What can GIS + 3D mean for landscape archaeology?

Until recently Geographic Information Systems (GIS) have held center stage in the archaeologist\u27s geospatial toolkit, and there is no doubt that archaeologists have moved beyond the mapdbut into what? In the early years, criticisms voicing GIS as environmentally-deterministic were abundant. What methods and tool have archaeologists used to overcome these criticisms? New geospatial technologies such as airborne lidar and aerial photogrammetry are allowing us to acquire inordinate amounts of georeferenced 3D datad but do these 3D technologies help overcome criticisms of environmental determinism? TogetherdGIS þ 3Dd can link georeferenced 3D models to underlying data adding a ground-based humanistic perspective lacking in the bird\u27s eye view of traditional GIS. This paper situates GIS and 3D within a semiotic framework to offer some ideas on using 3DGIS to intertwine environmental and cultural factors to work toward new approaches for landscape archaeology

ASTRAL PROJECTION: THEORIES OF METAPHOR, PHILOSOPHIES OF SCIENCE, AND THE ART O F SCIENTIFIC VISUALIZATION

This thesis provides an intellectual context for my work in computational scientific visualization for large-scale public outreach in venues such as digitaldome planetarium shows and high-definition public television documentaries. In my associated practicum, a DVD that provides video excerpts, 1 focus especially on work I have created with my Advanced Visualization Laboratory team at the National Center for Supercomputing Applications (Champaign, Illinois) from 2002-2007. 1 make three main contributions to knowledge within the field of computational scientific visualization. Firstly, I share the unique process 1 have pioneered for collaboratively producing and exhibiting this data-driven art when aimed at popular science education. The message of the art complements its means of production: Renaissance Team collaborations enact a cooperative paradigm of evolutionary sympathetic adaptation and co-creation. Secondly, 1 open up a positive, new space within computational scientific visualization's practice for artistic expression—especially in providing a theory of digi-epistemology that accounts for how this is possible given the limitations imposed by the demands of mapping numerical data and the computational models derived from them onto visual forms. I am concerned not only with liberating artists to enrich audience's aesthetic experiences of scientific visualization, to contribute their own vision, but also with conceiving of audiences as co-creators of the aesthetic significance of the work, to re-envision and re-circulate what they encounter there. Even more commonly than in the age of traditional media, on-line social computing and digital tools have empowered the public to capture and repurpose visual metaphors, circulating them within new contexts and telling new stories with them. Thirdly, I demonstrate the creative power of visaphors (see footnote, p. 1) to provide novel embodied experiences through my practicum as well as my thesis discussion. Specifically, I describe how the visaphors my Renaissance Teams and I create enrich the Environmentalist Story of Science, essentially promoting a counter-narrative to the Enlightenment Story of Science through articulating how humanity participates in an evolving universal consciousness through our embodied interaction and cooperative interdependence within nested, self-producing (autopoetic) systems, from the micro- to the macroscopic. This contemporary account of the natural world, its inter-related systems, and their dynamics may be understood as expressing a creative and generative energy—a kind of consciousness-that transcends the human yet also encompasses it

Software Visualization in 3D: Implementation, Evaluation, and Applicability

The focus of this thesis is on the implementation, the evaluation and the useful application of the third dimension in software visualization. Software engineering is characterized by a complex interplay of different stakeholders that produce and use several artifacts. Software visualization is used as one mean to address this increasing complexity. It provides role- and task-specific views of artifacts that contain information about structure, behavior, and evolution of a software system in its entirety. The main potential of the third dimension is the possibility to provide multiple views in one software visualization for all three aspects. However, empirical findings concerning the role of the third dimension in software visualization are rare. Furthermore, there are only few 3D software visualizations that provide multiple views of a software system including all three aspects. Finally, the current tool support lacks of generating easy integrateable, scalable, and platform independent 2D, 2.5D, and 3D software visualizations automatically. Hence, the objective is to develop a software visualization that represents all important structural entities and relations of a software system, that can display behavioral and evolutionary aspects of a software system as well, and that can be generated automatically. In order to achieve this objective the following research methods are applied. A literature study is conducted, a software visualization generator is conceptualized and prototypically implemented, a structured approach to plan and design controlled experiments in software visualization is developed, and a controlled experiment is designed and performed to investigate the role of the third dimension in software visualization. The main contributions are an overview of the state-of-the-art in 3D software visualization, a structured approach including a theoretical model to control influence factors during controlled experiments in software visualization, an Eclipse-based generator for producing automatically role- and task-specific 2D, 2.5D, and 3D software visualizations, the controlled experiment investigating the role of the third dimension in software visualization, and the recursive disk metaphor combining the findings with focus on the structure of software including useful applications of the third dimension regarding behavior and evolution

