced to enable any edge to be used as the slanted edge by defining the reconstruction pixel matrix in an arbitrary orientation. MTFs were estimated from the step response functions of the slanted edges. The obtained MTFs coincided with MTF values estimated from square-wave patterns milled on the aluminum surface. Although x-ray refraction influences should be taken into account to evaluate MTFs, any flat surfaces with nanometer roughness can be used to determine the spatial resolutions of microtomographs.

physics.data-an↗

arXiv2016

A method for estimating spatial resolution of real image in the Fourier domain

Spatial resolution is a fundamental parameter in structural sciences. In crystallography, the resolution is determined from the detection limit of high-angle diffraction in reciprocal space. In electron microscopy, correlation in the Fourier domain is used for estimating the resolution. In this paper, we report a method for estimating the spatial resolution of real images from a logarithmic intensity plot in the Fourier domain. The logarithmic intensity plots of test images indicated that the full width at half maximum of a Gaussian point-spread function can be estimated from the images. The spatial resolution of imaging X-ray microtomography using Fresnel zone-plate optics was also estimated with this method. A cross section of a test object visualized with the imaging microtomography indicated that square-wave patterns up to 120-nm pitch were resolved. The logarithmic intensity plot was calculated from a tomographic cross section of brain tissue. The full width at half maximum of the point spread function estimated from the plot coincided with the resolution determined from the test object. These results indicated that the logarithmic intensity plot in the Fourier domain provides an alternative measure of the spatial resolution without explicitly defining a noise criterion.

physics.data-an↗