Scaling Up Medical Visualization : Multi-Modal, Multi-Patient, and Multi-Audience Approaches for Medical Data Exploration, Analysis and Communication

Medisinsk visualisering er en av de mest applikasjonsrettede områdene av visualiseringsforsking. Tett samarbeid med medisinske eksperter er nødvendig for å tolke medisinsk bildedata og lage betydningsfulle visualiseringsteknikker og visualiseringsapplikasjoner. Kreft er en av de vanligste dødsårsakene, og med økende gjennomsnittsalder i i-land øker også antallet diagnoser av gynekologisk kreft. Moderne avbildningsteknikker er et viktig verktøy for å vurdere svulster og produsere et økende antall bildedata som radiologer må tolke. I tillegg til antallet bildemodaliteter, øker også antallet pasienter, noe som fører til at visualiseringsløsninger må bli skalert opp for å adressere den økende kompleksiteten av multimodal- og multipasientdata. Dessuten er ikke medisinsk visualisering kun tiltenkt medisinsk personale, men har også som mål å informere pasienter, pårørende, og offentligheten om risikoen relatert til visse sykdommer, og mulige behandlinger. Derfor har vi identifisert behovet for å skalere opp medisinske visualiseringsløsninger for å kunne håndtere multipublikumdata. Denne avhandlingen adresserer skaleringen av disse dimensjonene i forskjellige bidrag vi har kommet med. Først presenterer vi teknikkene våre for å skalere visualiseringer i flere modaliteter. Vi introduserer en visualiseringsteknikk som tar i bruk små multipler for å vise data fra flere modaliteter innenfor et bildesnitt. Dette lar radiologer utforske dataen effektivt uten å måtte bruke flere sidestilte vinduer. I det neste steget utviklet vi en analyseplatform ved å ta i bruk «radiomic tumor profiling» på forskjellige bildemodaliteter for å analysere kohortdata og finne nye biomarkører fra bilder. Biomarkører fra bilder er indikatorer basert på bildedata som kan forutsi variabler relatert til kliniske utfall. «Radiomic tumor profiling» er en teknikk som genererer mulige biomarkører fra bilder basert på første- og andregrads statistiske målinger. Applikasjonen lar medisinske eksperter analysere multiparametrisk bildedata for å finne mulige korrelasjoner mellom kliniske parameter og data fra «radiomic tumor profiling». Denne tilnærmingen skalerer i to dimensjoner, multimodal og multipasient. I en senere versjon la vi til funksjonalitet for å skalere multipublikumdimensjonen ved å gjøre applikasjonen vår anvendelig for livmorhalskreft- og prostatakreftdata, i tillegg til livmorkreftdataen som applikasjonen var designet for. I et senere bidrag fokuserer vi på svulstdata på en annen skala og muliggjør analysen av svulstdeler ved å bruke multimodal bildedata i en tilnærming basert på hierarkisk gruppering. Applikasjonen vår finner mulige interessante regioner som kan informere fremtidige behandlingsavgjørelser. I et annet bidrag, en digital sonderingsinteraksjon, fokuserer vi på multipasientdata. Bildedata fra flere pasienter kan sammenlignes for å finne interessante mønster i svulstene som kan være knyttet til hvor aggressive svulstene er. Til slutt skalerer vi multipublikumdimensjonen med en likhetsvisualisering som er anvendelig for forskning på livmorkreft, på bilder av nevrologisk kreft, og maskinlæringsforskning på automatisk segmentering av svulstdata. Som en kontrast til de allerede fremhevete bidragene, fokuserer vårt siste bidrag, ScrollyVis, hovedsakelig på multipublikumkommunikasjon. Vi muliggjør skapelsen av dynamiske og vitenskapelige “scrollytelling”-opplevelser for spesifikke eller generelle publikum. Slike historien kan bli brukt i spesifikke brukstilfeller som kommunikasjon mellom lege og pasient, eller for å kommunisere vitenskapelige resultater via historier til et generelt publikum i en digital museumsutstilling. Våre foreslåtte applikasjoner og interaksjonsteknikker har blitt demonstrert i brukstilfeller og evaluert med domeneeksperter og fokusgrupper. Dette har ført til at noen av våre bidrag allerede er i bruk på andre forskingsinstitusjoner. Vi ønsker å evaluere