From Molecules to the Masses : Visual Exploration, Analysis, and Communication of Human Physiology

Det overordnede målet med denne avhandlingen er tverrfaglig anvendelse av medisinske illustrasjons- og visualiseringsteknikker for å utforske, analysere og formidle aspekter ved fysiologi til publikum med ulik faglig nivå og bakgrunn. Fysiologi beskriver de biologiske prosessene som skjer i levende vesener over tid. Vitenskapen om fysiologi er kompleks, men samtidig kritisk for vår forståelse av hvordan levende organismer fungerer. Fysiologi dekker en stor bredde romlig-temporale skalaer og fordrer behovet for å kombinere og bygge bro mellom basalfagene (biologi, fysikk og kjemi) og medisin. De senere årene har det vært en eksplosjon av nye, avanserte eksperimentelle metoder for å detektere og karakterisere fysiologiske data. Volumet og kompleksiteten til fysiologiske data krever effektive strategier for visualisering for å komplementere dagens standard analyser. Hvilke tilnærminger som benyttes i visualiseringen må nøye balanseres og tilpasses formålet med bruken av dataene, enten dette er for å utforske dataene, analysere disse eller kommunisere og presentere dem. Arbeidet i denne avhandlingen bidrar med ny kunnskap innen teori, empiri, anvendelse og reproduserbarhet av visualiseringsmetoder innen fysiologi. Først i avhandlingen er en rapport som oppsummerer og utforsker dagens kunnskap om muligheter og utfordringer for visualisering innen fysiologi. Motivasjonen for arbeidet er behovet forskere innen visualiseringsfeltet, og forskere i ulike anvendelsesområder, har for en sammensatt oversikt over flerskala visualiseringsoppgaver og teknikker. Ved å bruke søk over et stort spekter av metodiske tilnærminger, er dette den første rapporten i sitt slag som kartlegger visualiseringsmulighetene innen fysiologi. I rapporten er faglitteraturen oppsummert slik at det skal være enkelt å gjøre oppslag innen ulike tema i rom-og-tid-skalaen, samtidig som litteraturen er delt inn i de tre høynivå visualiseringsoppgavene data utforsking, analyse og kommunikasjon. Dette danner et enkelt grunnlag for å navigere i litteraturen i feltet og slik danner rapporten et godt grunnlag for diskusjon og forskningsmuligheter innen feltet visualisering og fysiologi. Basert på arbeidet med rapporten var det særlig to områder som det er ønskelig for oss å fortsette å utforske: (1) utforskende analyse av mangefasetterte fysiologidata for ekspertbrukere, og (2) kommunikasjon av data til både eksperter og ikke-eksperter. Arbeidet vårt av mangefasetterte fysiologidata er oppsummert i to studier i avhandlingen. Hver studie omhandler prosesser som foregår på forskjellige romlig-temporale skalaer og inneholder konkrete eksempler på anvendelse av metodene vurdert av eksperter i feltet. I den første av de to studiene undersøkes konsentrasjonen av molekylære substanser (metabolitter) ut fra data innsamlet med magnetisk resonansspektroskopi (MRS), en avansert biokjemisk teknikk som brukes til å identifisere metabolske forbindelser i levende vev. Selv om MRS kan ha svært høy sensitivitet og spesifisitet i medisinske anvendelser, er analyseresultatene fra denne modaliteten abstrakte og vanskelige å forstå også for medisinskfaglige eksperter i feltet. Vår designstudie som undersøkte oppgavene og kravene til ekspertutforskende analyse av disse dataene førte til utviklingen av SpectraMosaic. Dette er en ny applikasjon som gjør det mulig for domeneeksperter å analysere konsentrasjonen av metabolitter normalisert for en hel kohort, eller etter prøveregion, individ, opptaksdato, eller status på hjernens aktivitetsnivå ved undersøkelsestidspunktet. I den andre studien foreslås en metode for å utføre utforskende analyser av flerdimensjonale fysiologiske data i motsatt ende av den romlig-temporale skalaen, nemlig på populasjonsnivå. En effektiv arbeidsflyt for utforskende dataanalyse må kritisk identifisere interessante mønstre og relasjoner, noe som blir stadig vanskeligere når dimensjonaliteten til dataene øker. Selv om dette delvis kan løses med eksisterende reduksjonsteknikker er det alltid en fare for at subtile mønstre kan gå tapt i reduksjonsprosessen. Isteden presenterer vi i studien DimLift, en iterativ dimensjonsreduksjonsteknikk som muliggjør brukeridentifikasjon av interessante mønstre og relasjoner som kan ligge subtilt i et datasett gjennom dimensjonale bunter. Nøkkelen til denne metoden er brukerens evne til å styre dimensjonalitetsreduksjonen slik at den følger brukerens egne undersøkelseslinjer. For videre å undersøke kommunikasjon til eksperter og ikke-eksperter, studeres i neste arbeid utformingen av visualiseringer for kommunikasjon til publikum med ulike nivåer av ekspertnivå. Det er naturlig å forvente at eksperter innen et emne kan ha ulike preferanser og kriterier for å vurdere en visuell kommunikasjon i forhold til et ikke-ekspertpublikum. Dette påvirker hvor effektivt et bilde kan benyttes til å formidle en gitt scenario. Med utgangspunkt i ulike teknikker innen biomedisinsk illustrasjon og visualisering, gjennomførte vi derfor en utforskende studie av kriteriene som publikum bruker når de evaluerer en biomedisinsk prosessvisualisering målrettet for kommunikasjon. Fra denne studien identifiserte vi muligheter for ytterligere konvergens av biomedisinsk illustrasjon og visualiseringsteknikker for mer målrettet visuell kommunikasjonsdesign. Særlig beskrives i større dybde utviklingen av semantisk konsistente retningslinjer for farging av molekylære scener. Hensikten med slike retningslinjer er å heve den vitenskapelige kompetansen til ikke-ekspertpublikum innen molekyler visualisering, som vil være spesielt relevant for kommunikasjon til befolkningen i forbindelse med folkehelseopplysning. All kode og empiriske funn utviklet i arbeidet med denne avhandlingen er åpen