共聚焦图像数据的三维重建和显示

本文介绍利用激光扫描共聚焦显微镜获得的共聚焦图像的三维重建和显示方法,并以ＡＣＡＳ Ｕｌｔｉｎａ３１２激光扫描共聚焦显微镜系统为例,分析了ＳＰＦ算法、投影算法和深度阴影算法等共聚焦图像数据的三维重建和图像显示方法的特点。     

Tinkerbell—A Tool for Interactive Segmentation of 3D Data

A software system for interactive manipulation of three-dimensional data has been developed, based on the Open Inventor tool kit. The primary use of this software system is in the segmentation of tomographic reconstructions of subcellular structures. To this end, the reconstruction is represented by volume rendering and displayed in stereo. A three-dimensional cursor with adjustable shape and size is used to define and isolate regions of interest inside the volume, based on the user's expert knowledge. Once isolated, the region of interest can be conveniently analyzed and displayed.     

Device Attitude and Real-Time 3D Visualization: An Interface for Elderly Care

Objectivethis paper presents an innovative graphical user interface to visualize the attitude of a sensing device in a three-dimensional space, serving a wide-range of medical applications.Material and methodsbased on inertial measurement units (IMU) or on magnetic, angular rate and gravity (MARG) sensors, a processing unit provides Euler angles using a sensor fusion technique to display the orientation of the device relative to the Earth frame in real-time. The device is schematized by linking six polygonal regions, and is subject to sequential rotations by updating the graph each 350 ms. We conduct comparative studies between the two sensing devices, i.e. IMUs and MARGs, as well as two orientation filters, namely Madgwick's algorithm and Mahony's algorithm.Resultsthe accuracy of the system is reported as a function of (i) the sampling frequency, (ii) the sensing unit, and (iii) the orientation filter, following two elderly care applications, namely fall risk assessment and body posture monitoring. The experiments are conducted using public datasets. The corresponding results show that Madgwick's algorithm is best suited for low sampling rates, whereas MARG sensors are best suited for the detection of postural transitions.Conclusionthis paper addresses the different aspects and discusses the limitations of attitude estimation systems, which are important tools to help clinicians in their diagnosis.     

MetaSee: An Interactive and Extendable Visualization Toolbox for Metagenomic Sample Analysis and Comparison

The NGS (next generation sequencing)-based metagenomic data analysis is becoming the mainstream for the study of microbial communities. Faced with a large amount of data in metagenomic research, effective data visualization is important for scientists to effectively explore, interpret and manipulate such rich information. The visualization of the metagenomic data, especially multi-sample data, is one of the most critical challenges. The different data sample sources, sequencing approaches and heterogeneous data formats make robust and seamless data visualization difficult. Moreover, researchers have different focuses on metagenomic studies: taxonomical or functional, sample-centric or genome-centric, single sample or multiple samples, etc. However, current efforts in metagenomic data visualization cannot fulfill all of these needs, and it is extremely hard to organize all of these visualization effects in a systematic manner. An extendable, interactive visualization tool would be the method of choice to fulfill all of these visualization needs. In this paper, we have present MetaSee, an extendable toolbox that facilitates the interactive visualization of metagenomic samples of interests. The main components of MetaSee include: (I) a core visualization engine that is composed of different views for comparison of multiple samples: Global view, Phylogenetic view, Sample view and Taxa view, as well as link-out for more in-depth analysis; (II) front-end user interface with real metagenomic models that connect to the above core visualization engine and (III) open-source portal for the development of plug-ins for MetaSee. This integrative visualization tool not only provides the visualization effects, but also enables researchers to perform in-depth analysis of the metagenomic samples of interests. Moreover, its open-source portal allows for the design of plug-ins for MetaSee, which would facilitate the development of any additional visualization effects.     

Visualization and analysis of 3D microscopic images

In a wide range of biological studies, it is highly desirable to visualize and analyze three-dimensional (3D) microscopic images. In this primer, we first introduce several major methods for visualizing typical 3D images and related multi-scale, multi-time-point, multi-color data sets. Then, we discuss three key categories of image analysis tasks, namely segmentation, registration, and annotation. We demonstrate how to pipeline these visualization and analysis modules using examples of profiling the single-cell gene-expression of C. elegans and constructing a map of stereotyped neurite tracts in a fruit fly brain.     

i2dash: Creation of Flexible,Interactive, and Web-based Dashboards for Visualization of Omics Data