innvirkningen deres på andre vitenskapelige felt og offentligheten i fremtidige arbeid.Medical visualization is one of the most application-oriented areas of visualization research. Close collaboration with medical experts is essential for interpreting medical imaging data and creating meaningful visualization techniques and visualization applications. Cancer is one of the most common causes of death, and with increasing average age in developed countries, gynecological malignancy case numbers are rising. Modern imaging techniques are an essential tool in assessing tumors and produce an increasing number of imaging data radiologists must interpret. Besides the number of imaging modalities, the number of patients is also rising, leading to visualization solutions that must be scaled up to address the rising complexity of multi-modal and multi-patient data. Furthermore, medical visualization is not only targeted toward medical professionals but also has the goal of informing patients, relatives, and the public about the risks of certain diseases and potential treatments. Therefore, we identify the need to scale medical visualization solutions to cope with multi-audience data. This thesis addresses the scaling of these dimensions in different contributions we made. First, we present our techniques to scale medical visualizations in multiple modalities. We introduced a visualization technique using small multiples to display the data of multiple modalities within one imaging slice. This allows radiologists to explore the data efficiently without having several juxtaposed windows. In the next step, we developed an analysis platform using radiomic tumor profiling on multiple imaging modalities to analyze cohort data and to find new imaging biomarkers. Imaging biomarkers are indicators based on imaging data that predict clinical outcome related variables. Radiomic tumor profiling is a technique that generates potential imaging biomarkers based on first and second-order statistical measurements. The application allows medical experts to analyze the multi-parametric imaging data to find potential correlations between clinical parameters and the radiomic tumor profiling data. This approach scales up in two dimensions, multi-modal and multi-patient. In a later version, we added features to scale the multi-audience dimension by making our application applicable to cervical and prostate cancer data and the endometrial cancer data the application was designed for. In a subsequent contribution, we focus on tumor data on another scale and enable the analysis of tumor sub-parts by using the multi-modal imaging data in a hierarchical clustering approach. Our application finds potentially interesting regions that could inform future treatment decisions. In another contribution, the digital probing interaction, we focus on multi-patient data. The imaging data of multiple patients can be compared to find interesting tumor patterns potentially linked to the aggressiveness of the tumors. Lastly, we scale the multi-audience dimension with our similarity visualization applicable to endometrial cancer research, neurological cancer imaging research, and machine learning research on the automatic segmentation of tumor data. In contrast to the previously highlighted contributions, our last contribution, ScrollyVis, focuses primarily on multi-audience communication. We enable the creation of dynamic scientific scrollytelling experiences for a specific or general audience. Such stories can be used for specific use cases such as patient-doctor communication or communicating scientific results via stories targeting the general audience in a digital museum exhibition. Our proposed applications and interaction techniques have been demonstrated in application use cases and evaluated with domain experts and focus groups. As a result, we brought some of our contributions to usage in practice at other research institutes. We want to evaluate their impact on other scientific fields and the general public in future work.Doktorgradsavhandlin

