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.     

Development and Optimization of Three-Dimensional Spatial EPR Imaging for Biological Organs and Tissues

The development and optimization procedures for obtaining high-quality three-dimensional spatial electron-paramagnetic-resonance images of large lossy samples at L band are described. Strategies for selecting optimized parameters for projection acquisition, instrumentation, and algorithms for correcting drifts in microwave frequency and inaccuracies in the static and gradient magnetic fields are described. Image reconstruction was performed using a two-stage filtered back-projection method with spectral deconvolution. With this instrumentation, correction algorithms, and image reconstruction method, spatially accurate 3D images of radical distribution were observed in complex phantoms using 0.5 mM nitroxide labels. The results indicate that high-quality images of lossy samples, including biological organs and tissues of up to 25 mm in size, could be obtained in a reasonable time with submillimeter resolution.     

血管内光声图像的建模与仿真

为了给血管内光声(intravascular photoacoustic,IVPA)成像的图像重建算法和图像后处理算法提供数据源,为培训医师提供图像库,提出一种二维IVPA图像的建模与仿真方法。建立包含斑块的血管横截面模型,并对成像导管发射激光脉冲照射血管壁组织、血管壁组织产生光声信号、利用得到的一组光声信号重建IVPA图像整个过程进行仿真,得到血管横截面模型的二维IVPA灰阶图像,同时根据冠状动脉血管随心脏搏动的规律,实现序列图像的仿真。利用仿真模型得到的IVPA图像与原电磁吸收分布图接近程度较高。仿真模型的物理意义清晰,可得到质量稳定的IVPA图像。     

Enhanced resolution for EPR imaging by two-step deblurring

The broad spectrum of spin probes used for electron paramagnetic resonance imaging (EPRI) result in poor spatial resolution of the reconstructed images. Conventional deconvolution procedures can enhance the resolution to some extent but obtaining high resolution EPR images is still a challenge. In this work, we have implemented and analyzed the performance of a postacquisition deblurring technique to enhance the spatial resolution of the EPR images. The technique consists of two steps; noniterative deconvolution followed by iterative deconvolution of the acquired projections which are then projected back using filtered backprojection (FBP) to reconstruct a high resolution image. Further, we have proposed an analogous technique for iterative reconstruction algorithms such as multiplicative simultaneous iterative reconstruction technique (MSIRT) which can be a method of choice for many applications. The performance of the suggested deblurring approach is evaluated using computer simulations and EPRI experiments. Results suggest that the proposed procedure is superior to the standard FBP and standard iterative reconstruction algorithms in terms of mean-square-error (MSE), spatial resolution, and visual judgment. Although the procedure is described for 2D imaging, it can be readily extended to 3D imaging.     

Three-dimensional recognition of occluded objects by using computational integral imaging

We have proposed a method to recognize partially occluded three-dimensional (3D) objects by using 3D volumetric reconstruction integral imaging (II). An II system captures multiple perspectives of occluded objects by using a microlens array. The reconstruction of the occluded 3D scene and target recognition are done digitally to reduce the effects of the occlusion. To verify system performance, we have implemented an optimum filter for object recognition. Both two-dimensional (2D) images and 3D II volumetric reconstructed images are considered. The correlation results of occluded 3D images for volumetric reconstruction show substantial improvements compared with those for conventional 2D imaging of occluded images.     

Cyber surgery: Parameterized mesh for multi-modal surgery simulation

This paper presents a new method for modeling of virtual organs for surgery simulation. The organ models have a parameterized representation that supports real-time interactive deformation. To accomplish real-time interaction with deformable organs, instead of computing the deformation on the 3D organ models in 3D space we use a novel yet simple and fast free-form deformation on the 2D parameterized representation itself. With the parameterized mesh, we also demonstrate that realistic visual and haptic rendering can be provided for interactive surgery simulation.     

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.     

A user-friendly nano-CT image alignment and 3D reconstruction platform based on Lab VIEW

X-ray computed tomography at the nanometer scale(nano-CT) offers a wide range of applications in scientific and industrial areas. Here we describe a reliable,user-friendly,and fast software package based on Lab VIEW that may allow us to perform all procedures after the acquisition of raw projection images in order to obtain the inner structure of the investigated sample. A suitable image alignment process to address misalignment problems among image series due to mechanical manufacturing errors,thermal expansion,and other external factors has been considered,together with a novel fast parallel beam 3D reconstruction procedure that was developed ad hoc to perform the tomographic reconstruction. We have obtained remarkably improved reconstruction results at the Beijing Synchrotron Radiation Facility after the image calibration,the fundamental role of this image alignment procedure was confirmed,which minimizes the unwanted blurs and additional streaking artifacts that are always present in reconstructed slices. Moreover,this nano-CT image alignment and its associated 3D reconstruction procedure are fully based on Lab VIEW routines,significantly reducing the data post-processing cycle,thus making the activity of the users faster and easier during experimental runs.     

