Diverging Color Maps for Scientific 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) .. -
Investigating the Effect of Color Gamut Mapping Quantitatively and Visually
Rochester Institute of Technology RIT Scholar Works Theses 5-2015 Investigating the Effect of Color Gamut Mapping Quantitatively and Visually Anupam Dhopade Follow this and additional works at: https://scholarworks.rit.edu/theses Recommended Citation Dhopade, Anupam, "Investigating the Effect of Color Gamut Mapping Quantitatively and Visually" (2015). Thesis. Rochester Institute of Technology. Accessed from This Thesis is brought to you for free and open access by RIT Scholar Works. It has been accepted for inclusion in Theses by an authorized administrator of RIT Scholar Works. For more information, please contact [email protected]. Investigating the Effect of Color Gamut Mapping Quantitatively and Visually by Anupam Dhopade A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Print Media in the School of Media Sciences in the College of Imaging Arts and Sciences of the Rochester Institute of Technology May 2015 Primary Thesis Advisor: Professor Robert Chung Secondary Thesis Advisor: Professor Christine Heusner School of Media Sciences Rochester Institute of Technology Rochester, New York Certificate of Approval Investigating the Effect of Color Gamut Mapping Quantitatively and Visually This is to certify that the Master’s Thesis of Anupam Dhopade has been approved by the Thesis Committee as satisfactory for the thesis requirement for the Master of Science degree at the convocation of May 2015 Thesis Committee: __________________________________________ Primary Thesis Advisor, Professor Robert Chung __________________________________________ Secondary Thesis Advisor, Professor Christine Heusner __________________________________________ Graduate Director, Professor Christine Heusner __________________________________________ Administrative Chair, School of Media Sciences, Professor Twyla Cummings ACKNOWLEDGEMENT I take this opportunity to express my sincere gratitude and thank all those who have supported me throughout the MS course here at RIT. -
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 -
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. -
Scientific Visualization for Secondary and Post–Secondary Schools Aaron C
24 Scientific Visualization for Secondary and Post–Secondary Schools Aaron C. Clark & Eric N. Wiebe North Carolina State University’s Department of marily brought about by advances in technology have Math, Science, and Technology Education along created new opportunities to use similar tools to pro- with Wake Technical Community College’s mote and enhance the study of the physical, biologi- Engineering Technology Division and North cal, and mathematical sciences. Carolina’s Department of Public Instruction These new courses are designed to articulate into (Vocational Education Division), sought ways in scientific visualization and technical graphics curric- which to build a strong secondary program in scien- ula at both two-year and four-year colleges and uni- tific and technical visualization, focusing on the use versities through the Tech-Prep initiative. of sophisticated graphics tools to study mathematics Articulation between schools allows for a broader and the sciences. Momentum for this high school- range of students to have a visual science course level scientific visualization curriculum developed out count for admission into a college or university. The of a revision of the complete high school technical courses have the potential to replace the fundamental graphics curriculum used throughout the state drafting course required for most degrees in engi- (North Carolina Public Schools, 1997). It became neering and technology. clear that a scientific visualization track could both The proposed student populations taking the sci- broaden the scope of the current technical graphics entific visualization courses are traditional vocational curriculum and attract a new group of students to track students and pre-college students who plan on technical graphics. -
NPR in Scientific Visualization
NPR Techniques for Scientific Visualization NPR Techniques for Scientific Visualization Victoria Interrante University of Minnesota 1 Introduction Visualization research is concerned with the design, implementation and evaluation of novel methods for effectively communicating information through images. For example: How do we determine how to portray a complicated set of data so that its essential information can be easily and accurately perceived and understood? How can we measure the success of our efforts? Where should we look for insight into the science behind the art of effective visual representation? For many years, photorealism was the gold standard, and the goal in visualization was to achieve renderings of scientific data that were as nearly indistinguishable as possible from a photograph. However in recent years, there has been an upsurge of interest in using non-photorealistic rendering (NPR) techniques in scientific visualization. What does NPR offer to visualization applications? What are some of the important research issues in developing NPR techniques for data visualization? What are the recent advances in this area? My presentation in this half-day course will attempt to survey these topics, beginning with a discussion of the motivation for using NPR in scientific visualization and continuing through an overview of recent research in the development and assessment of NPR techniques for visualization applications. 2 Motivation and Background Historical examples of the use of ‘non-photorealistic rendering’ techniques in scientific visualization can be found in the hand-drawn illustrations from scores of textbooks across multiple fields in the sciences [Loe64][Law71][Zwe61][Rid38]. The universal goal in such illustrations was to clarify the subject by emphasizing its most important or significant features, while de-emphasizing extraneous details [Hod89]. -