Data visualization and interactive data exploration are important aspects of illustrating complex concepts and results from analyses of omics data. A suitable visualization has to be intuitive and accessible. Web-based dashboards have become popular tools for the arrangement, consolidation, and display of such visualizations. However, the combination of automated data processing pipelines handling omics data and dynamically generated, interactive dashboards is poorly solved. Here, we present i2dash, an R package intended to encapsulate functionality for the programmatic creation of customized dashboards. It supports interactive and responsive (linked) visualizations across a set of predefined graphical layouts. i2dash addresses the needs of data analysts/software developers for a tool that is compatible and attachable to any R-based analysis pipeline, thereby fostering the separation of data visualization on one hand and data analysis tasks on the other hand. In addition, the generic design of i2dash enables the development of modular extensions for specific needs. As a proof of principle, we provide an extension of i2dash optimized for single-cell RNA sequencing analysis, supporting the creation of dashboards for the visualization needs of such experiments. Equipped with these features, i2dash is suitable for extensive use in large-scale sequencing/bioinformatics facilities. Along this line, we provide i2dash as a containerized solution, enabling a straightforward large-scale deployment and sharing of dashboards using cloud services. i2dash is freely available via the R package archive CRAN (https://CRAN.R-project.org/package=i2dash).     

多反应变量重复测量的混合效应模型及其应用

本文给出了多反应变量重复测量的协方差矩阵结构,探讨了用迭代广义最小二乘法来求解其带协变量和不带协变量的混合效应模型中固定效应和随机效应系数,并对１９９１年四川省高血压调查资料进行实例分析,得到其结论符合实际情况．     

GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data

Interactions between chromatin segments play a large role in functional genomic assays and developments in genomic interaction detection methods have shown interacting topological domains within the genome. Among these methods, Hi-C plays a key role. Here, we present the Genome Interaction Tools and Resources (GITAR), a software to perform a comprehensive Hi-C data analysis, including data preprocessing, normalization, and visualization, as well as analysis of topologically-associated domains (TADs). GITAR is composed of two main modules: (1) HiCtool, a Python library to process and visualize Hi-C data, including TAD analysis; and (2) processed data library, a large collection of human and mouse datasets processed using HiCtool. HiCtool leads the user step-by-step through a pipeline, which goes from the raw Hi-C data to the computation, visualization, and optimized storage of intra-chromosomal contact matrices and TAD coordinates. A large collection of standardized processed data allows the users to compare different datasets in a consistent way, while saving time to obtain data for visualization or additional analyses. More importantly, GITAR enables users without any programming or bioinformatic expertise to work with Hi-C data. GITAR is publicly available at http://genomegitar.org as an open-source software.     

Preparation and 3D Tracking of Catalytic Swimming Devices

We report a method to prepare catalytically active Janus colloids that "swim" in fluids and describe how to determine their 3D motion using fluorescence microscopy. One commonly deployed method for catalytically active colloids to produce enhanced motion is via an asymmetrical distribution of catalyst. Here this is achieved by spin coating a dispersed layer of fluorescent polymeric colloids onto a flat planar substrate, and then using directional platinum vapor deposition to half coat the exposed colloid surface, making a two faced "Janus" structure. The Janus colloids are then re-suspended from the planar substrate into an aqueous solution containing hydrogen peroxide. Hydrogen peroxide serves as a fuel for the platinum catalyst, which is decomposed into water and oxygen, but only on one side of the colloid. The asymmetry results in gradients that produce enhanced motion, or "swimming". A fluorescence microscope, together with a video camera is used to record the motion of individual colloids. The center of the fluorescent emission is found using image analysis to provide an x and y coordinate for each frame of the video. While keeping the microscope focal position fixed, the fluorescence emission from the colloid produces a characteristic concentric ring pattern which is subject to image analysis to determine the particles relative z position. In this way 3D trajectories for the swimming colloid are obtained, allowing swimming velocity to be accurately measured, and physical phenomena such as gravitaxis, which may bias the colloids motion to be detected.     

Application and Evaluation of Interactive 3D PDF for Presenting and Sharing Planning Results for Liver Surgery in Clinical Routine

MethodsWe developed an interactive 3D PDF report document format and implemented a software tool to create these reports automatically. After more than 1000 liver CASP cases that have been reported in clinical routine using our 3D PDF report, an international user survey was carried out online to evaluate the user experience.ResultsOur solution enables the user to interactively explore the anatomical configuration and to have different analyses and various resection proposals displayed within a 3D PDF document covering only a single page that acts more like a software application than like a typical PDF file (“PDF App”). The new 3D PDF report offers many advantages over the previous solutions. According to the results of the online survey, the users have assessed the pragmatic quality (functionality, usability, perspicuity, efficiency) as well as the hedonic quality (attractiveness, novelty) very positively.ConclusionThe usage of 3D PDF for reporting and sharing CASP results is feasible and well accepted by the target audience. Using interactive PDF with embedded 3D models is an enabler for presenting and exchanging complex medical information in an easy and platform-independent way. Medical staff as well as patients can benefit from the possibilities provided by 3D PDF. Our results open the door for a wider use of this new technology, since the basic idea can and should be applied for many medical disciplines and use cases.     

