江豚耳蜗切片的计算机三维重建

在自己组装的微型机图象系统上,实现了对生物组织连续切片的三维重建。重建结果以灰度阴影方式在彩色显示器上显示,并可在打印机上以多灰度等级方式打印输出。结合一例江豚内耳的连续切片,对其耳蜗骨迷路部份进行了三维重建。并将重建结果以动态形式在显示器上转动,以便观察其各个侧面的情况。     

Computerized method for analyzing maximum and partial expiratory flow-volume curves.

Computerized instrumentation and software have been developed to obtain maximum expiratory flow-volume (MEFV) and partial expiratory flow-volume (PEFV) curves. The computerized system calculates and prints out the flow at 25% and 40% of control vital capacity (VC), the expiratory volume, peak expiratory flow rate and expiratory volume at one second (FEV1) divided by VC, the latter expressed as a percent. The flow-volume curves can be displayed on an oscilloscope or plotter and stored on magnetic tape. A pilot study was completed to demonstrate the reliability and validity of the data obtained.     

Three-dimensional visualization of low-field MRI data using personal computer

An experience of three-dimensional reconstruction of low-field MRI data using a modern personal computer and Windows software is presented. A value of volume visualization in routine diagnostics and areas of its effective use are shown. Pulse sequences best suitable for volume reconstruction are selected. Performance of high-end PC in visualization of medical data is evaluated.     

Time-accurate,parallel, multi-zone,multi-block solver to study the human cardio-vascular system

A parallel, time-accurate flow solver is devised to study the human cardio-vascular system. The solver is capable of dealing with moving boundaries and moving grids. It is designed to handle complex, three-dimensional vascular systems. The computational domain is divided into multiple block subdomains. At each cross section the plane is divided into twelve sub-zones to allow flexibility for handling complex geometries and, if needed, appropriate parallel data partitioning. The unsteady, three-dimensional, incompressible Navier-Stokes equations are solved numerically. A second-order in time and third-order upwind finite volume method for solving time-accurate incompressible flows based on pseudo-compressibility and dual time-stepping technique is used. For parallel execution, the flow domain is partitioned. Communication between the subdomains of the flow on Riken's VPP/700E supercomputer is implemented using MPI message-passing library. A series of numerical simulations of biologically relevant flows is used to validate this code.     

High-throughput three-dimensional protein structure determination

In the wake of finished genomic sequencing projects, high-throughput analysis techniques are being developed in various fields of functional genomics. Of special interest in this regard is the three-dimensional structure analysis of proteins by X-ray crystallography and NMR spectroscopy, which has been characterized by distinctly low-throughput in the past. A number of recent advances in instrumentation and software are promising to radically change this situation, leaving the production of suitable protein samples as the sole rate-limiting step in structural analyses.     

Quality assurance procedure for a gamma guided stereotactic breast biopsy system

A quality assurance procedure has been developed for a prototype gamma-ray guided stereotactic biopsy system. The system consists of a compact small-field-of-view gamma-ray camera mounted to the rotational arm of a Lorad stereotactic biopsy system. The small-field-of-view gamma-ray camera has been developed for clinical applications where mammographic X-ray localization is not possible. Marker sources that can be imaged with the gamma-camera have been designed and built for quality assurance testing and to provide a fiducial reference mark. An algorithm for determining the three dimensional location of a region of interest, such as a lesion, relative to the fiducial mark has been implemented into the software control of the camera. This system can be used to determine the three-dimensional location of a region of interest from a stereo pair of images and that information can be used to guide a biopsy needle to that site. Point source phantom tests performed with the system have demonstrated that the camera can be used to localize a point of interest to within 1 mm, which is satisfactory for its use in needle localization.     

Efficient identification of critical residues based only on protein structure by network analysis

Despite the increasing number of published protein structures, and the fact that each protein's function relies on its three-dimensional structure, there is limited access to automatic programs used for the identification of critical residues from the protein structure, compared with those based on protein sequence. Here we present a new algorithm based on network analysis applied exclusively on protein structures to identify critical residues. Our results show that this method identifies critical residues for protein function with high reliability and improves automatic sequence-based approaches and previous network-based approaches. The reliability of the method depends on the conformational diversity screened for the protein of interest. We have designed a web site to give access to this software at http://bis.ifc.unam.mx/jamming/. In summary, a new method is presented that relates critical residues for protein function with the most traversed residues in networks derived from protein structures. A unique feature of the method is the inclusion of the conformational diversity of proteins in the prediction, thus reproducing a basic feature of the structure/function relationship of proteins.     

Protein-protein interaction between Bacillus stearothermophilus tyrosyl-tRNA synthetase subdomains revealed by a bacterial two-hybrid system

We have recently developed a bacterial two-hybrid system (BACTH), based on functional complementation between two fragments of the catalytic domain of Bordetella pertussis adenylate cyclase (AC), that allows an easy in vivo screening and selection of functional interactions between two proteins in Escherichia coli. In this work, we have further explored the potentialities of the BACTH system to study protein-protein interactions, using as a model, the interactions between various subdomains of the dimeric tyrosyl-tRNA synthetase (TyrRS) of Bacillus stearothermophilus. Using the BACTH system we confirmed the known interactions of the alpha/beta domains and those between the alpha/beta domain and the alpha domain that could be anticipated from the three-dimensional structure of TyrRS. Interestingly, the BACTH system revealed the unexpected interaction between the TyrRS alpha domains which is presumably mediated by a pseudo-leucine zipper motif. This study illustrates the interest of the bacterial two-hybrid system to delineate interacting domains of proteins and shows that it can reveal interactions that occur in vivo and that were not anticipated from the three-dimensional structure of the protein of interest.     

Micropilot: automation of fluorescence microscopy-based imaging for systems biology

Quantitative microscopy relies on imaging of large cell numbers but is often hampered by time-consuming manual selection of specific cells. The 'Micropilot' software automatically detects cells of interest and launches complex imaging experiments including three-dimensional multicolor time-lapse or fluorescence recovery after photobleaching in live cells. In three independent experimental setups this allowed us to statistically analyze biological processes in detail and is thus a powerful tool for systems biology.     

4D imaging to assay complex dynamics in live specimens

A full understanding of cellular dynamics is often difficult to obtain from time-lapse microscopy of single optical sections. New microscopes and image-processing software are now making it possible to rapidly record three-dimensional images over time. This four-dimensional imaging allows precise quantitative analysis and enhances visual exploration of data by allowing cellular structures to be interactively displayed from many angles. It has become a key tool for understanding the complex organization of biological processes in live specimens.     

Efficiently measuring complex sessile epibenthic organisms using a novel photogrammetric technique

This paper describes a stereo photogrammetry method that allows accurate measurements of volume for sessile epibenthic organisms. It represents a novel approach based on multiple views (five stereo image pairs) from a purpose built stereo digital still camera system combined with a three-dimensional reconstruction software program (CAM). The bias, accuracy, precision and efficiency of the method were assessed in the laboratory using models with three levels of morphological complexity (simple, moderate and complex morphologies) and two sizes (large and small). The technique did not show any biases to observer experience, with no significant difference among observers (p > 0.05). Volume measurements made with CAM were very accurate when compared with the water displacement volume of each model, with an overall mean error of about − 3% (S.E. ± 1%). The CAM volume measurements were more accurate on complex models and moderately complex models than on models with simple morphologies. Also, large models had a higher accuracy than small models. Volume measurements made with CAM were also highly precise with the lowest precision observed being ± 2% of the volume estimate. The time required for a volume estimation using the CAM method was also highly efficient, and the longest time taken for a volume estimation was on average 1 h and 36 min, making it the fastest reported three-dimensional reconstruction method. In field applications, volume estimations of four sponges were all within the observed accuracy, precision and efficiency established during laboratory trials. The accuracy, precision and efficiency demonstrated by the CAM method make this technique highly suitable for routine measurements of the volume of sessile epibenthic organisms.     

