Visualization
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Bio 219 Biomedical Imaging and Scientific Visualization
Bio 219 Biomedical Imaging and Scientific Visualization Ch. Zollikofer M. Ponce de León Organization • OLAT: – course scripts (pdf) • website: www.aim.uzh.ch/morpho/wiki/Teaching/SciVis – course scripts (pdf); passwd: scivisdocs – link collection (tutorials, applets, software/data downloads, ...) • book (background information): Zollikofer & Ponce de León, Virtual Reconstruction. A Primer in Computer-assisted Paleontology and Biomedicine (NY: Wiley, 2005) CHF 55 • final exam – Monday, 26. May 2014, 1015-1100 BioMedImg & SciVis • at the intersection between – theory/practice of image data acquisition – computer graphics – medical diagnostics – computer-assisted paleoanthropology Grotte Chauvet, France Biomedical Imaging • acquisition • processing • analysis • visualization ... of biomedical data Scientific Visualization visual... • representation (cf. data presentation) • exploration • analysis ...of scientific data aims of this course • provide theoretical (and practical) foundations of – image data acquisition, storage, retrieval – image data processing and analysis – image data visualization/rendering • establish links between – real-life vision and computer vision – computer science and biomedical sciences – theory and practice of handling biomedical data contents • real-life vision • computers and data representation • 2D image data acquisition • 3D image data acquisition • biomedical image processing in 2D and 3D • biomedical image data visualization and interaction biomedical data types of data data flow humans and computers facts and data • facts exist by definition (±independent of the observer): – females and males – humans and Neanderthals – dogs and wolves • data are generated through observation: – number of living human species: 1 – proportion of females to males at birth: 49/51 – nr. of wolves per square km biomedical data: general • physical/physiological data about the human body: – density – temperature – pressure – mass – chemical composition biomedical data: space and time • spatial – 1D – 2D – 3D • temporal • spatiotemporal (4D) .. -
ARTG-2306-CRN-11966-Graphic Design I Computer Graphics
Course Information Graphic Design 1: Computer Graphics ARTG 2306, CRN 11966, Section 001 FALL 2019 Class Hours: 1:30 pm - 4:20 pm, MW, Room LART 411 Instructor Contact Information Instructor: Nabil Gonzalez E-mail: [email protected] Office: Office Hours: Instructor Information Nabil Gonzalez is your instructor for this course. She holds an Associate of Arts degree from El Paso Community College, a double BFA degree in Graphic Design and Printmaking from the University of Texas at El Paso and an MFA degree in Printmaking from the Rhode Island School of Design. As a studio artist, Nabil’s work has been focused on social and political views affecting the borderland as well as the exploration of identity, repetition and erasure. Her work has been shown throughout the United State, Mexico, Colombia and China. Her artist books and prints are included in museum collections in the United States. Course Description Graphic Design 1: Computer Graphics is an introduction to graphics, illustration, and page layout software on Macintosh computers. Students scan, generate, import, process, and combine images and text in black and white and in color. Industry standard desktop publishing software and imaging programs are used. The essential applications taught in this course are: Adobe Illustrator, Adobe Photoshop and Adobe InDesign. Course Prerequisite Information Course prerequisites include ARTF 1301, ARTF 1302, and ARTF 1304 each with a grade of “C” or better. Students are required to have a foundational understanding of the elements of design, the principles of composition, style, and content. Additionally, students must have developed fundamental drawing skills. These skills and knowledge sets are provided through the Department of Art’s Foundational Courses. -
Scientific Visualization
GeoVisualization “Geovisualization integrates approaches from visualization in scientific computing (ViSC), cartography, image analysis, information systems (GISystems) to provide theory, methods, and tools for visual exploration, analysis, synthesis, and presentation of geospatial data” -- International cartographic association commission (2001) Point/line/surface, 3D, spatial-temporal 1 Point: gas stations on Google map Location information only. 2 Point: geo-temporal data 3 Point: vectors 4 Point: bricks & colors 5 Line: Google map 6 Line: Facebook (dense edges) 7 Line: bundling technique Population migration: Airline routes: 8 Region: contours (boundaries only) 9 Region: color (filled regions) 10 Health Data (Disease Distributions) 11 Cartogram: scale and deform regions to reflect the size of the attributes 12 Multi-relationship: line/bubble set Multiple relationships Avoid re-layout 13 3D Map (2.5 Dimension) 14 3D Map: issues Realism vs. Abstraction Distraction Occlusion Applications: – Travel guide – City planning/simulation 15 3D Map: occlusion & landmark 16 Spatial-temporal data Time stamps/labels on 2D map Space-time cube Color curves Attribute changes 17 Time-trajectory (Tornado path) 18 Space-Time Cube 19 Trajectory Wall (C. Tominsk, et al) 20 Color Curves Using curves in color space to represent time. 21 Using Color Curves to Draw Taxis Trajectories on 2D Maps 22 Attribute changes Robbery geo-temporal data 23 Attribute changes (Health Data) 24 Interactive Techniques in InfoVis Select: mark something as interesting -
Stardust: Accessible and Transparent GPU Support for Information Visualization Rendering
Eurographics Conference on Visualization (EuroVis) 2017 Volume 36 (2017), Number 3 J. Heer, T. Ropinski and J. van Wijk (Guest Editors) Stardust: Accessible and Transparent GPU Support for Information Visualization Rendering Donghao Ren1, Bongshin Lee2, and Tobias Höllerer1 1University of California, Santa Barbara, United States 2Microsoft Research, Redmond, United States Abstract Web-based visualization libraries are in wide use, but performance bottlenecks occur when rendering, and especially animating, a large number of graphical marks. While GPU-based rendering can drastically improve performance, that paradigm has a steep learning curve, usually requiring expertise in the computer graphics pipeline and shader programming. In addition, the recent growth of virtual and augmented reality poses a challenge for supporting multiple display environments beyond regular canvases, such as a Head Mounted Display (HMD) and Cave Automatic Virtual Environment (CAVE). In this paper, we introduce a new web-based visualization library called Stardust, which provides a familiar API while leveraging GPU’s processing power. Stardust also enables developers to create both 2D and 3D visualizations for diverse display environments using a uniform API. To demonstrate Stardust’s expressiveness and portability, we present five example visualizations and a coding playground for four display environments. We also evaluate its performance by comparing it against the standard HTML5 Canvas, D3, and Vega. Categories and Subject Descriptors (according to ACM CCS): -
Civic Participation and Empowerment Through Visualization
SIGRAD 2015 L. Kjelldahl and C. Peters (Editors) Civic Participation and Empowerment through Visualization Samuel Bohmany Department of Computer and Systems Sciences, Stockholm University, Sweden Abstract This article elaborates on the use of data visualization to promote civic participation and democratic engage- ment. The power and potential of data visualization is examined through a brief historical overview and four interconnected themes that provide new opportunities for electronic participation research: data storytelling, in- fographics, data physicalization, and quantified self. The goal is to call attention to this space and encourage a larger community of researchers to explore the possibilities that data visualization can bring. Categories and Subject Descriptors (according to ACM CCS): H.5.2 [Information Interfaces and Presentation]: Screen design—User-centered design 1. Introduction The authors acknowledge that the deliberative approach to civic dialogue is “unduly restrictive, discounting other im- Since the advent of the web in the early 1990s, prospects portant ways of making, receiving, and contesting public of electronic democracy have been viewed as heralding in claims”. They therefore encourage researchers in the field to a new era of political participation and civic engagement. be more open to a wider range of practices and technologies However, empirical studies suggest most initiatives to date and suggest some of the most innovative research is being have failed to live up to expectations despite large invest- done in the area of computer-supported argument mapping ments in research. For instance, Chadwick [Cha08] states and visualization. However, the visualization research they that “the reality of online deliberation, whether judged in are referring to have primarily focused on facilitating large- terms of quantity, its quality, or its impact on political be- scale online deliberation within a conventional rationalistic haviour and policy outcomes, is far removed from the ide- framework. -
4.3 Discovering Fractal Geometry in CAAD
4.3 Discovering Fractal Geometry in CAAD Francisco Garcia, Angel Fernandez*, Javier Barrallo* Facultad de Informatica. Universidad de Deusto Bilbao. SPAIN E.T.S. de Arquitectura. Universidad del Pais Vasco. San Sebastian. SPAIN * Fractal geometry provides a powerful tool to explore the world of non-integer dimensions. Very short programs, easily comprehensible, can generate an extensive range of shapes and colors that can help us to understand the world we are living. This shapes are specially interesting in the simulation of plants, mountains, clouds and any kind of landscape, from deserts to rain-forests. The environment design, aleatory or conditioned, is one of the most important contributions of fractal geometry to CAAD. On a small scale, the design of fractal textures makes possible the simulation, in a very concise way, of wood, vegetation, water, minerals and a long list of materials very useful in photorealistic modeling. Introduction Fractal Geometry constitutes today one of the most fertile areas of investigation nowadays. Practically all the branches of scientific knowledge, like biology, mathematics, geology, chemistry, engineering, medicine, etc. have applied fractals to simulate and explain behaviors difficult to understand through traditional methods. Also in the world of computer aided design, fractal sets have shown up with strength, with numerous software applications using design tools based on fractal techniques. These techniques basically allow the effective and realistic reproduction of any kind of forms and textures that appear in nature: trees and plants, rocks and minerals, clouds, water, etc. For modern computer graphics, the access to these techniques, combined with ray tracing allow to create incredible landscapes and effects. -
Daftar Program Untuk Komputer Grafik Dan Pengolahan Citra
Daftar program untuk Komputer Grafik dan Pengolahan Citra I Made Wiryana 1 Nopember 2012 Daftar Isi 1 OpenCV 1 2 Scilab Image Processing Toolbox 2 3 VIPS 2 4 ImageJ 2 5 Marvin 2 6 MeVisLab 3 7 MVTH 3 8 Gephex 3 9 Fiji 3 10 MathMap 4 11 VTK 4 12 Tulip 4 13 PreFuse 4 1 OpenCV OpenCV - Open Source Computer Vision Library [http://www.opencv.org] is an open-source BSD- licensed library that includes several hundreds of computer vision algorithms. The document de- scribes the so-called OpenCV 2.x API, which is essentially a C++ API, as opposite to the C-based OpenCV 1.x API. The latter is described in opencv1x.pdf. OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. Being a BSD-licensed product, OpenCV makes it easy for businesses to utilize and modify the code. The library has more than 2500 optimized algorithms, which includes a comprehensive set of both classic and state-of-the-art computer vision and machine learning algorithms. These algori- thms can be used to detect and recognize faces, identify objects, classify human actions in videos, track camera movements, track moving objects, extract 3D models of objects, produce 3D point clouds from stereo cameras, stitch images together to produce a high resolution image of an entire 1 scene, find similar images from an image database, remove red eyes from images taken using flash, follow eye movements, recognize scenery and establish markers to overlay it with augmented reali- ty, etc. -
Volume Rendering
Volume Rendering 1.1. Introduction Rapid advances in hardware have been transforming revolutionary approaches in computer graphics into reality. One typical example is the raster graphics that took place in the seventies, when hardware innovations enabled the transition from vector graphics to raster graphics. Another example which has a similar potential is currently shaping up in the field of volume graphics. This trend is rooted in the extensive research and development effort in scientific visualization in general and in volume visualization in particular. Visualization is the usage of computer-supported, interactive, visual representations of data to amplify cognition. Scientific visualization is the visualization of physically based data. Volume visualization is a method of extracting meaningful information from volumetric datasets through the use of interactive graphics and imaging, and is concerned with the representation, manipulation, and rendering of volumetric datasets. Its objective is to provide mechanisms for peering inside volumetric datasets and to enhance the visual understanding. Traditional 3D graphics is based on surface representation. Most common form is polygon-based surfaces for which affordable special-purpose rendering hardware have been developed in the recent years. Volume graphics has the potential to greatly advance the field of 3D graphics by offering a comprehensive alternative to conventional surface representation methods. The object of this thesis is to examine the existing methods for volume visualization and to find a way of efficiently rendering scientific data with commercially available hardware, like PC’s, without requiring dedicated systems. 1.2. Volume Rendering Our display screens are composed of a two-dimensional array of pixels each representing a unit area. -
Course Title: Principles of Scientific Visualization Course Number: 9400110 Course Credit: 1 Course Description: This Course
Course Title: Principles of Scientific Visualization Course Number: 9400110 Course Credit: 1 Course Description: This course provides students with instruction in the evolution and underlying principles of scientific visualization, including two-dimensional representation of scientific and other forms of data. Included in the content is the use of color and other graphical elements such as vector and bitmap images in different presentation techniques. Students will also learn about the use of charts and graphs in representing data and the software tools used to produce them. The ultimate output of this course is a design portfolio created by the student from a scenario. The portfolio should include a narrative description of the scenario, the approach to data collection, resulting charts and graphs, and an interpretation of each chart/graph. Research references should be cited appropriately. Consideration should be given to having students produce the portfolio using presentation software. CTE Standards and Benchmarks NGSSS-Sci 28.0 Describe scientific & technical visualization. – The student will be able to: 28.01 Define scientific and technical visualization and provide examples of each. 28.02 Explain the importance of scientific visualization and its applicability to various industries. 28.03 Provide examples of 2-D and 3D rendered visualizations. 29.0 Describe the historical significance of scientific & technical visualization. – The student will be able to: 29.01 Describe the evolution of drawings from cave through perspective drawings to photography, television, and the Internet. 29.02 Define and describe the elements contained on various types of maps (e.g., road, topographic, aeronautical, weather, concept, and gene). SC.912.L.14.4; SC.912.E.5.8; 30.0 Describe the technological advancements of scientific & technical visualization. -
Cryptic Inoviruses Revealed As Pervasive in Bacteria and Archaea Across Earth’S Biomes