Scientific Visualization
0 Introduction CEG790 Introduction to Scientific Visualization Department of Computer Science and Engineering 0-1 0 Introduction Outline • Introduction • The visualization pipeline • Basic data representations • Fundamental algorithms • Advanced computer graphics • Advanced data representations • Advanced algorithms Department of Computer Science and Engineering 0-2 0 Introduction Literature • Will Schroeder, Ken Martin, Bill Lorenson, The Visualization Toolkit - An Object-Oriented Approach To 3D Graphics, Kitware, 2004 • Charles D. Hansen, Chris Johnson, Visualization Handbook, First Edition, Academic Press, 2004 • Scientific visualization: overviews, methodologies, and techniques, Gregory M. Nielson, Hans Hagen, Heinrich Müller, Los Alamitos, Calif., IEEE Computer Society Press, 1997 • Woo, Neider, Davis, Shreiner, OpenGL Programming Guide, Addison Wesley, 2000, http://www.opengl.org/documentation/red_book_1.0 • http://www-static.cc.gatech.edu/scivis/tutorial/linked/ classification.html Department of Computer Science and Engineering 0-3 0 Introduction What is Scientific Visualization? Scientific visualization, sometimes referred to in shorthand as SciVis, is the representation of data graphically as a means of gaining understanding and insight into the data. It is sometimes referred to as visual data analysis. This allows the researcher to gain insight into the system that is studied in ways previously impossible. Department of Computer Science and Engineering 0-4 0 Introduction What it is not It is important to differentiate between scientific visualization and presentation graphics. Presentation graphics is primarily concerned with the communication of information and results in ways that are easily understood. In scientific visualization, we seek to understand the data. However, often the two methods are intertwined. Department of Computer Science and Engineering 0-5 0 Introduction What is Scientific Visualization? From a computing perspective, SciVis is part of a greater field called visualization. -
Fast and Stable Color Balancing for Images and Augmented Reality
Fast and Stable Color Balancing for Images and Augmented Reality Thomas Oskam 1,2 Alexander Hornung 1 Robert W. Sumner 1 Markus Gross 1,2 1 Disney Research Zurich 2 ETH Zurich Abstract This paper addresses the problem of globally balanc- ing colors between images. The input to our algorithm is a sparse set of desired color correspondences between a source and a target image. The global color space trans- formation problem is then solved by computing a smooth Source Image Target Image Color Balanced vector field in CIE Lab color space that maps the gamut of the source to that of the target. We employ normalized ra- dial basis functions for which we compute optimized shape parameters based on the input images, allowing for more faithful and flexible color matching compared to existing RBF-, regression- or histogram-based techniques. Further- more, we show how the basic per-image matching can be Rendered Objects efficiently and robustly extended to the temporal domain us- Tracked Colors balancing Augmented Image ing RANSAC-based correspondence classification. Besides Figure 1. Two applications of our color balancing algorithm. Top: interactive color balancing for images, these properties ren- an underexposed image is balanced using only three user selected der our method extremely useful for automatic, consistent correspondences to a target image. Bottom: our extension for embedding of synthetic graphics in video, as required by temporally stable color balancing enables seamless compositing applications such as augmented reality. in augmented reality applications by using known colors in the scene as constraints. 1. Introduction even for different scenes. With today’s tools this process re- quires considerable, cost-intensive manual efforts. -
Hiding Color Watermarks in Halftone Images Using Maximum-Similarity
Signal Processing: Image Communication 48 (2016) 1–11 Contents lists available at ScienceDirect Signal Processing: Image Communication journal homepage: www.elsevier.com/locate/image Hiding color watermarks in halftone images using maximum- similarity binary patterns Pedro Garcia Freitas a,n, Mylène C.Q. Farias b, Aletéia P.F. Araújo a a Department of Computer Science, University of Brasília (UnB), Brasília, Brazil b Department of Electrical Engineering, University of Brasília (UnB), Brasília, Brazil article info abstract Article history: This paper presents a halftoning-based watermarking method that enables the embedding of a color Received 3 June 2016 image into binary black-and-white images. To maintain the quality of halftone images, the method maps Received in revised form watermarks to halftone channels using homogeneous dot patterns. These patterns use a different binary 25 August 2016 texture arrangement to embed the watermark. To prevent a degradation of the host image, a max- Accepted 25 August 2016 imization problem is solved to reduce the associated noise. The objective function of this maximization Available online 26 August 2016 problem is the binary similarity measure between the original binary halftone and a set of randomly Keywords: generated patterns. This optimization problem needs to be solved for each dot pattern, resulting in Color embedding processing overhead and a long running time. To overcome this restriction, parallel computing techni- Halftone ques are used to decrease the processing time. More specifically, the method is tested using a CUDA- Color restoration based parallel implementation, running on GPUs. The proposed technique produces results with high Watermarking Enhancement visual quality and acceptable processing time. -