Visualisation of Large-Scale Call-Centre Data

The contact centre industry employs 4% of the entire United King-dom and United States’ working population and generates gigabytes of operational data that require analysis, to provide insight and to improve efficiency. This thesis is the result of a collaboration with QPC Limited who provide data collection and analysis products for call centres. They provided a large data-set featuring almost 5 million calls to be analysed. This thesis utilises novel visualisation techniques to create tools for the exploration of the large, complex call centre data-set and to facilitate unique observations into the data.A survey of information visualisation books is presented, provid-ing a thorough background of the field. Following this, a feature-rich application that visualises large call centre data sets using scatterplots that support millions of points is presented. The application utilises both the CPU and GPU acceleration for processing and filtering and is exhibited with millions of call events.This is expanded upon with the use of glyphs to depict agent behaviour in a call centre. A technique is developed to cluster over-lapping glyphs into a single parent glyph dependant on zoom level and a customizable distance metric. This hierarchical glyph repre-sents the mean value of all child agent glyphs, removing overlap and reducing visual clutter. A novel technique for visualising individually tailored glyphs using a Graphics Processing Unit is also presented, and demonstrated rendering over 100,000 glyphs at interactive frame rates. An open-source code example is provided for reproducibility.Finally, a novel interaction and layout method is introduced for improving the scalability of chord diagrams to visualise call transfers. An exploration of sketch-based methods for showing multiple links and direction is made, and a sketch-based brushing technique for filtering is proposed. Feedback from domain experts in the call centre industry is reported for all applications developed

Travails in the third dimension: a critical evaluation of three-dimensional geographical visualization

Several broad questions are posed about the role of the third dimension in data visualization. First, how far have we come in developing effective 3D displays for the analysis of spatial and other data? Second, when is it appropriate to use 3D techniques in visualising data, which 3D techniques are most appropriate for particular applications, and when might 2D approaches be more appropriate? (Indeed, is 3D always better than 2D?) Third, what can we learn from other communities in which 3D graphics and visualization technologies have been developed? And finally, what are the key R&D challenges in making effective use of the third dimension for visualising data across the spatial and related sciences? Answers to these questions will be based on several lines of evidence: the extensive literature on data and information visualization; visual perception research; computer games technology; and the author’s experiments with a prototype 3D data visualization system

WHIDE—a web tool for visual data mining colocation patterns in multivariate bioimages

Motivation: Bioimaging techniques rapidly develop toward higher resolution and dimension. The increase in dimension is achieved by different techniques such as multitag fluorescence imaging, Matrix Assisted Laser Desorption / Ionization (MALDI) imaging or Raman imaging, which record for each pixel an N-dimensional intensity array, representing local abundances of molecules, residues or interaction patterns. The analysis of such multivariate bioimages (MBIs) calls for new approaches to support users in the analysis of both feature domains: space (i.e. sample morphology) and molecular colocation or interaction. In this article, we present our approach WHIDE (Web-based Hyperbolic Image Data Explorer) that combines principles from computational learning, dimension reduction and visualization in a free web application

Visualization of multidimensional data with collocated paired coordinates and general line coordinates

Often multidimensional data are visualized by splitting n-D data to a set of low dimensional data. While it is useful it destroys integrity of n-D data, and leads to a shallow understanding complex n-D data. To mitigate this challenge a difficult perceptual task of assembling low-dimensional visualized pieces to the whole n-D vectors must be solved. Another way is a lossy dimension reduction by mapping n-D vectors to 2-D vectors (e.g., Principal Component Analysis). Such 2-D vectors carry only a part of information from n-D vectors, without a way to restore n-D vectors exactly from it. An alternative way for deeper understanding of n-D data is visual representations in 2-D that fully preserve n-D data. Methods of Parallel and Radial coordinates are such methods. Developing new methods that preserve dimensions is a long standing and challenging task that we address by proposing Paired Coordinates that is a new type of n-D data visual representation and by generalizing Parallel and Radial coordinates as a General Line coordinates. The important novelty of the concept of the Paired Coordinates is that it uses a single 2-D plot to represent n-D data as an oriented graph based on the idea of collocation of pairs of attributes. The advantage of the General Line Coordinates and Paired Coordinates is in providing a common framework that includes Parallel and Radial coordinates and generating a large number of new visual representations of multidimensional data without lossy dimension reduction