ARTICLES https://doi.org/10.1038/s41564-019-0510-x Corrected: Author Correction Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes Simon Roux 1*, Mart Krupovic 2, Rebecca A. Daly3, Adair L. Borges4, Stephen Nayfach1, Frederik Schulz 1, Allison Sharrar5, Paula B. Matheus Carnevali 5, Jan-Fang Cheng1, Natalia N. Ivanova 1, Joseph Bondy-Denomy4,6, Kelly C. Wrighton3, Tanja Woyke 1, Axel Visel 1, Nikos C. Kyrpides1 and Emiley A. Eloe-Fadrosh 1* Bacteriophages from the Inoviridae family (inoviruses) are characterized by their unique morphology, genome content and infection cycle. One of the most striking features of inoviruses is their ability to establish a chronic infection whereby the viral genome resides within the cell in either an exclusively episomal state or integrated into the host chromosome and virions are continuously released without killing the host. To date, a relatively small number of inovirus isolates have been extensively studied, either for biotechnological applications, such as phage display, or because of their effect on the toxicity of known bacterial pathogens including Vibrio cholerae and Neisseria meningitidis. Here, we show that the current 56 members of the Inoviridae family represent a minute fraction of a highly diverse group of inoviruses. Using a machine learning approach lever- aging a combination of marker gene and genome features, we identified 10,295 inovirus-like sequences from microbial genomes and metagenomes. Collectively, our results call for reclassification of the current Inoviridae family into a viral order including six distinct proposed families associated with nearly all bacterial phyla across virtually every ecosystem. -
Animated Presentation of Static Infographics with Infomotion
Eurographics Conference on Visualization (EuroVis) 2021 Volume 40 (2021), Number 3 R. Borgo, G. E. Marai, and T. von Landesberger (Guest Editors) Animated Presentation of Static Infographics with InfoMotion Yun Wang1, Yi Gao1;2, Ray Huang1, Weiwei Cui1, Haidong Zhang1, and Dongmei Zhang1 1Microsoft Research Asia 2Nanjing University (a) 5% (b) time Element Animation effect Meats, sweets slice spin link wipe dot zoom 35% icon zoom 10% Whole grains, title zoom OliVer oil pasta, beans, description wipe whole grain bread Mediterranean Diet 20% 30% 30% Vegetables and fruits Fish, seafood, poultry, Vegetables and fruits dairy food, eggs Figure 1: (a) An example infographic design. (b) The animated presentations for this infographic show the start time, duration, and animation effects applied to the visual elements. InfoMotion automatically generates animated presentations of static infographics. Abstract By displaying visual elements logically in temporal order, animated infographics can help readers better understand layers of information expressed in an infographic. While many techniques and tools target the quick generation of static infographics, few support animation designs. We propose InfoMotion that automatically generates animated presentations of static infographics. We first conduct a survey to explore the design space of animated infographics. Based on this survey, InfoMotion extracts graphical properties of an infographic to analyze the underlying information structures; then, animation effects are applied to the visual elements in the infographic in temporal order to present the infographic. The generated animations can be used in data videos or presentations. We demonstrate the utility of InfoMotion with two example applications, including mixed-initiative animation authoring and animation recommendation. -
Information Graphics Design Challenges and Workflow Management Marco Giardina, University of Neuchâtel, Switzerland, Pablo Medi
Online Journal of Communication and Media Technologies Volume: 3 – Issue: 1 – January - 2013 Information Graphics Design Challenges and Workflow Management Marco Giardina, University of Neuchâtel, Switzerland, Pablo Medina, Sensiel Research, Switzerland Abstract Infographics, though still in its infancy in the digital world, may offer an opportunity for media companies to enhance their business processes and value creation activities. This paper describes research about the influence of infographics production and dissemination on media companies’ workflow management. Drawing on infographics examples from New York Times print and online version, this contribution empirically explores the evolution from static to interactive multimedia infographics, the possibilities and design challenges of this journalistic emerging field and its impact on media companies’ activities in relation to technology changes and media-use patterns. Findings highlight some explorative ideas about the required workflow and journalism activities for a successful inception of infographics into online news dissemination practices of media companies. Conclusions suggest that delivering infographics represents a yet not fully tapped opportunity for media companies, but its successful inception on news production routines requires skilled professionals in audiovisual journalism and revised business models. Keywords: newspapers, visual communication, infographics, digital media technology © Online Journal of Communication and Media Technologies 108 Online Journal of Communication and Media Technologies Volume: 3 – Issue: 1 – January - 2013 During this time of unprecedented change in journalism, media practitioners and scholars find themselves mired in a new debate on the storytelling potential of data visualization narratives. News organization including the New York Times, Washington Post and The Guardian are at the fore of innovation and experimentation and regularly incorporate dynamic graphics into their journalism products (Segel, 2011).