Scientific Visualization
Introduction to Scientific Visualization Data Sources Scientific Visualization Pipelines VTK System 1 Scientific Data Sources Common data sources: Scanning devices Computation (mathematical) processes Measuring Application tools usually coupled with Haptic feedback devices Stereo output (glasses) Interactivity ---- demanding of the rendering algorithm 2 Scanning - Domains Biomedical scanners: MRI, CT, SPECT, PET, Ultrasound, confocal microscopes. Surface scanner (range data, surface details) Geospatial sensor 3 Surface Scanner Laser Scanner Structured Light Scanner 4 Scanning - Applications Medical education, illustration and training Biomedical research 5 6 Scanning – Applications (2) Surgical simulation for treatment planning Medical diagnosis and Tele-medicine Inter-operative visualization in brain surgery, biopsies, etc. (computer-aided surgery) Industrial purposes (quality control, security) Games with realistic 3D effects? 7 Scanning – Applications (3) Range data: Digital library, Virtual museum, etc. Geographical Information Systems Terracotta army 8 Scientific Computation Data sources (domain): Mathematical analysis, ODE/PDE, Finite element analysis (FE), Supercomputer simulations, etc Applications: Scientific simulation, Computational fluid dynamics (CFD), etc. 9 Measuring - Domains Data sources (domain): Orbiting satellites, Spacecraft, Seismic devices, Statistical Data. Applications: for military intelligence, weather and atmospheric studies, planetary and interplanetary exploration, oil exploitation, -
14. Color Mapping
14. Color Mapping Jacobs University Visualization and Computer Graphics Lab Recall: RGB color model Jacobs University Visualization and Computer Graphics Lab Data Analytics 691 CMY color model • The CMY color model is related to the RGB color model. •Itsbasecolorsare –cyan(C) –magenta(M) –yellow(Y) • They are arranged in a 3D Cartesian coordinate system. • The scheme is subtractive. Jacobs University Visualization and Computer Graphics Lab Data Analytics 692 Subtractive color scheme • CMY color model is subtractive, i.e., adding colors makes the resulting color darker. • Application: color printers. • As it only works perfectly in theory, typically a black cartridge is added in practice (CMYK color model). Jacobs University Visualization and Computer Graphics Lab Data Analytics 693 CMY color cube • All colors c that can be generated are represented by the unit cube in the 3D Cartesian coordinate system. magenta blue red black grey white cyan yellow green Jacobs University Visualization and Computer Graphics Lab Data Analytics 694 CMY color cube Jacobs University Visualization and Computer Graphics Lab Data Analytics 695 CMY color model Jacobs University Visualization and Computer Graphics Lab Data Analytics 696 CMYK color model Jacobs University Visualization and Computer Graphics Lab Data Analytics 697 Conversion • RGB -> CMY: • CMY -> RGB: Jacobs University Visualization and Computer Graphics Lab Data Analytics 698 Conversion • CMY -> CMYK: • CMYK -> CMY: Jacobs University Visualization and Computer Graphics Lab Data Analytics 699 HSV color model • While RGB and CMY color models have their application in hardware implementations, the HSV color model is based on properties of human perception. • Its application is for human interfaces. Jacobs University Visualization and Computer Graphics Lab Data Analytics 700 HSV color model The HSV color model also consists of 3 channels: • H: When perceiving a color, we perceive the dominant wavelength. -
GS9 Color Management
Ghostscript 9.21 Color Management Michael J. Vrhel, Ph.D. Artifex Software 7 Mt. Lassen Drive, A-134 San Rafael, CA 94903, USA www.artifex.com Abstract This document provides information about the color architecture in Ghostscript 9.21. The document is suitable for users who wish to obtain accurate color with their output device as well as for developers who wish to customize Ghostscript to achieve a higher level of control and/or interface with a different color management module. Revision 1.6 Artifex Software Inc. www.artifex.com 1 1 Introduction With release 9.0, the color architecture of Ghostscript was updated to primarily use the ICC[1] format for its color management needs. Prior to this release, Ghostscript's color architecture was based heavily upon PostScript[2] Color Management (PCM). This is due to the fact that Ghostscript was designed prior to the ICC format and likely even before there was much thought about digital color management. At that point in time, color management was very much an art with someone adjusting controls to achieve the proper output color. Today, almost all print color management is performed using ICC profiles as opposed to PCM. This fact along with the desire to create a faster, more flexible design was the motivation for the color architectural changes in release 9.0. Since 9.0, several new features and capabilities have been added. As of the 9.21 release, features of the color architecture include: • Easy to interface different CMMs (Color Management Modules) with Ghostscript. • ALL color spaces are defined in terms of ICC profiles.