基于机器视觉的三维灰度重构技术

基于双目立体视觉三维重构原理,采用主动扫描实现特征匹配的三维灰度重构技术,通过特征结构光扫描物体表面,由经过预标定的两套成像传感器拍摄其图像,经过图像处理程序提取出特征点,完成特征匹配,再计算出物体表面三维轮廓,同时将成像传感器中的灰度信息映射到相应的特征点,从而实现特征点的三维信息和颜色信息的重构和匹配。该技术为三维彩色逼真场景的重构奠定了基础。     

代数迭代重建算法在折射衬度CT中的应用

X射线折射衬度CT是一种基于相位衬度的断层成像技术,特别适合对由轻元素组成的生物、医学样品进行成像,可以观察到常规吸收衬度CT无法观察到的软组织内部微细结构,是一种具有巨大发展潜力的新成像方法.迭代重建算法和解析重建算法是计算机断层成像技术中并行发展的两种算法,虽然已经提出了几种X射线折射衬度CT的解析重建算法,可是还未见X射线折射衬度CT迭代重建算法的报道.研究了代数迭代重建算法在X射线折射衬度CT中的应用,比较分析了不同的投影数据排列方式对于折射衬度CT重建图像的影响,并对实验数据进行了图像重建,获得了满意的CT图像.研究结果表明,在相位衬度CT中,迭代重建算法相对于解析重建算法而言,能减少投影次数,降低曝光剂量,减少对生物样品的辐射损伤,在生物样品成像和投影数据不完整的情况下具有明显的优势. 关键词： 衍射增强成像 代数迭代算法 CT重建 同步辐射     

First-order kernel density estimation of abdomen medical image intensity and spatial information and application to segmentation

Kernel density estimators (KDE) used for many medical image applications only consider the intensity information of each pixel or its neighbors without the ability of expressing the structure and shape of tissues and organs, and they suffer from boundary bias problem. In this paper, we propose a new first-order kernel density estimation (FOKDE) method for 1D intensity information and 2D spatial information of medical image in two steps. First, the FOKDE of intensity information is estimated and applied to medical image segmentation with the multi-thresholding algorithm. Second, we estimate the FOKDE of spatial information on the initial segmentation, which can express the structure and shape of organs and tissues. In order to evaluate the FOKDE and KDE of the 2D spatial information, we apply them to medical image segmentation with the hill-climbing strategy. Density estimation experiments and segmentation application results on the simulated dataset and real abdomen CT images show us that the FOKDE has smaller boundary bias than the KDE, and that it can estimate the structure and shape of tissues and organs with spatial information effectively.     

Orthoscopic integral imaging display by use of the computational method based on lenslet model

In this paper, we propose a computational depth conversion method based on the lenslet model to display the orthoscopic 3D images in 3D integral imaging display. The proposed method permits the synthesis of elemental images for the orthoscopic 3D images at any arbitrary position without any restrictions and requires no additional procedure during the depth conversion process. Due to the lenslet model involved in the depth conversion procedure, the proposed method can broaden the flexibility of 3D image reconstruction in the integral imaging display system. We carry out the preliminary experiments to prove the feasibility of the proposed method. The experimental results reveal that the proposed method is an effective depth conversion method that allows the reconstruction of the orthoscopic 3D images at any arbitrary position.     

Use of Autostitch for automatic stitching of microscope images

Image stitching is the process of combining multiple images to produce a panorama or larger image. In many biomedical studies, including those of cancer and infection, the use of this approach is highly desirable in order to acquire large areas of certain structures or whole sections, while retaining microscopic resolution. In this study, we describe the application of Autostitch, viz. software that is normally used for the generation of panoramas in photography, in the seamless stitching of microscope images. First, we tested this software on image sets manually acquired by normal light microscopy and compared the performance with a manual stitching approach performed with Paint Shop Pro. Secondly, this software was applied to an image stack acquired by an automatic microscope. The stitching results were then compared with that generated by a self-programmed rectangular tiling macro integrated in Image J. Thirdly, this program was applied in the image stitching of images from electron microscopy. Thus, the automatic stitching program described here may find applications in convenient image stitching and virtual microscopy in the biomedical research.     

Segmentation of holographic images using the level set method

Image segmentation, which is to distinguish objects from background, has played an important role in holographic image processing. In this work, we propose a technique that uses the combination of rough segmentation and the level set methods for segmentation of holographic images with zero-order diffraction interference. To improve the image quality, we eliminate the interference of zero-order diffraction in digital holography using Sobel differential gradient algorithm based on digital image processing. After reconstruction, the rough segmentation including intensity transformations and Morphology methods is applied to acquire the rough contour of the reconstruction image. Finally, we adopt level set methods to smooth the object contour and improve its accuracy. Segmentation results for objects in holographic images are presented.     