Correlation of Atmospheric Spore Frequencies with Meteorological Data

Correlation and regression analyses have found wide application, even in aerobiology. Their application is, however, closely related to the purpose of the study: (a) to find which has caused the present phenomenon, (b) to find which will be the consequences, or (c) to make predictions—for instance for pollen and spore forecasts. In (a ), it is useless to study simple or even multiple correlations alone. For example, the presence of allergenic alder pollen in the air in May, 1977, was the result of numerous developmental stages, either dependent or independent of each other; and yet many correlation studies neglect that there is a complete life cycle. It is conceivable that a positive correlation exists between the alder pollen count and an increase in temperature, but it cannot be asserted that the increase in temperature is the cause of the pollen peak, since many other factors are involved. (c) If the aim is to predict, it is not necessary to know anything about the causal relationships. We may calculate all sorts of multiregression equations, and these may be of a great value in making estimates; but they do not necessarily indicate true biological dependence or true causal relationships. The use of regression analysis—and the perhaps very significant regression coefficients—certainly to not necessarily explain anything about the cause.     

ArrayOU: A Web Application for Microarray Data Analysis and Visualization

A web-based microarray data analysis tool, ArrayOU (freely available at www.bioinformatics.plantbio.ohiou.edu.), has been developed at the Ohio University Genomics Facility for the research and education community to analyze Agilent microarray data. Agilent''s microarray pipeline has gained in popularity as a result of its ease of use and low cost of customized arrays. The current version of the ArrayOU pipeline allows users to visualize, analyze, and annotate microarray data from commercially available and customized Agilent expression arrays and is extendable for further implementations.     

基于VTK的医学图像三维可视化系统

医学图像的三维可视化可以通过可视化工具包（VTK）提供的API实现。VTK是医学图像可视化的开法工具包,它把可视化的算法封装起来,利用简单的代码生成所需图形。基于VTK的医学图像三维可视化系统阐述了如何借助VTKAPI读入二维医学图像序列、操作二维图像、重建三维图像以及进行三维图像可视化的全套方案,为临床医生的诊断、治疗提供了有益的途径。     

iMAR: An Interactive Web-Based Application for Mapping Herbicide Resistant Weeds

Herbicides are the major weed control tool in most cropping systems worldwide. However, the high reliance on herbicides has led to environmental issues as well as to the evolution of herbicide-resistant biotypes. Resistance is a major concern in modern agriculture and early detection of resistant biotypes is therefore crucial for its management and prevention. In this context, a timely update of resistance biotypes distribution is fundamental to devise and implement efficient resistance management strategies. Here we present an innovative web-based application called iMAR (interactive MApping of Resistance) for the mapping of herbicide resistant biotypes. It is based on open source software tools and translates into maps the data reported in the GIRE (Italian herbicide resistance working group) database of herbicide resistance at national level. iMAR allows an automatic, easy and cost-effective updating of the maps a nd provides two different systems, “static” and “dynamic”. In the first one, the user choices are guided by a hierarchical tree menu, whereas the latter is more flexible and includes a multiple choice criteria (type of resistance, weed species, region, cropping systems) that permits customized maps to be created. The generated information can be useful to various stakeholders who are involved in weed resistance management: farmers, advisors, national and local decision makers as well as the agrochemical industry. iMAR is freely available, and the system has the potential to handle large datasets and to be used for other purposes with geographical implications, such as the mapping of invasive plants or pests.     

RGB Plots as a Tool for the Simultaneous Visualization of Multiple Data Layers in a Two Dimensional Space

Visualization of multidimensional data helps in understanding complex systems and environments. We present here a red, green, blue (RGB) visualization method that can serve to display environmental properties. The saturation of each color is used to represent the concentration of a given property. The implementation of that figure is illustrated through visualization of three dissolved inorganic nutrient concentrations along a vertical transect of the Mediterranean, as well as through a vertical time series of three phytoplankton group cell numbers. The RGB figures show well known properties of the water column. In addition, they reveal some lesser-known properties, such as regions in shallow water in which the ratio of phosphorus and silica to nitrogen is high, and a deep eukariotic phytoplankton community. Visualization of such data is usually performed with three separate contour or surface plots, and occasionally two properties are presented as an overlay in a single figure. The RGB figure offers a better way to visualize the interactions among the three separate plots than is commonly available.     

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

Background

The analysis of microbial communities through DNA sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data.

Results

Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research.

Conclusions

The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor.