Automatic registration of serial sections of mouse lymph node by using Image-Reg

The first step towards the three-dimensional (3D) reconstruction of histological structures from serial sectioned tissue blocks is the proper alignment of microscope image sequences. We have accomplished an automatic rigid registration program, named Image-Reg, to align serial sections from mouse lymph node and Peyer's patch. Our approach is based on the calculation of the pixel-correlation of objects in adjacent images. The registration process is mainly divided into two steps. Once the foreground images have been segmented from the original images, the first step (primary alignment) is performed on the binary images of segmented objects; this process includes rotation by using the moments and translation through the X, Y axes by using the centroid. In the second step, the matching error of two binary images is calculated and the registration results are refined through multi-scale iterations. In order to test the registration performance, Image-Reg has been applied to an image and its transformed (rotated) version and subsequently to an image sequence of three serial sections of mouse lymph node. In addition, to compare our algorithm with other registration methods, three other approaches, viz. manual registration with Reconstruct, semi-automatic landmark registration with Image-Pro Plus and the automatic phase-correlation method with Image-Pro Plus, have also been applied to these three sections. The performance of our program has been also tested on other two-image data sets. These include: (a) two light microscopic images acquired by the automatic microscope (stitched with other software); (b) two images fluorescent images acquired by confocal microscopy (tiled with other software). Our proposed approach provides a fast and accurate linear alignment of serial image sequences for the 3D reconstruction of tissues and organs.     

Synchronization phenomena in nephron-nephron interaction

Experimental data for tubular pressure oscillations in rat kidneys are analyzed in order to examine the different types of synchronization that can arise between neighboring functional units. For rats with normal blood pressure, the individual unit (the nephron) typically exhibits regular oscillations in its tubular pressure and flow variations. For such rats, both in-phase and antiphase synchronization can be demonstrated in the experimental data. For spontaneously hypertensive rats, where the pressure variations in the individual nephrons are highly irregular, signs of chaotic phase and frequency synchronization can be observed. Accounting for a hemodynamic as well as for a vascular coupling between nephrons that share a common interlobular artery, we develop a mathematical model of the pressure and flow regulation in a pair of adjacent nephrons. We show that this model, for appropriate values of the parameters, can reproduce the different types of experimentally observed synchronization. (c) 2001 American Institute of Physics.     

Fractal microstructures of light-emitting porous silicon films

By means of scanning electron microscopy and computer simulation, we have investigated the microstructures of a 23-μm-thick porous silicon (PS) film and a 6-μm-thick PS film. The two films give off strong visible emissions when excited by the 254 nm light. For the 23-μm-thick PS film, both of its cross-sectional and top-surface morphologies exhibit self-similarity whose small-scale and large-scale microstructures resemble one another. For the 6-μm-thick PS film, self-similar cracks are developed on its top surface. Our results have demonstrated that the microstructures of PS films exhibit the characteristics of fractals. With box counting method, the fractal dimensions of the PS films are calculated to be about 2.3-2.6. Based on the model of diffusion-limited aggregation, the fractal growth processes have been simulated for the PS films.     

Computer-generated, three-dimensional reconstruction of histological parallel serial sections displaying microvascular and glandular structures in human endometrium

This paper describes a technique to develop high-resolution three-dimensional (3D) images of microvasculature structures in curettage, hysterectomy or endometrial resection biopsies using parallel histological serial sections. Employing a labelled streptavidin-biotin-alkaline phosphatase (LSAB(+)) method and visualising by using DAB(+) with the primary antibody, mouse anti human Q-Bend-10, the images were directly digitised from a light microscope into the KS400 Universal Image Processing and Analysis software via a CCD colour camera; binary images of the structures were created and the binary images were exported into VoxBlast 3D rendering software to view still and rotating 3D images on a computer monitor. This in turn enabled hard copies of the full sequence to be printed.     

Three-dimensional holographic reconstruction of two-dimensional image information from serial sections and its applications in biomedicine

An experimental study to synthesize holographically two-dimensional projections of serial sections at various depths into three-dimensional images is described. The effects caused by the position, size and resolution of virtual images during reconstruction are analysed, and the advantages and limitations of this method are discussed. An application of this experimental method — the three-dimensional reconstruction of serial sections of a newt embryo — is presented.     