kildekode og tilgjengelig for gjenbruk av det vitenskapelige miljøet og offentligheten. Metodene og funnene presentert i denne avhandlingen danner et grunnlag for tverrfaglig biomedisinsk illustrasjon og visualiseringsforskning, og åpner flere muligheter for fortsatt arbeid med visualisering av fysiologiske prosesser.The overarching theme of this thesis is the cross-disciplinary application of medical illustration and visualization techniques to address challenges in exploring, analyzing, and communicating aspects of physiology to audiences with differing expertise. Describing the myriad biological processes occurring in living beings over time, the science of physiology is complex and critical to our understanding of how life works. It spans many spatio-temporal scales to combine and bridge the basic sciences (biology, physics, and chemistry) to medicine. Recent years have seen an explosion of new and finer-grained experimental and acquisition methods to characterize these data. The volume and complexity of these data necessitate effective visualizations to complement standard analysis practice. Visualization approaches must carefully consider and be adaptable to the user's main task, be it exploratory, analytical, or communication-oriented. This thesis contributes to the areas of theory, empirical findings, methods, applications, and research replicability in visualizing physiology. Our contributions open with a state-of-the-art report exploring the challenges and opportunities in visualization for physiology. This report is motivated by the need for visualization researchers, as well as researchers in various application domains, to have a centralized, multiscale overview of visualization tasks and techniques. Using a mixed-methods search approach, this is the first report of its kind to broadly survey the space of visualization for physiology. Our approach to organizing the literature in this report enables the lookup of topics of interest according to spatio-temporal scale. It further subdivides works according to any combination of three high-level visualization tasks: exploration, analysis, and communication. This provides an easily-navigable foundation for discussion and future research opportunities for audience- and task-appropriate visualization for physiology. From this report, we identify two key areas for continued research that begin narrowly and subsequently broaden in scope: (1) exploratory analysis of multifaceted physiology data for expert users, and (2) communication for experts and non-experts alike. Our investigation of multifaceted physiology data takes place over two studies. Each targets processes occurring at different spatio-temporal scales and includes a case study with experts to assess the applicability of our proposed method. At the molecular scale, we examine data from magnetic resonance spectroscopy (MRS), an advanced biochemical technique used to identify small molecules (metabolites) in living tissue that are indicative of metabolic pathway activity. Although highly sensitive and specific, the output of this modality is abstract and difficult to interpret. Our design study investigating the tasks and requirements for expert exploratory analysis of these data led to SpectraMosaic, a novel application enabling domain researchers to analyze any permutation of metabolites in ratio form for an entire cohort, or by sample region, individual, acquisition date, or brain activity status at the time of acquisition. A second approach considers the exploratory analysis of multidimensional physiological data at the opposite end of the spatio-temporal scale: population. An effective exploratory data analysis workflow critically must identify interesting patterns and relationships, which becomes increasingly difficult as data dimensionality increases. Although this can be partially addressed with existing dimensionality reduction techniques, the nature of these techniques means that subtle patterns may be lost in the process. In this approach, we describe DimLift, an iterative dimensionality reduction technique enabling user identification of interesting patterns and relationships that may lie subtly within a dataset through dimensional bundles. Key to this method is the user's ability to steer the dimensionality reduction technique to follow their own lines of inquiry. Our third question considers the crafting of visualizations for communication to audiences with different levels of expertise. It is natural to expect that experts in a topic may have different preferences and criteria to evaluate a visual communication relative to a non-expert audience. This impacts the success of an image in communicating a given scenario. Drawing from diverse techniques in biomedical illustration and visualization, we conducted an exploratory study of the criteria that audiences use when evaluating a biomedical process visualization targeted for communication. From this study, we identify opportunities for further convergence of biomedical illustration and visualization techniques for more targeted visual communication design. One opportunity that we discuss in greater depth is the development of semantically-consistent guidelines for the coloring of molecular scenes. The intent of such guidelines is to elevate the scientific literacy of non-expert audiences in the context of molecular visualization, which is particularly relevant to public health communication. All application code and empirical findings are open-sourced and available for reuse by the scientific community and public. The methods and findings presented in this thesis contribute to a foundation of cross-disciplinary biomedical illustration and visualization research, opening several opportunities for continued work in visualization for physiology.Doktorgradsavhandlin

