Interactive 3D visualization and post-processing analysis of vertex-based unstructured polyhedral meshes with ParaView

The development of physics-based 3D models that investigate the behavior of biological tissues requires effective and efficient visualization tools. The open-source software ParaView has such capabilities, but often impose a steep learning curve due to the use of the Visualization Toolkit (VTK) data structures. To overcome this, I show how to setup the components of 3D vertex-like models, i.e., vertices, faces, and polyhedra, into the VTK data format and then output as ParaView unstructured grid files. I present a few relevant tools to visualize and analyze the files in ParaView. All sample codes are available in the Github repository vis3Dvertex.

Robotic Obstacle Avoidance: A Virtual Modeling And Reinforcement Learning

This study developed a robotic arm self-learning system based on virtual modeling and reinforcement learning. Using the model of a robotic arm, information concerning obstacles in the environment, initial coordinates of the robotic arm, and the target position, this system automatically generated a set of rotational angles to enable a robotic arm to be positioned such that it can avoid all obstacles and reach a target. The developed program was divided into three parts. The first part involves robotic arm simulation and collision detection; specifically, images of a six-axis robotic arm and obstacles were input to the Visualization ToolKit library to visualize the movements and surrounding environment of the robotic arm. Subsequently, an oriented bounding box algorithm was used to determine whether collisions had occurred. The second part concerned machine-learning–based route planning. The TensorFlow was used to establish a deep deterministic policy gradient model, and reinforcement learning was employed for the response to environmental variables. Different reward functions were designed for tests and discussions, and the program’s practicality was verified through actual machine operations. Finally, the application of reinforcement learning in route planning for a robotic arm was proved feasible by the experiment. Such an application facilitated automatic route planning and achieved an error of less than 10 mm from the target position.

Visual representation of CORDEX climate data by using QGIS

<p>The majority of studies are dedicated to the analysis of climate change and climate models with no regard for data visualization part. Therefore, this research is aimed at highlighting challenges, with an emphasis on spatial referencing that can occur while visualizing CORDEX data. CORDEX data are stored in NetCDF file format, and sometimes georeferencing may be misconceived in QGIS software. For this reason, two techniques of georeferencing data are examined in this work. The first way of data georeferencing is re-projecting coordinates from original projection to an interpolated latitude/longitude grid. The second way is re-encrypting initial data file so that QGIS is able to interpret projection information. Preference of using QGIS explained by two reasons: it is open source GIS application and it has expanded visualization toolkit.</p><p>In addition, there are a great deal of climate models based on CORDEX data for some regions whereas there is a lack of climate projections for particular areas. In this regard, carrying out analysis for the region of Kazakhstan is beneficial. Outcomes of this research may stimulate spreading local climate models for Kazakhstan territory. Results are represented in the form of maps of Kazakhstan illustrating temperature change over 21<sup>st</sup> century time period.</p>

Using Gaming Technology to Explore and Visualize Management Impacts on Marine Ecosystems

We have developed an approach that connects a complex and widely used scientific ecosystem modeling approach with a game engine for real-time communication and visualization of scientific results. The approach, OceanViz, focuses on communicating scientific data to non-scientific audiences to foster dialogue, offering experimental, immersive approaches to visualizing complex ecosystems whilst avoiding information overload. Within the context of ecosystem-based fisheries management, OceanViz can engage decision makers into the implicit operation of scientific software as an aid during the decision process, and it can be of direct use for public communication through appealing and informative visualizations. Beside a server-client architecture to centralize decision making around an ecosystem model, OceanViz includes an extensive visualization toolkit capable of accurately reflecting marine ecosystem changes through a simulated three-dimensional (3D) underwater environment. Here we outline the ideas and concepts that went into OceanViz, its implementation and its related challenges. We reflect on challenges to scientific visualization and communication as food-for-thought for the marine ecosystem modeling community and beyond.

dittoSeq: universal user-friendly single-cell and bulk RNA sequencing visualization toolkit

Summary A visualization suite for major forms of bulk and single-cell RNAseq data in R. dittoSeq is color blindness-friendly by default, robustly documented to power ease-of-use and allows highly customizable generation of both daily-use and publication-quality figures. Availability and implementation dittoSeq is an R package available through Bioconductor via an open source MIT license. Supplementary information Supplementary data are available at Bioinformatics online.

Optimization of Breast Tomosynthesis Visualization through 3D Volume Rendering

3D volume rendering may represent a complementary option in the visualization of Digital Breast Tomosynthesis (DBT) examinations by providing an understanding of the underlying data at once. Rendering parameters directly influence the quality of rendered images. The purpose of this work is to study the influence of two of these parameters (voxel dimension in z direction and sampling distance) on DBT rendered data. Both parameters were studied with a real phantom and one clinical DBT data set. The voxel size was changed from 0.085 × 0.085 × 1.0 mm3 to 0.085 × 0.085 × 0.085 mm3 using ten interpolation functions available in the Visualization Toolkit library (VTK) and several sampling distance values were evaluated. The results were investigated at 90º using volume rendering visualization with composite technique. For phantom quantitative analysis, degree of smoothness, contrast-to-noise ratio, and full width at half maximum of a Gaussian curve fitted to the profile of one disk were used. Additionally, the time required for each visualization was also recorded. Hamming interpolation function presented the best compromise in image quality. The sampling distance values that showed a better balance between time and image quality were 0.025 mm and 0.05 mm. With the appropriate rendering parameters, a significant improvement in rendered images was achieved.

Offline programming method and implementation of industrial robot grinding based on VTK

Purpose The purpose of this paper is to present a robotic off-line programming method for freeform surface grinding based on visualization toolkit (VTK). Nowadays, manual grinding and traditional robot on-line programming are difficult to ensure the surface grinding accuracy, thus off-line programming is gradually used in grinding, however, several problems are needed to be resolved which include: off-programming environment depends on the third-party CAD software, leads to insufficient self-development flexibility; single support for robot type or workpiece model format contributes to lack of versatility; grinding point data depends on external data calculation and import process, causes human-computer interaction deterioration. Design/methodology/approach In this method, the visualization pipeline and observer/command mode of VTK are used to display the 3D model of the robot grinding system and pick up the workpiece surfaces to be grinded respectively. Two groups of cutter planes with equidistant spacing are created to form the grinding nodes on the surface, and the extraction method for the position and posture of the nodes is proposed. Furthermore, the position and posture of discretized points along the grinding curve are obtained by B-spline curve interpolation and quaternion spherical linear interpolation respectively. Finally, the motion simulation is realized by robot inverse kinematics. Findings Through a watch case grinding experiment, the results show that the proposed method based on VTK can achieving high precision grinding effect, which is obviously better than traditional method. Originality/value The proposed method is universal which does not depend on the specific forms of surface, and all calculations in simulation are completed within the system, avoiding tedious external data calculation and import process. The grinding trajectory can be generated only by the mouse picking operation without relying on the other third-party CAD software.