Improved detection of molecularly targeted iron oxide particles in mouse brain using B0 field stabilised high resolution MRI

PurposeHigh resolution multi-gradient echo (MGE) scanning is typically used for detection of molecularly targeted iron oxide particles. The images of individual echoes are often combined to generate a composite image with improved SNR from the early echoes and boosted contrast from later echoes. In 3D implementations prolonged scanning at high gradient duty cycles induces a B₀ shift that predominantly affects image alignment in the slow phase encoding dimension of 3D MGE images. The effect corrupts the composite echo image and limits the image resolution that is realised. A real-time adaptive B₀ stabilisation during respiration gated 3D MGE scanning is shown to reduce image misalignment and improve detection of molecularly targeted iron oxide particles in composite images of the mouse brain.MethodsAn optional B₀ measurement block consisting of a 16 μs hard pulse with FA 1°, an acquisition delay of 3.2 ms, followed by gradient spoiling in all three axes was added to a respiration gated 3D MGE scan. During the acquisition delay of each B₀ measurement block the NMR signal was routed to a custom built B₀ stabilisation unit which mixed the signal to an audio frequency nominally centred around 1000 Hz to enable an Arduino based single channel receiver to measure frequency shifts. The frequency shift was used to effect correction to the main magnetic field via the B₀ coil. The efficacy of B₀ stabilisation and respiration gating was validated in vivo and used to improve detection of molecularly targeted microparticles of iron oxide (MPIO) in a mouse model of acute neuroinflammation.ResultsWithout B₀ stabilisation 3D MGE image data exhibit varying mixtures of translation, scaling and blurring, which compromise the fidelity of the composite image. The real-time adaptive B₀ stabilisation minimises corruption of the composite image as the images from the different echoes are properly aligned. The improved detection of molecularly targeted MPIO easily compensates for the scan time penalty of 14% incurred by the B₀ stabilisation method employed. Respiration gating of the B₀ measurement and the MRI scan was required to preserve high resolution detail, especially towards the back of the brain.ConclusionsHigh resolution imaging for the detection of molecularly targeted iron oxide particles in the mouse brain requires good stabilisation of the main B₀ field, and can benefit from a respiration gated image acquisition strategy.     

Crystal-dithering method applied to spectral phase interferometry for direct electric-field reconstruction (SPIDER) for sensitivity enhancement of the pulse phase measurement

The application of a crystal-dithering technique to the spectral phase interferometry for direct electric-field reconstruction (SPIDER) was experimentally demonstrated. Applying a crystal-dithering technique to SPIDER resulted in the improvement of the measurement sensitivity. In our approach, a 20 μm-thick nonlinear crystal for a thin-crystal SPIDER method was replaced by a 100 μm-thick crystal, and the crystal was dithered. The improvement was confirmed by comparing the statistical error of the crystal-dithering SPIDER to the statistical error of the thin-crystal SPIDER method. The dispersion of a BK7 plate was investigated to evaluate the reliability of the proposed approach.     

Comparative study of InGaP/GaAs heterojunction bipolar transistors (HBTs) with different base surface treatments

The interesting InGaP/GaAs heterojunction bipolar transistors (HBTs) with different surface passivations on the base surface are fabricated and studied. Experimentally, the HBT device with sulfur treatment passivation displays the lowest offset voltage. However, the device with a 0.02 μm-thick emitter ledge structure reveals better transistor behaviors such as higher current gain and lower base surface recombination current. In addition, it also exhibits improved thermal stability. For the reliability test, the device with a 0.02 μm-thick emitter ledge structure shows the best performance. Therefore, from experimental results, the HBT device performance could be improved by appropriate base surface treatments, e.g., sulfur passivation and emitter ledge structure.     

Finite element modelling of ion transport in the electrolyte of a 3D-microbattery

A mathematical model describing ionic transport in a 3D-microbattery (3D-MB) electrolyte is developed here using finite element methodology. The model is then exploited to study a 3D-MB based on an interdigitated plate (“trench”) architecture for a 10 μm-thick electrolyte layer separating 10 μm-thick graphite anode and LiCoO₂ cathode plates. The effect of varying plate length, end-shape and electronic conductivity is also modelled. It is shown that the 3D-MB architecture gives rise to qualitatively non-uniform current densities, leading to sub-optimal surface utilization. This can, in turn, be optimized by varying electrode geometries and/or material properties.     

Thickness effect of the TiO2 nanofiber scattering layer on the performance of the TiO2 nanoparticle/TiO2 nanofiber-structured dye-sensitized solar cells

TiO₂ nanofibers (NFs) were fabricated by an electrospinning process and were used as scattering layers in dye-sensitized solar cells (DSSCs). The NF-coated photoanodes of the DSSCs were prepared with a variety of scattering layer thicknesses. The thickness effect of the scattering layer on the double-layered TiO₂ nanoparticle (NP)/TiO₂ NF structure was investigated through structural, morphological, and optical measurements. In the double-layered photoanode, the TiO₂ NP layer plays a major role in dye adsorption and light transmission, and the TiO₂ NF scattering layer improves the absorption of visible light due to the light scattering effects. The scattering effect of TiO₂ NFs layer was examined by the incident monochromatic photon-to-electron conversion efficiency (IPCE) and UV–Vis spectrometry. The conversion efficiency for the 12 μm-thick photoanode composed of a 2 μm-thick TiO₂ NF layer and 10 μm-thick TiO₂ NP layer was higher than that of DSSCs with only TiO₂ NPs photoanode by approximately 33%.     

In vivo hypoxia characterization using blood oxygen level dependent magnetic resonance imaging in a preclinical glioblastoma mouse model

PurposeHypoxia measurements can provide crucial information regarding tumor aggressiveness, however current preclinical approaches are limited. Blood oxygen level dependent (BOLD) Magnetic Resonance Imaging (MRI) has the potential to continuously monitor tumor pathophysiology (including hypoxia). The aim of this preliminary work was to develop and evaluate BOLD MRI followed by post-image analysis to identify regions of hypoxia in a murine glioblastoma (GBM) model.MethodsA murine orthotopic GBM model (GL261-luc2) was used and independent images were generated from multiple slices in four different mice. Image slices were randomized and split into training and validation cohorts. A 7 T MRI was used to acquire anatomical images using a fast-spin-echo (FSE) T2-weighted sequence. BOLD images were taken with a T2*-weighted gradient echo (GRE) and an oxygen challenge. Thirteen images were evaluated in a training cohort to develop the MRI sequence and optimize post-image analysis. An in-house MATLAB code was used to evaluate MR images and generate hypoxia maps for a range of thresholding and ΔT2* values, which were compared against respective pimonidazole sections to optimize image processing parameters. The remaining (n = 6) images were used as a validation group. Following imaging, mice were injected with pimonidazole and collected for immunohistochemistry (IHC). A test of correlation (Pearson's coefficient) and agreement (Bland-Altman plot) were conducted to evaluate the respective MRI slices and pimonidazole IHC sections.ResultsFor the training cohort, the optimized parameters of “thresholding” (20 ≤ T2* ≤ 35 ms) and ΔT2* (±4 ms) yielded a Pearson's correlation of 0.697. These parameters were applied to the validation cohort confirming a strong Pearson's correlation (0.749) when comparing the respective analyzed MR and pimonidazole images.ConclusionOur preliminary study supports the hypothesis that BOLD MRI is correlated with pimonidazole measurements of hypoxia in an orthotopic GBM mouse model. This technique has further potential to monitor hypoxia during tumor development and therapy.     

A nonlinear mesh-warping technique for correcting brain deformation after stroke

This article presents a warping technique for correcting brain tissue distortion on magnetic resonance imaging (MRI) scans due to stroke lesion growth and for mapping MRI scans to histological sections. Meshes are imposed upon the images for feature specification, and these features are exactly matched in the different images to be mapped, while the other voxels are matched by interpolation. This technique was tested on serial MR images and histological sections that were acquired in a nonhuman primate model of stroke. This technique was able to deliver satisfactory warping results. It is simple and robust and can be utilized in many applications for comparison of multimodality medical images and histological sections.     

Complex cylindrical vector beam excludes the orientation dependence of the intensity of scanning fluorescence images of single molecules

A polarization inhomogeneous vector beam, which is the complex superposition of radially and azimuthally polarized beams, has been studied computationally and theoretically in application to scanning fluorescence microscopy of single molecules. It has been shown that its application makes it possible to almost exclude the dependence of the intensity maximum of the scanning fluorescence image of a single molecule on its orientation. It has been demonstrated that the scanning of one horizontal plane of a solid matrix containing impurity luminescent molecules provides images of all molecules located in a 1-μm-thick layer, replacing three-dimensional scanning. Recommendations on the technical implementation of the proposed beam have been given.     

Phase transitions in KNO3 embedded in MCM-41 films with regular nanopores

This paper reports on a comparative study of phase transitions in nanocomposites made up of KNO₃ embedded in 10-μm-thick MCM-41 films with unidirectional pores 4.0 nm in size on an aluminum substrate and of nanocomposites prepared in the form of potassium-nitrate-filled pressed MCM-41 powders with 3.7-nm pores. The temperature dependences of linear permittivity and the amplitude of third harmonic generation have been measured under heating and cooling. The structural transition from phase II to phase I shifts under heating relative to that occurring in bulk KNO₃ toward lower temperatures for potassium nitrate in the film and toward higher temperatures for the pressed MCM-41-based nanocomposite. A significant difference has been observed also within the region of existence of ferroelectric phase III. The data obtained suggest that the shifts of phase transition temperatures observed in the conditions of nanoconfinement are influenced markedly not only by pore size and geometry but also by other factors.     

宽沟道SI-GaAs衬底上适于光发射机的BH激光器

目前,光发射机中的激光器有采用MOCVD和MBE方法生长的多量子阱激光器,用LPE法生长的BH激光器。我们根据现有的实验条件,为了制作单片集成的光发射机,在沟道SI-GaAs衬底上采用两次液相外延生长BH激光器,实现了表面平面化。在800℃一次外延生长四层。第一层n⁺-GaAs缓冲层,第二层N-GaAlAs下限制层,第三层非掺杂构GaAs有源层,第四层为P-GaAlAs上限制层。采用适当的腐蚀条件刻蚀出有源区最窄的燕尾形隐埋条。在二次外延中,我们仅装一槽GaAlAs源液,在晶片上仅停留一次便生长出两个掩埋层,且层间界面与有源区自对准。上层为N-GaAlAs,载流子浓度为10¹⁶cm^-3,下层为高阻伴随生长层。由于高阻伴随层的存在对电流产生了有有效的侧向限制作用,因此避免了通常的SiO₂膜沉积等一系列工艺,提高了成品率,减化了工艺程序。利用n型掩埋层和隐埋条区P型上限制层之间铝组分及载流子类型、浓度的差异,虽然做一种宽接触电极,但由于隐埋条区上有良好的欧姆接触,而在掩埋层上为非良欧姆接触,所以起到了一定的电流外限制作用。n型电极是从n⁺-GaAs层引出的。 这种沟道SI-GaAs衬底正装GaAlAs/GaAs BH激光器室温连续工作阈值电流为55mA,P-I曲线在100℃仍有良好的线性关系。     

Magnetic resonance imaging (MRI) and pathophysiology of the rat kidney in streptozotocin-induced diabetes.

Proton magnetic resonance imaging was performed on rats before induction of diabetes with streptozotocin (STZ) and at 2 and 12 days postinduction. Images revealed an increase in maximal longitudinal and axial dimensions of the kidneys at 2 days and a further increase at 12 days. Similarly, an increase in the size of the remaining kidney was seen in a rat which underwent uninephrectomy as a positive control. Two major differences were observed between the kidney undergoing compensatory hypertrophy and those developing diabetic nephropathy: (i) Expansion of the renal vasculature was seen only in images of the diabetic rat; (ii) A loss in conspicuity of the normal corticomedullary junction was seen in the T2-weighted images of the diabetic rat but not in the uninephrectomized rat. Histologic examination revealed that the medulla increased to a size greater than the cortex during diabetic nephropathy whereas the medullary volume was less than that of the cortex during compensatory hypertrophy. In vitro T1 relaxation times in cortex, outer medulla and inner medulla of kidneys from control rats were measured and compared with the same respective regions in diabetic rats. When these values were correlated with tissue water content, a linear increase in relaxation rate versus percent water content from cortex to inner medulla was found in the control kidneys, but this correlation was absent in diabetic nephropathy. These studies demonstrate that MRI is an effective noninvasive tool for studying the course of renal hypertrophy and hydration changes in the development of renal disease in STZ-induced diabetes in the rat.     

Rat brain digital stereotaxic white matter atlas with fine tract delineation in Paxinos space and its automated applications in DTI data analysis

PurposeTo automatically analyze diffusion tensor images of the rat brain via both voxel-based and ROI-based approaches, we constructed a new white matter atlas of the rat brain with fine tracts delineation in the Paxinos and Watson space.Materials and methodsUnlike in previous studies, we constructed a digital atlas image from the latest edition of the Paxinos and Watson. This atlas contains 111 carefully delineated white matter fibers. A white matter network of rat brain based on anatomy was constructed by locating the intersection of all these tracts and recording the nuclei on the pathway of each white matter tract. Moreover, a compatible rat brain template from DTI images was created and standardized into the atlas space. To evaluate the automated application of the atlas in DTI data analysis, a group of rats with right-side middle cerebral artery occlusion (MCAO) and those without were enrolled in this study.ResultsThe voxel-based analysis result shows that the brain region showing significant declines in signal in the MCAO rats was consistent with the occlusion position.ConclusionWe constructed a stereotaxic white matter atlas of the rat brain with fine tract delineation and a compatible template for the data analysis of DTI images of the rat brain.     