Advanced 3D-Sonographic Imaging as a Precise Technique to Evaluate Tumor Volume

Determination of tumor volume in subcutaneously inoculated xenograft models is a standard procedure for clinical and preclinical evaluation of tumor response to treatment. Practitioners frequently use a hands-on caliper method in conjunction with a simplified formula to assess tumor volume. Non-invasive and more precise techniques as investigation by MR or (μ)CT exist but come with various adverse effects in terms of radiation, complex setup or elevated cost of investigations. Therefore, we propose an advanced three-dimensional sonographic imaging technique to determine small tumor volumes in xenografts with high precision and minimized observer variability. We present a study on xenograft carcinoma tumors from which volumes and shapes were calculated with the standard caliper method as well as with a clinically available three-dimensional ultrasound scanner and subsequent processing software. Statistical analysis reveals the suitability of this non-invasive approach for the purpose of a quick and precise calculation of tumor volume in small rodents.     

Limitations on cell volume determination using three-dimensional optical microscopy

One important application for three-dimensional microscopy is the determination of the volumes of biological cells. In this paper we investigate the application of three-dimensional deconvolution techniques to the problem of cell volume determination. The theoretical discussion is based on a Fourier sampling condition for reliable image reconstruction and it is shown, using this condition and simulated images, that the cell volume determination is reliable only for cells with a shape and orientation such that their length along the optic axis is much greater than their width.     

Morphogenesis and oncogenesis of MCF-10A mammary epithelial acini grown in three-dimensional basement membrane cultures

The three-dimensional culture of MCF-10A mammary epithelial cells on a reconstituted basement membrane results in formation of polarized, growth-arrested acini-like spheroids that recapitulate several aspects of glandular architecture in vivo. Oncogenes introduced into MCF-10A cells disrupt this morphogenetic process, and elicit distinct morphological phenotypes. Recent studies analyzing the mechanistic basis for phenotypic heterogeneity observed among different oncogenes (e.g., ErbB2, cyclin D1) have illustrated the utility of this three-dimensional culture system in modeling the biological activities of cancer genes, particularly with regard to their ability to disrupt epithelial architecture during the early aspects of carcinoma formation. Here we provide a collection of protocols to culture MCF-10A cells, to establish stable pools expressing a gene of interest via retroviral infection, as well as to grow and analyze MCF-10A cells in three-dimensional basement membrane culture.     

Dosimetry with radiosensitive gels in radiotherapy. Methods

The goal of conformal radiotherapy is to concentrate the dose in a well-defined volume by avoiding the neighbouring healthy structures. This technique requires powerful treatment planning software and a rigorous control of estimated dosimetry. The usual dosimetric tools are not adapted to visualize and validate complex 3D treatment. Dosimetry by radiosensitive gel permits visualization and measurement of the three-dimensional dose distribution. The objective of this work is to report on current work in this field and, based on our results and our experience, to draw prospects for an optimal use of this technique. Further developments will relate to the realization of new radiosensitive gels satisfying, as well as possible, cost requirements, easy realization and use, magnetic resonance imagery (MRI) sensitivity, tissue equivalence, and stability. Other developments focus on scanning methods, especially in MRI to measure T1 and T2.     

髋关节假体脱位分析软件的设计与开发

目的研发了髋关节假体脱位分析软件。软件基于ADAMS/VIEW软件进行二次开发,能够可视化的构建三维参数化的髋关节假体模型,模型能够模拟假体的六种运动。应用此软件可以为病人更好的选择和植入假体,评估各种髋关节假体的安全活动范围,用来设计新的关节假体。     

An accurate and effective FMM-based approach for freehand 3D ultrasound reconstruction

Freehand three-dimensional ultrasound imaging is a highly attractive research area because it is capable of volumetric visualization and analysis of tissues and organs. The reconstruction algorithm plays a key role to the construction of three-dimensional ultrasound volume data with higher image quality and faster reconstruction speed. However, a systematic approach to such problem is still missing. A new fast marching method (FMM) for three-dimensional ultrasound volume reconstruction using the tracked and hand-held probe is proposed in this paper. Our reconstruction approach consists of two stages: bin-filling stage and hole-filling stage. Each pixel in the B-scan images is traversed and its intensity value is assigned to its nearest voxel in the bin-filling stage. For the efficient and accurate reconstruction, we present a new hole-filling algorithm based on the fast marching method. Our algorithm advances the interpolation boundary along its normal direction and fills the area closest to known voxel points in first, which ensure that the structural details of image can be preserved. Experimental results on both ultrasonic abdominal phantom and in vivo urinary bladder of human subject and comparisons with some popular algorithms are used to demonstrate its improvement in both reconstruction accuracy and efficiency.     

MR 脑图像海马自动分割法在AD 早期诊断中的应用研究

目的:研究磁共振(Magnetic resonance,MR)脑图像中海马的自动分割方法及海马的形态学分析方法,为阿尔茨海默病(Alzheimer’s disease,AD)的早期诊断提供依据。方法:对20例AD患者和60名正常对照者行MRI T1 WI 3D容积扫描,建立海马的三维主动表观模型,并以此模型对每个个体脑部磁共振图像上的海马进行自动识别和三维分割,分别建立正常对照组和AD组的海马统计形状模型,比较AD组与正常对照组间海马形状的差异性。结果:海马三维分割方法与手动分割方法在海马体积测量上无统计学差别(P>0.05);AD患者海马头部发生萎缩(P<0.05)。结论:基于主动表观模型的MR脑图像海马自动识别和三维分割法是准确可靠的;海马头部萎缩可作为AD诊断的依据之一。     

Optical sectioning microscopy with planar or structured illumination

A key requirement for performing three-dimensional (3D) imaging using optical microscopes is that they be capable of optical sectioning by distinguishing in-focus signal from out-of-focus background. Common techniques for fluorescence optical sectioning are confocal laser scanning microscopy and two-photon microscopy. But there is increasing interest in alternative optical sectioning techniques, particularly for applications involving high speeds, large fields of view or long-term imaging. In this Review, I examine two such techniques, based on planar illumination or structured illumination. The goal is to describe the advantages and disadvantages of these techniques.     

UCSF tomography: an integrated software suite for real-time electron microscopic tomographic data collection, alignment, and reconstruction

A real-time alignment and reconstruction scheme for electron microscopic tomography (EMT) has been developed and integrated within our UCSF tomography data collection software. This newly integrated software suite provides full automation from data collection to real-time reconstruction by which the three-dimensional (3D) reconstructed volume is immediately made available at the end of each data collection. Real-time reconstruction is achieved by calculating a weighted back-projection on a small Linux cluster (five dual-processor compute nodes) concurrently with the UCSF tomography data collection running on the microscope's computer, and using the fiducial-marker free alignment data generated during the data collection process. The real-time reconstructed 3D volume provides users with immediate feedback to fully asses all aspects of the experiment ranging from sample choice, ice thickness, experimental parameters to the quality of specimen preparation. This information can be used to guide subsequent data collections. Access to the reconstruction is especially useful in low-dose cryo EMT where such information is very difficult to obtain due to extraordinary low signal to noise ratio in each 2D image. In our environment, we generally collect 2048 x 2048 pixel images which are subsequently computationally binned four-fold for the on-line reconstruction. Based upon experiments performed with thick and cryo specimens at various CCD magnifications (50000x-80000x), alignment accuracy is sufficient to support this reduced resolution but should be refined before calculating a full resolution reconstruction. The reduced resolution has proven to be quite adequate to assess sample quality, or to screen for the best data set for full-resolution reconstruction, significantly improving both productivity and efficiency of system resources. The total time from start of data collection to a final reconstructed volume (512 x 512 x 256 pixels) is about 50 min for a +/-70 degrees 2k x 2k pixel tilt series acquired at every 1 degrees.