New insights into the suitability of the third dimension for visualizing multivariate/multidimensional data: a study based on loss of quality quantification

Most visualization techniques have traditionally used two-dimensional, instead of three-dimensional representations to visualize multidimensional and multivariate data. In this article, a way to demonstrate the underlying superiority of three-dimensional, with respect to two-dimensional, representation is proposed. Specifically, it is based on the inevitable quality degradation produced when reducing the data dimensionality. The problem is tackled from two different approaches: a visual and an analytical approach. First, a set of statistical tests (point classification, distance perception, and outlier identification) using the two-dimensional and three-dimensional visualization are carried out on a group of 40 users. The results indicate that there is an improvement in the accuracy introduced by the inclusion of a third dimension; however, these results do not allow to obtain definitive conclusions on the superiority of three-dimensional representation. Therefore, in order to draw further conclusions, a deeper study based on an analytical approach is proposed. The aim is to quantify the real loss of quality produced when the data are visualized in two-dimensional and three-dimensional spaces, in relation to the original data dimensionality, to analyze the difference between them. To achieve this, a recently proposed methodology is used. The results obtained by the analytical approach reported that the loss of quality reaches significantly high values only when switching from three-dimensional to two-dimensional representation. The considerable quality degradation suffered in the two-dimensional visualization strongly suggests the suitability of the third dimension to visualize data

Designing a 3D visualization for exploring relations between semantically similar brain diseases in Augmented Reality

As more papers are published and the body of knowledge increases, it becomes difficult to maintain a sense of overview and recognize relations between discussed topics. In order to assist neuroscientists with their task of finding unexplored relations between brain diseases, the DatAR project provides a topic model which allows neuroscientists to see at a glance which brain diseases are semantically similar and thus likely correlated. However, this topic model lacks the ability to explain why and how these brain diseases are semantically similar. We set out to design the Brain Disease Co-occurrence Explorer (BDCE), a 3D visualization which visualizes the number of co-occurrences between two brain diseases and any other brain topic in literature, with co-occurrence defined as two topics mentioned in the same sentence or body of text. We design two iterations of the BDCE, the first of which is evaluated by interviewing two experts in the field of 3D data visualization and immersive analytics. Based on the results from these interviews, we improve upon the design and perform user evaluations of the final iteration with participants from a neuroscience background or different related biology field. The user evaluations show that the BDCE is capable of explaining the topic model and encouraging further investigation into potentially interesting relations between brain diseases. Finally, we propose some avenues for future research regarding additional BDCE features, different visualization designs for visualizing co-occurrences in 3D space and improvements to our number visualization style