空间目标天基光学观测的序列图像仿真方法

利用STK和OpenGL,提出了一种能体现空间目标天基光学观测系统真实成像距离和系统性能的序列图像仿真方法。首先建立空间目标的三维模型和轨道模型,利用STK预测目标卫星和观测卫星的相对几何关系,然后在分析相机针孔成像和OpenGL透视投影成像模型关系的基础上,通过设置OpenGL的有关参数生成了包含目标和成像系统信息在内的目标仿真图像,最后生成运动空间目标近距离光学观测的二维图像序列,可为天基空间目标识别研究提供数据基础。     

Radiation-induced kidney injury: a role for chronic oxidative stress?

Kidney irradiation clearly leads to a progressive reduction in function associated with concomitant glomerulosclerosis and/or tubulointerstitial fibrosis. However, the particular cell types, mediators and/or mechanisms involved in the development and progression of radiation nephropathy remain ill defined. Angiotensin II (Ang II) plays a major pathogenic role; administration of Ang II blockers markedly abrogates the severity of radiation nephropathy in experimental models. Both ionizing radiation and Ang II signal via generation of reactive oxygen species (ROS). Thus, we hypothesized that localized kidney irradiation might lead to a chronic oxidative stress. In view of the difficulty in measuring ROS in vivo we adopted an indirect immunohistochemical approach in which we used a monoclonal antibody specific for 8-hydroxy-2'-deoxyguanosine (8-OHdG), one of the most commonly used markers of DNA oxidation.The right kidney of 7-8 week-old male Sprague-Dawley rats was removed. Five to 6 weeks later the remaining hypertrophied kidney was irradiated with single doses of 0-20.0 Gy X-rays. Groups of rats, three per dose, were killed at 4, 8, 16 and 24 weeks post-irradiation, their kidneys fixed, and sections stained with the 8-OHdG-specific antibody N45.1.For quantitation of glomerular DNA oxidation with the N45.1 antibody stained sections, 50 glomeruli/animal were counted. The presence of any intensely stained nuclei within the glomerular tuft was scored as positive. Quantitation of tubular DNA oxidation employed a 10 x 10 point ocular grid. Sections were examined at 400 magnification; 250 tubular profiles were counted. All tubules with any nuclear staining were scored as positive.Sham-irradiated kidneys showed little evidence of DNA oxidation over the experimental period. In contrast, localized kidney irradiation led to a marked, dose-independent increase in glomerular and tubular cell nuclear DNA oxidation. This increase was evident at the first time point studied, i.e. 4 weeks after irradiation, and persisted for up to 24 weeks postirradiation. DNA oxidation in the irradiated kidney was only seen in apparently viable glomerular and tubular cells. Thus, while from 16 to 24 weeks post-irradiation structural alterations had progressed to glomerular sclerosis and tubular atrophy, positive staining for 8-OHdG was not observed in severely atrophic tubules. Similarly, fewer positive staining cells were noted in glomeruli undergoing sclerosis, while none were seen in totally sclerotic glomeruli. These data support the hypothesis that renal irradiation is associated with a chronic and persistent oxidative stress.     

Indirect optical crosstalk reduction by highly-doped backside layer in single-photon avalanche diode arrays

A method of reducing indirect optical crosstalk in single-photon avalanche diode arrays is investigated by TCAD simulations. The reduction is accomplished by taking advantage of an enhanced optical absorption in a highly-doped Si layer on the backside of the wafer. A simulation environment was developed to give information about optical crosstalk by incorporating the experimental optical constants of the materials constituting the crosstalk-reduction layer. It is shown that the indirect optical crosstalk is greatly reduced by increasing the thickness and doping of the layer. A crosstalk reduction of 5 orders of magnitude is gained with addition of 1-μm-thick \(\hbox {PureB}/\upalpha \hbox {-Si}\) stack for the array processed on a p-type substrate, while the same reduction is achieved with a 1-μm-thick highly-doped Si layer (As, \(1.1\times 10^{20}\, \hbox {cm}^{-3}\)) for an array processed on an n-type substrate.