Improvement of 1D off-axis computer-generated holograms

Creation of Fresnel off-axis computer-generated holograms and improvement of images reconstructed from the holograms are described. To improve the reconstructed images, we have created the holograms with high construct diffraction patterns by using a histogram method. From reconstruction experiments of the holograms, clear images have been obtained and 3D images have been seen directly with eyes.     

基于视场拼接的全视差三维显示系统

提出了一种新的基于视场拼接的全视差三维显示方法及图像生成方案.系统核心部分由一个微投影机阵列、一个反射光路和一个散射屏组构成,图像生成方案采用基于OpenGL的算法实现.为了验证所提出的基于视场拼接理论的正确性,利用液晶显示器、菲涅耳镜组、定向散射屏和背投式反射光路搭建了实验样机.该装置可以在更紧凑的系统结构下显示包括横向视差和纵向视差在内的三维图像,并且通过图像生成算法的配合实现了动态三维显示效果.     

Non-rigid landmark-based large-scale image registration in 3-D reconstruction of mouse and rat kidney nephrons

BackgroundSerial histological sections are suffering from mechanical distortions that disturb the reconstruction of 3-D objects. We have corrected such artifacts with a non-rigid landmark-based method that respects the original geometry in the tissue block. The method is exemplified on a large scale in the registration of semi-thin serial sections of the mouse and rat kidneys, and has been tested on FFPE-sections.AimIn this study of mouse and rat kidneys, we have measured and characterized the deformations introduced in the preparation of 2.5-μm-thick Epon sections and then eliminated them by a landmark-based non-rigid transformation (NRT).MethodsWe obtained 2.5-μm-thick serial Epon sections from three mouse kidneys and three rat kidneys for 3-D reconstruction of the nephron tubules. First, the images from 3000 serial mouse and 13,000 serial rat sections underwent a classic rigid registration (CRR), and the distortions were measured and indexed. The section images underwent a further NRT in order to compensate for the deformations. The NRT used is a classic interactive landmark-based approach. The quality of the NRT was verified by comparing the geometry of the transformed images with corresponding block images.ResultsAfter CRR, the 2.5-μm-thick sections had a linear deformation of up to 2%, the tubular lengths were overestimated with up to 1.5×, and it was most difficult to trace the tubules from section to section. After the additional NRT, the geometry of the images reflected the original geometry in the block, the tubular lengths were no longer overestimated, and the NRT highly facilitated the tracing of the tubular system.ConclusionsNRT has facilitated the tracing of the tubular system in kidneys, a tracing, which would otherwise have been most difficult to perform. NRT has yielded substantial new knowledge to segmental and spatial nephron organization in the mouse and rat kidneys.     

基于Matlab的计算全息图的制作与数字再现的研究

 应用Matlab语言,结合博奇型计算全息的编码方法,利用计算机分别绘制了菲涅耳全息图和傅里叶变换全息图,实现了计算全息图的快速制作,讨论了制作计算全息图的原理、方法和步骤。利用CGH技术和数字全息技术所生成的全息图再现出原始图像,完成了全息图的数字重现,实现了整个全息记录和再现过程的计算机模拟。与传统的编程语言和绘图方法相比较,该算法在实现上更加简单和快捷,并且带有一系列提高计算全息图质量的措施,有效地消除了零级像和孪生像的影响,获得了清晰的数字再现图像。     

Recording of PIV images on photothermoplastic plates

In this paper we explore the possibility of utilizing commercially available photothermoplastic plates as recording support in Particle Image Velocimetry (PIV), to allow real time analysis of recorded data. An experimental apparatus has been developed which allows holographic recording and reconstruction of simulated PIV images. We show that double exposed photothermoplastic plates can successfully be analysed provided that a suitable recording/reconstruction scheme is used.     

Three-dimensional free view reconstruction in axially distributed image sensing

In this Letter, we propose a three-dimensional(3D) free view reconstruction technique in axially distributed image sensing(ADS). In typical integral imaging, free view reconstructed images can be obtained by tilting all elemental images or tilting the reconstruction plane due to large lateral perspectives for 3D objects. In conventional ADS, the reconstructed images at only a front view can be generated since the sensor is moved along with its optical axis so that it has small lateral perspectives for 3D objects. However, the reconstructed 3D images at any viewing point may be obtained because the virtual viewing camera may capture these slightly different perspectives for 3D objects. Therefore, in this Letter, we employ the virtual viewing camera to visualize the 3D images at the arbitrary viewing point. To support our proposed method, we show the experimental results.