Digital Documentation and Reconstruction of an Ancient Maya Temple and Prototype of Internet GIS Database of Maya Architectur

This is a request for Level II Start-Up funding for an international project to develop and test a working prototype for a new platform for an online, searchable database that can bring together GIS maps, 3D models, and virtual environments for teaching and research. (The planning phase was funded by a Level I Start-Up Grant in 2009.) The prototype will employ existing digital collections on Maya architecture at the UNESCO World Heritage Site of Copan, Honduras and a highly-accurate, hybrid 3D model being developed by the project that will test and demonstrate the platform???s capabilities. Art historians and archaeologists from the University of New Mexico (UNM) and the Honduran Institute of Anthropology and History will work with computer experts from ETH Zurich, FBK Trento, and the University of California to design this online tool

Dataremix: Aesthetic Experiences of Big Data and Data Abstraction

This PhD by published work expands on the contribution to knowledge in two recent large-scale transdisciplinary artistic research projects: ATLAS in silico and INSTRUMENT | One Antarctic Night and their exhibited and published outputs. The thesis reflects upon this practice-based artistic research that interrogates data abstraction: the digitization, datafication and abstraction of culture and nature, as vast and abstract digital data. The research is situated in digital arts practices that engage a combination of big (scientific) data as artistic material, embodied interaction in virtual environments, and poetic recombination. A transdisciplinary and collaborative artistic practice, x-resonance, provides a framework for the hybrid processes, outcomes, and contributions to knowledge from the research. These are purposefully and productively situated at the objective | subjective interface, have potential to convey multiple meanings simultaneously to a variety of audiences and resist disciplinary definition. In the course of the research, a novel methodology emerges, dataremix, which is employed and iteratively evolved through artistic practice to address the research questions: 1) How can a visceral and poetic experience of data abstraction be created? and 2) How would one go about generating an artistically-informed (scientific) discovery? Several interconnected contributions to knowledge arise through the first research question: creation of representational elements for artistic visualization of big (scientific) data that includes four new forms (genomic calligraphy, algorithmic objects as natural specimens, scalable auditory data signatures, and signal objects); an aesthetic of slowness that contributes an extension to the operative forces in Jevbratt’s inverted sublime of looking down and in to also include looking fast and slow; an extension of Corby’s objective and subjective image consisting of “informational and aesthetic components” to novel virtual environments created from big 3 (scientific) data that extend Davies’ poetic virtual spatiality to poetic objective | subjective generative virtual spaces; and an extension of Seaman’s embodied interactive recombinant poetics through embodied interaction in virtual environments as a recapitulation of scientific (objective) and algorithmic processes through aesthetic (subjective) physical gestures. These contributions holistically combine in the artworks ATLAS in silico and INSTRUMENT | One Antarctic Night to create visceral poetic experiences of big data abstraction. Contributions to knowledge from the first research question develop artworks that are visceral and poetic experiences of data abstraction, and which manifest the objective | subjective through art. Contributions to knowledge from the second research question occur through the process of the artworks functioning as experimental systems in which experiments using analytical tools from the scientific domain are enacted within the process of creation of the artwork. The results are “returned” into the artwork. These contributions are: elucidating differences in DNA helix bending and curvature along regions of gene sequences specified as either introns or exons, revealing nuanced differences in BLAST results in relation to genomics sequence metadata, and cross-correlation of astronomical data to identify putative variable signals from astronomical objects for further scientific evaluation

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future.

"Α picture is worth a thousand words." This widely used adage sums up in a few words the notion that a successful visual representation of a concept should enable easy and rapid absorption of large amounts of information. Although, in general, the notion of capturing complex ideas using images is very appealing, would 1000 words be enough to describe the unknown in a research field such as the life sciences? Life sciences is one of the biggest generators of enormous datasets, mainly as a result of recent and rapid technological advances; their complexity can make these datasets incomprehensible without effective visualization methods. Here we discuss the past, present and future of genomic and systems biology visualization. We briefly comment on many visualization and analysis tools and the purposes that they serve. We focus on the latest libraries and programming languages that enable more effective, efficient and faster approaches for visualizing biological concepts, and also comment on the future human-computer interaction trends that would enable for enhancing visualization further